Starting phenix.real_space_refine on Thu Feb 22 01:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqy_24640/02_2024/7rqy_24640_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqy_24640/02_2024/7rqy_24640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqy_24640/02_2024/7rqy_24640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqy_24640/02_2024/7rqy_24640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqy_24640/02_2024/7rqy_24640_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqy_24640/02_2024/7rqy_24640_neut_trim_updated.pdb" } resolution = 3.04 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= 0.011 sd= 0.135 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 80 5.16 5 C 11016 2.51 5 N 2620 2.21 5 O 2940 1.98 5 H 15388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32052 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 138 Chain: "B" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 138 Chain: "C" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 7877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 7877 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 511} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 301 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 168 Unusual residues: {'6EU': 1, '6OU': 3, 'LBN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'LBN:plan-3': 1, '6OU:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {'6EU': 1, '6OU': 2, 'LBN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'6OU:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 104 Unusual residues: {'6EU': 1, '6OU': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 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 B 204 " occ=0.50 ... (8 atoms not shown) pdb=" HB3 ALA B 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 Time building chain proxies: 14.05, per 1000 atoms: 0.44 Number of scatterers: 32052 At special positions: 0 Unit cell: (124.509, 123.48, 109.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 8 15.00 O 2940 8.00 N 2620 7.00 C 11016 6.00 H 15388 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=2.07 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.07 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.07 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.07 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: 25.46 Conformation dependent library (CDL) restraints added in 3.5 seconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 12 sheets defined 57.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'A' and resid 204 through 211 Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.609A pdb=" N LYS A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.597A pdb=" N ILE A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 428 removed outlier: 4.019A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.501A pdb=" N TYR A 435 " --> pdb=" O LYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 removed outlier: 3.609A pdb=" N PHE A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 removed outlier: 3.670A pdb=" N LEU A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE A 507 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 508 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP A 509 " --> pdb=" O LEU A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 509' Processing helix chain 'A' and resid 511 through 531 removed outlier: 3.583A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 520 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 558 removed outlier: 3.547A pdb=" N VAL A 538 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 543 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A 547 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 550 " --> pdb=" O MET A 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 581 through 598 removed outlier: 3.607A pdb=" N VAL A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.690A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 removed outlier: 3.574A pdb=" N ILE A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 690 removed outlier: 3.527A pdb=" N LEU A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 711 removed outlier: 3.639A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 718 Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 removed outlier: 3.609A pdb=" N LYS B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.597A pdb=" N ILE B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 428 removed outlier: 4.018A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 removed outlier: 3.609A pdb=" N PHE B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 removed outlier: 3.670A pdb=" N LEU B 506 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE B 507 " --> pdb=" O LYS B 504 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 508 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP B 509 " --> pdb=" O LEU B 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 503 through 509' Processing helix chain 'B' and resid 511 through 531 removed outlier: 3.584A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 520 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 558 removed outlier: 3.547A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 550 " --> pdb=" O MET B 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 553 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'B' and resid 581 through 598 removed outlier: 3.607A pdb=" N VAL B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.690A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 removed outlier: 3.574A pdb=" N ILE B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 690 removed outlier: 3.527A pdb=" N LEU B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 711 removed outlier: 3.639A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 Processing helix chain 'C' and resid 204 through 211 Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 removed outlier: 3.609A pdb=" N LYS C 303 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 removed outlier: 3.597A pdb=" N ILE C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.019A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.501A