Starting phenix.real_space_refine on Thu Mar 21 22:18:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/03_2024/7rqx_24639_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/03_2024/7rqx_24639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/03_2024/7rqx_24639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/03_2024/7rqx_24639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/03_2024/7rqx_24639_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/03_2024/7rqx_24639_trim_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 S 92 5.16 5 Na 2 4.78 5 C 10612 2.51 5 N 2504 2.21 5 O 2880 1.98 5 H 14344 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 478": "OE1" <-> "OE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 576": "OD1" <-> "OD2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 576": "OD1" <-> "OD2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 576": "OD1" <-> "OD2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 709": "OE1" <-> "OE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 576": "OD1" <-> "OD2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 709": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30450 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 135 Chain: "C" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 135 Chain: "D" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 7413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 7413 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 135 Chain: "A" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 201 Unusual residues: {' NA': 2, '6EU': 1, '6OU': 3, 'LBN': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 199 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 166 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 232 Unusual residues: {'6EU': 1, '6OU': 4, 'LBN': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-2': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 13 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALA A 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA A 204 " occ=0.50 residue: pdb=" N ALA C 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA C 204 " occ=0.50 residue: pdb=" N ALA D 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA D 204 " occ=0.50 residue: pdb=" N ALA B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 204 " occ=0.50 Time building chain proxies: 13.30, per 1000 atoms: 0.44 Number of scatterers: 30450 At special positions: 0 Unit cell: (121.422, 121.422, 111.132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 92 16.00 P 16 15.00 Na 2 11.00 O 2880 8.00 N 2504 7.00 C 10612 6.00 H 14344 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.04 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.04 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 23.40 Conformation dependent library (CDL) restraints added in 3.4 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 8 sheets defined 58.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.781A pdb=" N ILE A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.723A pdb=" N THR A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 268 Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 320 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 397 through 400 No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 416 through 429 removed outlier: 3.870A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.619A pdb=" N ASN A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 503 through 509 removed outlier: 5.230A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 508 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP A 509 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 531 removed outlier: 3.611A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.561A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 558 removed outlier: 3.902A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 555 through 558' Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.538A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.812A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 3.854A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 691 removed outlier: 3.814A pdb=" N ALA A 680 " --> pdb=" O ASN A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 711 Processing helix chain 'A' and resid 713 through 716 No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.781A pdb=" N ILE C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.723A pdb=" N THR C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 268 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 320 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 397 through 400 No H-bonds generated for 'chain 'C' and resid 397 through 400' Processing helix chain 'C' and resid 416 through 429 removed outlier: 3.870A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 453 removed outlier: 3.619A pdb=" N ASN C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 503 through 509 removed outlier: 5.230A pdb=" N PHE C 507 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP C 509 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 531 removed outlier: 3.611A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 553 removed outlier: 3.560A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 558 removed outlier: 3.902A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 555 through 558' Processing helix chain 'C' and resid 565 through 574 removed outlier: 3.538A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 598 removed outlier: 3.812A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 3.854A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 691 removed outlier: 3.814A pdb=" N