Starting phenix.real_space_refine on Fri Dec 15 12:10:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/12_2023/7rqx_24639_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/12_2023/7rqx_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_24639/12_2023/7rqx_24639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/12_2023/7rqx_24639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/12_2023/7rqx_24639_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqx_24639/12_2023/7rqx_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-1.21rc1-5172/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: 13.13, per 1000 atoms: 0.43 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: 25.16 Conformation dependent library (CDL) restraints added in 3.6 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: 4.53 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: 10.32 Time building geometry restraints manager: 25.73 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: 14568 35.29 - 70.58: 380 70.58 - 105.86: 36 105.86 - 141.15: 12 141.15 - 176.44: 8 Dihedral angle restraints: 15004 sinusoidal: 7716 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 15001 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: 0.850 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: 0.510 Extract box with map and model: 5.510 Check model and map are aligned: 0.460 Set scattering table: 0.310 Process input model: 94.330 Find NCS groups from input model: 1.590 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.460 ------------------------------------------------------------------------------- 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 : 2.539 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 outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.5738 time to fit residues: 188.5552 Evaluate side-chains 163 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3101 ------------------------------------------------------------------------------- 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: 4.9990 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: 10.0000 chunk 181 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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: 0.7451 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16472 Z= 0.311 Angle : 0.540 4.230 22372 Z= 0.284 Chirality : 0.036 0.144 2524 Planarity : 0.004 0.075 2736 Dihedral : 18.084 179.326 3068 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.74 % Allowed : 7.42 % Favored : 90.84 % 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: -0.30 (0.19), residues: 1992 helix: 0.61 (0.15), residues: 1220 sheet: -2.32 (0.58), residues: 56 loop : -1.37 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 697 HIS 0.006 0.001 HIS C 364 PHE 0.022 0.002 PHE D 473 TYR 0.013 0.001 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 198 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.261 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 outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.5374 time to fit residues: 154.1123 Evaluate side-chains 169 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 2.549 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4079 time to fit residues: 16.3024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 40.0000 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 B 364 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16472 Z= 0.293 Angle : 0.505 4.826 22372 Z= 0.269 Chirality : 0.035 0.125 2524 Planarity : 0.004 0.070 2736 Dihedral : 17.237 179.490 3068 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.07 % Allowed : 9.29 % Favored : 89.64 % 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: -0.08 (0.19), residues: 1992 helix: 0.81 (0.15), residues: 1220 sheet: -2.40 (0.55), residues: 56 loop : -1.30 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 697 HIS 0.006 0.001 HIS D 364 PHE 0.019 0.001 PHE A 473 TYR 0.012 0.001 TYR D 530 ARG 0.004 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 181 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 2.412 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 outliers start: 16 outliers final: 6 residues processed: 169 average time/residue: 0.5146 time to fit residues: 139.0290 Evaluate side-chains 159 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 153 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3877 time to fit residues: 6.6675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7442 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16472 Z= 0.196 Angle : 0.458 4.216 22372 Z= 0.245 Chirality : 0.034 0.133 2524 Planarity : 0.004 0.063 2736 Dihedral : 16.234 173.904 3068 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.94 % Allowed : 10.49 % Favored : 88.57 % 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: 0.25 (0.19), residues: 1992 helix: 1.07 (0.16), residues: 1220 sheet: -2.09 (0.56), residues: 56 loop : -1.19 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 697 HIS 0.006 0.001 HIS D 364 PHE 0.016 0.001 PHE A 429 TYR 0.011 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 176 