pdb=" N TYR C 435 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 499 removed outlier: 3.609A pdb=" N PHE C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 509 removed outlier: 3.670A pdb=" N LEU C 506 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE C 507 " --> pdb=" O LYS C 504 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP C 509 " --> pdb=" O LEU C 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 503 through 509' Processing helix chain 'C' and resid 511 through 531 removed outlier: 3.583A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER C 520 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 558 removed outlier: 3.547A pdb=" N VAL C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 543 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 550 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 553 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 574 Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.606A pdb=" N VAL C 586 " --> pdb=" O PHE C 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.690A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.574A pdb=" N ILE C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 690 removed outlier: 3.527A pdb=" N LEU C 678 " --> pdb=" O LEU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 711 removed outlier: 3.640A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 718 Processing helix chain 'D' and resid 204 through 211 Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 removed outlier: 3.608A pdb=" N LYS D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 removed outlier: 3.597A pdb=" N ILE D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 removed outlier: 4.018A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 removed outlier: 3.501A pdb=" N TYR D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 removed outlier: 3.608A pdb=" N PHE D 489 " --> pdb=" O GLY D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 509 removed outlier: 3.670A pdb=" N LEU D 506 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE D 507 " --> pdb=" O LYS D 504 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL D 508 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP D 509 " --> pdb=" O LEU D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 509' Processing helix chain 'D' and resid 511 through 531 removed outlier: 3.584A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER D 520 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET D 523 " --> pdb=" O GLN D 519 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 558 removed outlier: 3.548A pdb=" N VAL D 538 " --> pdb=" O LYS D 535 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 543 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR D 550 " --> pdb=" O MET D 547 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 553 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 574 Processing helix chain 'D' and resid 581 through 598 removed outlier: 3.607A pdb=" N VAL D 586 " --> pdb=" O PHE D 582 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.691A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.574A pdb=" N ILE D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 690 removed outlier: 3.527A pdb=" N LEU D 678 " --> pdb=" O LEU D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 711 removed outlier: 3.640A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 718 Processing sheet with id= A, first strand: chain 'A' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 377 " --> pdb=" O TYR A 374 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 380 through 382 Processing sheet with id= C, first strand: chain 'A' and resid 724 through 730 removed outlier: 3.943A pdb=" N VAL A 728 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 377 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 380 through 382 Processing sheet with id= F, first strand: chain 'B' and resid 724 through 730 removed outlier: 3.942A pdb=" N VAL B 728 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 372 through 374 removed outlier: 3.638A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 377 " --> pdb=" O TYR C 374 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 380 through 382 Processing sheet with id= I, first strand: chain 'C' and resid 724 through 730 removed outlier: 3.943A pdb=" N VAL C 728 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 372 through 374 removed outlier: 3.639A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 377 " --> pdb=" O TYR D 374 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 380 through 382 Processing sheet with id= L, first strand: chain 'D' and resid 724 through 730 removed outlier: 3.942A pdb=" N VAL D 728 " --> pdb=" O ASP D 737 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) 781 hydrogen bonds defined for protein. 2187 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: 11.45 Time building geometry restraints manager: 26.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15368 1.04 - 1.23: 601 1.23 - 1.43: 6749 1.43 - 1.63: 9570 1.63 - 1.83: 160 Bond restraints: 32448 Sorted by residual: bond pdb=" CAS 6EU A 901 " pdb=" CAX 6EU A 901 " ideal model delta sigma weight residual 1.334 1.606 -0.272 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU D 901 " pdb=" CAX 6EU D 901 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU B 901 " pdb=" CAX 6EU B 901 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAS 6EU C 902 " pdb=" CAX 6EU C 902 " ideal model delta sigma weight residual 1.334 1.605 -0.271 2.00e-02 2.50e+03 1.84e+02 bond pdb=" CAW 6EU C 902 " pdb=" CBA 6EU C 902 " ideal model delta sigma weight residual 1.339 1.519 -0.180 2.00e-02 2.50e+03 8.10e+01 ... (remaining 32443 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.79: 289 105.79 - 112.86: 35814 112.86 - 119.93: 9658 119.93 - 127.00: 12105 127.00 - 134.07: 150 Bond angle restraints: 58016 Sorted by residual: angle pdb=" N GLU B 391 " pdb=" CA GLU B 391 " pdb=" C GLU B 391 " ideal model delta sigma weight residual 111.02 118.42 -7.40 1.22e+00 6.72e-01 3.68e+01 angle pdb=" N GLU C 391 " pdb=" CA GLU C 391 " pdb=" C GLU C 391 " ideal model delta sigma weight residual 