ALA C 680 " --> pdb=" O ASN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 711 Processing helix chain 'C' and resid 713 through 716 No H-bonds generated for 'chain 'C' and resid 713 through 716' Processing helix chain 'D' and resid 204 through 210 removed outlier: 3.782A pdb=" N ILE D 209 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.723A pdb=" N THR D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 268 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 320 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 397 through 400 No H-bonds generated for 'chain 'D' and resid 397 through 400' Processing helix chain 'D' and resid 416 through 429 removed outlier: 3.870A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 453 removed outlier: 3.619A pdb=" N ASN D 437 " --> pdb=" O ILE D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 509 removed outlier: 5.230A pdb=" N PHE D 507 " --> pdb=" O LYS D 504 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL D 508 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP D 509 " --> pdb=" O LEU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 531 removed outlier: 3.612A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 553 removed outlier: 3.560A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 558 removed outlier: 3.902A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 555 through 558' Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.538A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 598 removed outlier: 3.812A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 removed outlier: 3.855A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 691 removed outlier: 3.814A pdb=" N ALA D 680 " --> pdb=" O ASN D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 711 Processing helix chain 'D' and resid 713 through 716 No H-bonds generated for 'chain 'D' and resid 713 through 716' Processing helix chain 'B' and resid 204 through 210 removed outlier: 3.781A pdb=" N ILE B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.722A pdb=" N THR B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 268 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 320 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 397 through 400 No H-bonds generated for 'chain 'B' and resid 397 through 400' Processing helix chain 'B' and resid 416 through 429 removed outlier: 3.870A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.619A pdb=" N ASN B 437 " --> pdb=" O ILE B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 503 through 509 removed outlier: 5.230A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 508 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP B 509 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 removed outlier: 3.611A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 553 removed outlier: 3.560A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 558 removed outlier: 3.902A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 555 through 558' Processing helix chain 'B' and resid 565 through 574 removed outlier: 3.538A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 598 removed outlier: 3.813A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.855A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 691 removed outlier: 3.814A pdb=" N ALA B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 711 Processing helix chain 'B' and resid 713 through 716 No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing sheet with id= A, first strand: chain 'A' and resid 380 through 382 removed outlier: 3.549A pdb=" N TYR A 382 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 724 through 730 removed outlier: 3.780A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 380 through 382 removed outlier: 3.549A pdb=" N TYR C 382 " --> pdb=" O PHE C 742 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 724 through 730 removed outlier: 3.781A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 380 through 382 removed outlier: 3.549A pdb=" N TYR D 382 " --> pdb=" O PHE D 742 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 724 through 730 removed outlier: 3.781A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 380 through 382 removed outlier: 3.550A pdb=" N TYR B 382 " --> pdb=" O PHE B 742 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 724 through 730 removed outlier: 3.780A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.02 Time building geometry restraints manager: 24.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14316 1.02 - 1.22: 75 1.22 - 1.41: 6843 1.41 - 1.61: 9381 1.61 - 1.81: 201 Bond restraints: 30816 Sorted by residual: bond pdb=" CAS 6EU C 904 " pdb=" CAX 6EU C 904 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAS 6EU D 905 " pdb=" CAX 6EU D 905 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAS 6EU B 907 " pdb=" CAX 6EU B 907 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAS 6EU A 903 " pdb=" CAX 6EU A 903 " ideal model delta sigma weight residual 1.334 1.612 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" CAW 6EU C 904 " pdb=" CBA 6EU C 904 " ideal model delta sigma weight residual 1.339 1.520 -0.181 2.00e-02 2.50e+03 8.16e+01 ... (remaining 30811 not shown) Histogram of bond angle deviations from ideal: 79.53 - 90.42: 16 90.42 - 101.31: 68 101.31 - 112.20: 33179 112.20 - 123.09: 18699 123.09 - 133.98: 2870 Bond angle restraints: 54832 Sorted by residual: angle pdb=" CG1 ILE D 679 " pdb=" CD1 ILE D 679 " pdb="HD11 ILE D 679 " ideal model delta sigma weight residual 109.00 79.53 29.47 3.00e+00 1.11e-01 9.65e+01 angle pdb=" CG1 ILE C 679 " pdb=" CD1 ILE C 679 " pdb="HD11 ILE C 679 " ideal model delta sigma weight residual 109.00 79.54 