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 2.733 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 outliers start: 14 outliers final: 5 residues processed: 168 average time/residue: 0.5292 time to fit residues: 138.3559 Evaluate side-chains 158 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 2.469 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4053 time to fit residues: 6.4098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 2 optimal weight: 30.0000 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 B 364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16472 Z= 0.212 Angle : 0.461 6.400 22372 Z= 0.245 Chirality : 0.034 0.134 2524 Planarity : 0.003 0.057 2736 Dihedral : 15.429 170.691 3068 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.87 % Allowed : 10.49 % Favored : 88.64 % 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: 0.39 (0.19), residues: 1992 helix: 1.21 (0.16), residues: 1220 sheet: -2.01 (0.56), residues: 56 loop : -1.19 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 749 HIS 0.006 0.001 HIS B 364 PHE 0.013 0.001 PHE A 473 TYR 0.013 0.001 TYR D 309 ARG 0.002 0.000 ARG C 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 175 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 2.478 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 outliers start: 13 outliers final: 7 residues processed: 166 average time/residue: 0.5498 time to fit residues: 142.7345 Evaluate side-chains 163 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3759 time to fit residues: 7.7639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 47 optimal weight: 20.0000 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.7472 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16472 Z= 0.271 Angle : 0.483 5.968 22372 Z= 0.256 Chirality : 0.035 0.138 2524 Planarity : 0.003 0.055 2736 Dihedral : 14.919 169.468 3068 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.40 % Allowed : 11.97 % Favored : 87.63 % 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: 1.15 (0.16), residues: 1220 sheet: -2.08 (0.56), residues: 56 loop : -1.26 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 749 HIS 0.004 0.001 HIS D 364 PHE 0.014 0.001 PHE A 473 TYR 0.013 0.001 TYR A 309 ARG 0.001 0.000 ARG B 499 *********************** 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 166 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 2.594 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 outliers start: 6 outliers final: 3 residues processed: 161 average time/residue: 0.5439 time to fit residues: 136.3586 Evaluate side-chains 156 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3781 time to fit residues: 4.8837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 110 optimal weight: 0.0020 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 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: 5.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 364 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16472 Z= 0.151 Angle : 0.438 6.188 22372 Z= 0.232 Chirality : 0.033 0.169 2524 Planarity : 0.003 0.050 2736 Dihedral : 14.309 167.646 3068 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.40 % Allowed : 12.57 % 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: 0.59 (0.20), residues: 1992 helix: 1.38 (0.16), residues: 1220 sheet: -1.92 (0.57), residues: 56 loop : -1.13 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 749 HIS 0.007 0.001 HIS B 364 PHE 0.012 0.001 PHE A 473 TYR 0.011 0.001 TYR B 309 ARG 0.002 0.000 ARG D 701 *********************** 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 173 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 167 time to evaluate : 2.635 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 outliers start: 6 outliers final: 6 residues processed: 168 average time/residue: 0.5843 time to fit residues: 152.6037 Evaluate side-chains 161 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4373 time to fit residues: 7.3869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 58 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 151 optimal weight: 40.0000 chunk 175 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.2102 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= 0.271 Angle : 0.476 4.873 22372 Z= 0.251 Chirality : 0.035 0.144 2524 Planarity : 0.003 0.048 2736 Dihedral : 14.159 168.498 3068 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.33 % Allowed : 12.70 % Favored : 86.97 % 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: 1220 sheet: -2.10 (0.57), residues: 56 loop : -1.23 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 749 HIS 0.003 0.001 HIS C 320 PHE 0.014 0.001 PHE B 649 TYR 0.013 0.001 TYR D 309 ARG 0.002 0.000 ARG D 575 *********************** 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 166 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 2.677 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 outliers start: 5 outliers final: 4 residues processed: 162 average time/residue: 0.5500 time to fit residues: 137.7358 Evaluate side-chains 159 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3189 time to fit residues: 5.1578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 189 optimal weight: 0.0370 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 423 GLN B 364 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16472 Z= 0.187 Angle : 0.447 4.749 22372 Z= 0.236 Chirality : 0.034 0.186 2524 Planarity : 0.003 0.049 2736 Dihedral : 13.614 167.230 3068 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.40 % Allowed : 12.57 % 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: 0.61 (0.20), residues: 1992 helix: 1.40 (0.16), residues: 1220 sheet: -1.95 (0.57), residues: 56 loop : -1.14 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 749 HIS 0.008 0.001 HIS B 364 PHE 0.012 0.001 PHE B 429 TYR 0.012 0.001 TYR D 309 ARG 0.001 0.000 ARG A 355 *********************** 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 168 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 2.699 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 outliers start: 6 outliers final: 3 residues processed: 164 average time/residue: 0.5650 time to fit residues: 142.1539 Evaluate side-chains 161 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3135 time to fit residues: 4.3663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.5773 > 50: distance: 306 - 348: 17.600 distance: 314 - 358: 32.576 distance: 324 - 375: 23.417 distance: 331 - 348: 14.230 distance: 332 - 382: 23.257 distance: 348 - 349: 15.332 distance: 348 - 353: 4.895 distance: 349 - 350: 30.128 distance: 349 - 352: 41.636 distance: 349 - 354: 18.559 distance: 350 - 351: 37.606 distance: 350 - 358: 40.555 distance: 351 - 406: 22.869 distance: 352 - 355: 37.307 distance: 352 - 356: 27.233 distance: 352 - 357: 40.559 distance: 358 - 359: 57.889 distance: 358 - 366: 25.652 distance: 359 - 360: 58.476 distance: 359 - 362: 57.422 distance: 359 - 367: 43.164 distance: 360 - 361: 42.721 distance: 360 - 375: 49.763 distance: 361 - 420: 47.288 distance: 362 - 363: 43.320 distance: 362 - 368: 41.099 distance: 362 - 369: 33.029 distance: 363 - 364: 23.254 distance: 363 - 370: 29.835 distance: 363 - 371: 32.642 distance: 364 - 365: 16.810 distance: 365 - 372: 5.593 distance: 365 - 373: 6.147 distance: 365 - 374: 6.458 distance: 375 - 376: 36.146 distance: 375 - 379: 18.986 distance: 376 - 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412: 28.277 distance: 410 - 415: 53.349 distance: 411 - 416: 21.764 distance: 412 - 417: 24.835 distance: 412 - 418: 5.329 distance: 412 - 419: 13.812 distance: 420 - 421: 18.807 distance: 420 - 428: 49.800 distance: 421 - 422: 39.672 distance: 421 - 424: 12.909 distance: 421 - 429: 24.137 distance: 422 - 423: 40.295 distance: 422 - 434: 59.442 distance: 424 - 425: 33.732 distance: 424 - 430: 39.826 distance: 424 - 431: 16.267 distance: 425 - 426: 17.041 distance: 425 - 427: 28.103 distance: 427 - 432: 20.851 distance: 427 - 433: 30.566 distance: 434 - 435: 56.947 distance: 434 - 442: 58.751 distance: 435 - 436: 16.616 distance: 435 - 438: 27.175 distance: 435 - 443: 48.274 distance: 436 - 437: 47.228 distance: 436 - 451: 7.538 distance: 438 - 439: 28.959 distance: 438 - 444: 38.445 distance: 438 - 445: 37.463 distance: 439 - 440: 25.892 distance: 439 - 446: 28.306 distance: 439 - 447: 28.211 distance: 440 - 441: 43.543 distance: 441 - 448: 10.295 distance: 441 - 449: 7.081 distance: 441 - 450: 5.751 distance: 451 - 452: 17.933 distance: 451 - 459: 11.386 distance: 452 - 453: 25.593 distance: 452 - 455: 39.344 distance: 452 - 460: 29.521 distance: 453 - 454: 27.062 distance: 453 - 470: 25.637 distance: 455 - 456: 12.535 distance: 455 - 461: 22.951 distance: 455 - 462: 18.159 distance: 456 - 457: 13.231 distance: 456 - 458: 10.426 distance: 456 - 463: 11.605 distance: 457 - 464: 15.053 distance: 457 - 465: 9.359 distance: 457 - 466: 11.568 distance: 458 - 467: 7.469 distance: 458 - 468: 3.602 distance: 458 - 469: 8.188 distance: 470 - 471: 17.560 distance: 470 - 482: 32.966 distance: 471 - 472: 40.334 distance: 471 - 474: 17.354 distance: 471 - 483: 31.366 distance: 472 - 473: 18.174 distance: 472 - 491: 34.135 distance: 474 - 475: 22.089 distance: 474 - 484: 25.212 distance: 474 - 485: 21.903 distance: 475 - 476: 27.032 distance: 475 - 477: 13.459 distance: 476 - 478: 9.309 distance: 476 - 486: 18.667 distance: 477 - 479: 8.623 distance: 477 - 487: 12.844 distance: 478 - 480: 13.070 distance: 478 - 488: 17.981 distance: 479 - 480: 7.028 distance: 479 - 489: 3.073 distance: 480 - 481: 12.942 distance: 481 - 490: 5.478 distance: 491 - 492: 40.040 distance: 491 - 503: 25.583 distance: 492 - 493: 18.110 distance: 492 - 495: 43.436 distance: 492 - 504: 31.012 distance: 493 - 494: 12.919 distance: 493 - 512: 15.962 distance: 495 - 496: 40.418 distance: 495 - 505: 10.473 distance: 495 - 506: 13.593 distance: 496 - 497: 15.163 distance: 496 - 498: 13.522 distance: 497 - 499: 20.045 distance: 497 - 507: 6.613 distance: 498 - 500: 29.573 distance: 498 - 508: 6.970 distance: 499 - 501: 35.808 distance: 499 - 509: 17.407 distance: 500 - 501: 35.285 distance: 500 - 510: 22.626 distance: 501 - 502: 29.481 distance: 502 - 511: 20.990