29.46 3.00e+00 1.11e-01 9.65e+01 angle pdb=" CG1 ILE A 679 " pdb=" CD1 ILE A 679 " pdb="HD11 ILE A 679 " ideal model delta sigma weight residual 109.00 79.56 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" CG1 ILE C 679 " pdb=" CD1 ILE C 679 " pdb="HD13 ILE C 679 " ideal model delta sigma weight residual 109.00 79.56 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" CG1 ILE B 679 " pdb=" CD1 ILE B 679 " pdb="HD11 ILE B 679 " ideal model delta sigma weight residual 109.00 79.59 29.41 3.00e+00 1.11e-01 9.61e+01 ... (remaining 54827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 14760 35.29 - 70.58: 492 70.58 - 105.86: 36 105.86 - 141.15: 12 141.15 - 176.44: 8 Dihedral angle restraints: 15308 sinusoidal: 8020 harmonic: 7288 Sorted by residual: dihedral pdb=" C1 LBN C 901 " pdb=" O1 LBN C 901 " pdb=" P1 LBN C 901 " pdb=" O3 LBN C 901 " ideal model delta sinusoidal sigma weight residual 275.40 98.96 176.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN D 903 " pdb=" O1 LBN D 903 " pdb=" P1 LBN D 903 " pdb=" O3 LBN D 903 " ideal model delta sinusoidal sigma weight residual 275.40 98.98 176.42 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 LBN A 901 " pdb=" O1 LBN A 901 " pdb=" P1 LBN A 901 " pdb=" O3 LBN A 901 " ideal model delta sinusoidal sigma weight residual 275.40 99.02 176.38 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 15305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2399 0.094 - 0.187: 77 0.187 - 0.281: 12 0.281 - 0.374: 13 0.374 - 0.468: 23 Chirality restraints: 2524 Sorted by residual: chirality pdb=" C2 LBN A 905 " pdb=" C1 LBN A 905 " pdb=" C3 LBN A 905 " pdb=" O7 LBN A 905 " both_signs ideal model delta sigma weight residual False -2.36 -2.83 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" C2 LBN B 902 " pdb=" C1 LBN B 902 " pdb=" C3 LBN B 902 " pdb=" O7 LBN B 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.83 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C2 LBN D 902 " pdb=" C1 LBN D 902 " pdb=" C3 LBN D 902 " pdb=" O7 LBN D 902 " both_signs ideal model delta sigma weight residual False -2.36 -2.83 0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 2521 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 403 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.32e+00 pdb=" C SER B 403 " 0.047 2.00e-02 2.50e+03 pdb=" O SER B 403 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 404 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 403 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C SER A 403 " 0.047 2.00e-02 2.50e+03 pdb=" O SER A 403 " -0.017 2.00e-02 2.50e+03 pdb=" N SER A 404 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 403 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C SER D 403 " 0.046 2.00e-02 2.50e+03 pdb=" O SER D 403 " -0.017 2.00e-02 2.50e+03 pdb=" N SER D 404 " -0.016 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.08: 404 2.08 - 2.71: 46928 2.71 - 3.34: 86381 3.34 - 3.97: 105687 3.97 - 4.60: 168822 Nonbonded interactions: 408222 Sorted by model distance: nonbonded pdb=" O THR D 298 " pdb=" H THR D 302 " model vdw 1.445 1.850 nonbonded pdb=" O THR A 298 " pdb=" H THR A 302 " model vdw 1.445 1.850 nonbonded pdb=" O THR B 298 " pdb=" H THR B 302 " model vdw 1.445 1.850 nonbonded pdb=" O THR C 298 " pdb=" H THR C 302 " model vdw 1.446 1.850 nonbonded pdb=" OE2 GLU C 600 " pdb="HH22 ARG D 455 " model vdw 1.501 1.850 ... (remaining 408217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 203 through 752) selection = (chain 'B' and resid 203 through 752) selection = (chain 'C' and resid 203 through 752) selection = (chain 'D' and resid 203 through 752) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.430 Extract box with map and model: 5.080 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 91.530 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.278 16472 Z= 0.741 Angle : 1.058 16.769 22372 Z= 0.464 Chirality : 0.062 0.468 2524 Planarity : 0.005 0.094 2736 Dihedral : 19.015 176.441 6144 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1992 helix: 0.66 (0.16), residues: 1204 sheet: -2.16 (0.60), residues: 56 loop : -1.43 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 697 HIS 0.003 0.001 HIS A 320 PHE 0.028 0.001 PHE C 473 TYR 0.013 0.001 TYR D 401 ARG 0.004 0.001 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 GLN cc_start: 0.8516 (pp30) cc_final: 0.8160 (pp30) REVERT: C 443 LEU cc_start: 0.7998 (tt) cc_final: 0.7648 (tp) REVERT: D 519 GLN cc_start: 0.8557 (pp30) cc_final: 0.8207 (pp30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5381 time to fit residues: 176.0447 Evaluate side-chains 165 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 9.9990 chunk 151 optimal weight: 40.0000 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 30.0000 chunk 102 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 181 optimal weight: 0.4980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS C 297 ASN C 364 HIS C 423 GLN D 364 HIS D 423 GLN B 364 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16472 Z= 0.399 Angle : 0.575 4.312 22372 Z= 0.303 Chirality : 0.038 0.155 2524 Planarity : 0.004 0.076 2736 Dihedral : 18.109 179.147 3068 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.74 % Allowed : 7.69 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1992 helix: 0.47 (0.15), residues: 1220 sheet: -2.53 (0.57), residues: 56 loop : -1.43 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 697 HIS 0.006 0.002 HIS C 364 PHE 0.024 0.002 PHE B 473 TYR 0.015 0.002 TYR C 530 ARG 0.004 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 TRP cc_start: 0.4892 (OUTLIER) cc_final: 0.4679 (t-100) REVERT: B 644 MET cc_start: 0.7255 (ptt) cc_final: 0.6881 (ptt) outliers start: 26 outliers final: 19 residues processed: 181 average time/residue: 0.5422 time to fit residues: 157.2849 Evaluate side-chains 169 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain B residue 364 HIS Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 696 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS D 364 HIS D 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16472 Z= 0.277 Angle : 0.505 5.694 22372 Z= 0.271 Chirality : 0.035 0.121 2524 Planarity : 0.004 0.071 2736 Dihedral : 17.232 178.976 3068 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.94 % Allowed : 9.63 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 1992 helix: 0.78 (0.15), residues: 1220 sheet: -2.47 (0.56), residues: 56 loop : -1.30 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 697 HIS 0.018 0.002 HIS B 364 PHE 0.020 0.001 PHE D 429 TYR 0.012 0.001 TYR A 309 ARG 0.003 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 TRP cc_start: 0.4894 (OUTLIER) cc_final: 0.4669 (t-100) REVERT: C 308 MET cc_start: 0.7247 (tmm) cc_final: 0.6966 (tmm) REVERT: D 473 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: B 473 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6501 (m-80) outliers start: 29 outliers final: 18 residues processed: 174 average time/residue: 0.5169 time to fit residues: 142.1385 Evaluate side-chains 170 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 749 TRP Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 696 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS D 364 HIS D 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16472 Z= 0.240 Angle : 0.474 5.422 22372 Z= 0.252 Chirality : 0.034 0.152 2524 Planarity : 0.004 0.067 2736 Dihedral : 15.972 171.790 3068 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.34 % Allowed : 10.09 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1992 helix: 1.01 (0.15), residues: 1220 sheet: -2.20 (0.56), residues: 56 loop : -1.20 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 697 HIS 0.007 0.001 HIS D 364 PHE 0.018 0.001 PHE A 429 TYR 0.012 0.001 TYR A 309 ARG 0.003 0.000 ARG C 701 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 160 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 473 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: C 631 TYR cc_start: 0.7247 (t80) cc_final: 0.6895 (t80) REVERT: D 473 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: D 631 TYR cc_start: 0.7358 (t80) cc_final: 0.7026 (t80) outliers start: 35 outliers final: 17 residues processed: 179 average time/residue: 0.4890 time to fit residues: 138.1538 Evaluate side-chains 170 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN D 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16472 Z= 0.280 Angle : 0.488 7.152 22372 Z= 0.259 Chirality : 0.035 0.139 2524 Planarity : 0.004 0.058 2736 Dihedral : 15.404 170.751 3068 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.94 % Allowed : 10.56 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1992 helix: 1.03 (0.16), residues: 1220 sheet: -2.30 (0.56), residues: 56 loop : -1.24 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 697 HIS 0.003 0.001 HIS C 320 PHE 0.014 0.001 PHE A 473 TYR 0.016 0.001 TYR D 309 ARG 0.002 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 631 TYR cc_start: 0.7246 (t80) cc_final: 0.6900 (t80) REVERT: D 291 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6985 (tt) REVERT: D 631 TYR cc_start: 0.7351 (t80) cc_final: 0.7021 (t80) REVERT: B 684 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7090 (mp0) outliers start: 29 outliers final: 21 residues processed: 170 average time/residue: 0.5093 time to fit residues: 136.1429 Evaluate side-chains 173 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 50.0000 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16472 Z= 0.184 Angle : 0.449 4.906 22372 Z= 0.238 Chirality : 0.034 0.146 2524 Planarity : 0.003 0.051 2736 Dihedral : 14.656 168.694 3068 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.40 % Allowed : 11.56 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 1992 helix: 1.25 (0.16), residues: 1220 sheet: -2.04 (0.57), residues: 56 loop : -1.18 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 749 HIS 0.003 0.001 HIS D 364 PHE 0.013 0.001 PHE A 473 TYR 0.012 0.001 TYR A 309 ARG 0.002 0.000 ARG D 701 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 631 TYR cc_start: 0.7233 (t80) cc_final: 0.6894 (t80) REVERT: D 631 TYR cc_start: 0.7334 (t80) cc_final: 0.7015 (t80) REVERT: B 684 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7085 (mp0) outliers start: 21 outliers final: 19 residues processed: 175 average time/residue: 0.5199 time to fit residues: 140.0693 Evaluate side-chains 170 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 110 optimal weight: 0.0370 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.4980 chunk 162 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16472 Z= 0.164 Angle : 0.432 5.187 22372 Z= 0.229 Chirality : 0.033 0.163 2524 Planarity : 0.003 0.049 2736 Dihedral : 14.109 167.395 3068 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.40 % Allowed : 11.70 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1992 helix: 1.41 (0.16), residues: 1212 sheet: -1.91 (0.57), residues: 56 loop : -1.07 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 749 HIS 0.003 0.001 HIS D 364 PHE 0.011 0.001 PHE A 473 TYR 0.012 0.001 TYR A 309 ARG 0.001 0.000 ARG B 499 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 631 TYR cc_start: 0.7303 (t80) cc_final: 0.6998 (t80) REVERT: B 684 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7095 (mp0) outliers start: 21 outliers final: 19 residues processed: 176 average time/residue: 0.5855 time to fit residues: 160.6621 Evaluate side-chains 174 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 40.0000 chunk 175 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN D 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16472 Z= 0.274 Angle : 0.479 4.342 22372 Z= 0.253 Chirality : 0.035 0.204 2524 Planarity : 0.003 0.049 2736 Dihedral : 14.028 168.461 3068 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.67 % Allowed : 12.10 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1992 helix: 1.26 (0.16), residues: 1212 sheet: -2.15 (0.57), residues: 56 loop : -1.18 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.003 0.001 HIS C 320 PHE 0.015 0.001 PHE B 649 TYR 0.013 0.001 TYR D 530 ARG 0.002 0.000 ARG C 499 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 159 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 631 TYR cc_start: 0.7290 (t80) cc_final: 0.6960 (t80) REVERT: B 684 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7089 (mp0) outliers start: 25 outliers final: 23 residues processed: 173 average time/residue: 0.5388 time to fit residues: 143.6963 Evaluate side-chains 174 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16472 Z= 0.225 Angle : 0.455 3.955 22372 Z= 0.240 Chirality : 0.034 0.179 2524 Planarity : 0.003 0.049 2736 Dihedral : 13.591 168.102 3068 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.67 % Allowed : 12.37 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1992 helix: 1.31 (0.16), residues: 1220 sheet: -2.09 (0.57), residues: 56 loop : -1.15 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.003 0.001 HIS A 364 PHE 0.012 0.001 PHE A 649 TYR 0.012 0.001 TYR D 309 ARG 0.001 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 631 TYR cc_start: 0.7331 (t80) cc_final: 0.7009 (t80) REVERT: B 684 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6900 (mp0) outliers start: 25 outliers final: 23 residues processed: 171 average time/residue: 0.5424 time to fit residues: 141.7489 Evaluate side-chains 175 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.0010 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 687 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16472 Z= 0.166 Angle : 0.434 3.727 22372 Z= 0.229 Chirality : 0.033 0.178 2524 Planarity : 0.003 0.048 2736 Dihedral : 13.107 166.853 3068 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.54 % Allowed : 12.63 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1992 helix: 1.48 (0.16), residues: 1212 sheet: -1.97 (0.58), residues: 56 loop : -1.04 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE C 429 TYR 0.012 0.001 TYR B 309 ARG 0.001 0.000 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue ILE 207 is missing expected H atoms. Skipping. Residue MET 214 is missing expected H atoms. Skipping. Residue THR 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue VAL 221 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 252 is missing expected H atoms. Skipping. Residue LEU 254 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 265 is missing expected H atoms. Skipping. Residue LEU 268 is missing expected H atoms. Skipping. Residue VAL 287 is missing expected H atoms. Skipping. Residue THR 298 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue THR 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue LYS 324 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue ILE 328 is missing expected H atoms. Skipping. Residue LYS 345 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue ILE 387 is missing expected H atoms. Skipping. Residue THR 389 is missing expected H atoms. Skipping. Residue LYS 392 is missing expected H atoms. Skipping. Residue VAL 395 is missing expected H atoms. Skipping. Residue SER 404 is missing expected H atoms. Skipping. Residue LEU 414 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LEU 465 is missing expected H atoms. Skipping. Residue LYS 466 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue LYS 504 is missing expected H atoms. Skipping. Residue LYS 714 is missing expected H atoms. Skipping. Residue MET 716 is missing expected H atoms. Skipping. Residue LYS 718 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue VAL 728 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 397 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 631 TYR cc_start: 0.7345 (t80) cc_final: 0.7048 (t80) REVERT: B 684 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6561 (mp0) outliers start: 23 outliers final: 20 residues processed: 171 average time/residue: 0.5423 time to fit residues: 141.5255 Evaluate side-chains 171 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 689 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 749 TRP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 689 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.187315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.144203 restraints weight = 53776.278| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.34 r_work: 0.3280 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16472 Z= 0.150 Angle : 0.429 4.300 22372 Z= 0.225 Chirality : 0.033 0.173 2524 Planarity : 0.003 0.047 2736 Dihedral : 12.696 165.636 3068 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.20 % Allowed : 13.10 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1992 helix: 1.68 (0.16), residues: 1200 sheet: -1.84 (0.59), residues: 56 loop : -0.99 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 697 HIS 0.003 0.001 HIS A 364 PHE 0.014 0.001 PHE C 429 TYR 0.011 0.001 TYR B 309 ARG 0.001 0.000 ARG B 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5231.95 seconds wall clock time: 93 minutes 34.41 seconds (5614.41 seconds total)