111.02 118.40 -7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" N GLU A 391 " pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 111.02 118.37 -7.35 1.22e+00 6.72e-01 3.63e+01 angle pdb=" N GLU D 391 " pdb=" CA GLU D 391 " pdb=" C GLU D 391 " ideal model delta sigma weight residual 111.02 118.36 -7.34 1.22e+00 6.72e-01 3.62e+01 angle pdb=" CAM 6EU B 901 " pdb=" CAV 6EU B 901 " pdb=" CBD 6EU B 901 " ideal model delta sigma weight residual 115.62 99.79 15.83 3.00e+00 1.11e-01 2.78e+01 ... (remaining 58011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 15356 33.05 - 66.11: 500 66.11 - 99.16: 44 99.16 - 132.21: 12 132.21 - 165.27: 8 Dihedral angle restraints: 15920 sinusoidal: 8304 harmonic: 7616 Sorted by residual: dihedral pdb=" C1 LBN B 902 " pdb=" O1 LBN B 902 " pdb=" P1 LBN B 902 " pdb=" O3 LBN B 902 " ideal model delta sinusoidal sigma weight residual -84.60 80.67 -165.27 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 LBN A 902 " pdb=" O1 LBN A 902 " pdb=" P1 LBN A 902 " pdb=" O3 LBN A 902 " ideal model delta sinusoidal sigma weight residual -84.60 80.64 -165.24 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 LBN C 903 " pdb=" O1 LBN C 903 " pdb=" P1 LBN C 903 " pdb=" O3 LBN C 903 " ideal model delta sinusoidal sigma weight residual -84.60 80.62 -165.22 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 15917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2563 0.089 - 0.178: 53 0.178 - 0.267: 12 0.267 - 0.357: 14 0.357 - 0.446: 14 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.44 2.00e-01 2.50e+01 4.93e+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 -2.81 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 2653 not shown) Planarity restraints: 4880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 687 " 0.158 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN B 687 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 687 " -0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN B 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 687 " -0.221 2.00e-02 2.50e+03 pdb="HD22 ASN B 687 " 0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 687 " -0.157 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN D 687 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN D 687 " 0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN D 687 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 687 " 0.221 2.00e-02 2.50e+03 pdb="HD22 ASN D 687 " -0.226 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 687 " 0.158 2.00e-02 2.50e+03 1.57e-01 3.69e+02 pdb=" CG ASN C 687 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 687 " -0.150 2.00e-02 2.50e+03 pdb=" ND2 ASN C 687 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 687 " -0.221 2.00e-02 2.50e+03 pdb="HD22 ASN C 687 " 0.226 2.00e-02 2.50e+03 ... (remaining 4877 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1901 2.20 - 2.80: 63375 2.80 - 3.40: 86275 3.40 - 4.00: 111839 4.00 - 4.60: 173591 Nonbonded interactions: 436981 Sorted by model distance: nonbonded pdb=" O ILE B 209 " pdb="HE22 GLN B 260 " model vdw 1.600 1.850 nonbonded pdb=" O ILE C 209 " pdb="HE22 GLN C 260 " model vdw 1.600 1.850 nonbonded pdb=" O ILE A 209 " pdb="HE22 GLN A 260 " model vdw 1.600 1.850 nonbonded pdb=" O ILE D 209 " pdb="HE22 GLN D 260 " model vdw 1.601 1.850 nonbonded pdb=" OD1 ASP B 296 " pdb=" HG1 THR B 298 " model vdw 1.621 1.850 ... (remaining 436976 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 197 through 752) selection = (chain 'B' and resid 197 through 752) selection = (chain 'C' and resid 197 through 752) selection = (chain 'D' and resid 197 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: 0.740 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: 0.490 Extract box with map and model: 5.340 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 98.560 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.011 0.272 17060 Z= 0.677 Angle : 0.942 15.830 23204 Z= 0.431 Chirality : 0.054 0.446 2656 Planarity : 0.004 0.055 2844 Dihedral : 17.875 165.267 6260 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -0.70 (0.18), residues: 2076 helix: 0.13 (0.15), residues: 1288 sheet: -4.09 (0.44), residues: 56 loop : -1.06 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 372 HIS 0.002 0.001 HIS C 364 PHE 0.013 0.001 PHE D 448 TYR 0.010 0.001 TYR C 309 ARG 0.003 0.001 ARG D 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.8034 (mp10) cc_final: 0.7426 (pm20) REVERT: A 677 MET cc_start: 0.8428 (ttp) cc_final: 0.8028 (ttm) REVERT: B 552 MET cc_start: 0.8883 (mtt) cc_final: 0.8452 (mtt) REVERT: B 677 MET cc_start: 0.8374 (ttp) cc_final: 0.8057 (ttm) REVERT: C 552 MET cc_start: 0.8818 (mtt) cc_final: 0.8434 (mtt) REVERT: C 677 MET cc_start: 0.8330 (ttp) cc_final: 0.7935 (ttm) REVERT: C 703 ILE cc_start: 0.8639 (mt) cc_final: 0.8375 (mt) REVERT: D 592 SER cc_start: 0.8910 (t) cc_final: 0.8471 (m) REVERT: D 677 MET cc_start: 0.8404 (ttp) cc_final: 0.8083 (ttm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.5270 time to fit residues: 169.7708 Evaluate side-chains 164 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS A 378 HIS A 561 GLN A 687 ASN B 498 GLN B 687 ASN C 378 HIS C 498 GLN C 687 ASN D 206 HIS D 320 HIS D 378 HIS D 561 GLN D 687 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17060 Z= 0.281 Angle : 0.574 7.897 23204 Z= 0.289 Chirality : 0.035 0.134 2656 Planarity : 0.004 0.054 2844 Dihedral : 16.314 165.356 2952 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.50 % Allowed : 7.08 % Favored : 92.42 % 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: -0.41 (0.18), residues: 2076 helix: 0.40 (0.15), residues: 1296 sheet: -4.12 (0.39), residues: 56 loop : -1.03 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 697 HIS 0.008 0.001 HIS D 320 PHE 0.012 0.001 PHE B 448 TYR 0.014 0.002 TYR D 309 ARG 0.002 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7450 (mp-120) REVERT: A 677 MET cc_start: 0.8565 (ttp) cc_final: 0.8248 (ttm) REVERT: B 677 MET cc_start: 0.8459 (ttp) cc_final: 0.8180 (ttm) REVERT: C 677 MET cc_start: 0.8440 (ttp) cc_final: 0.8078 (ttm) REVERT: D 561 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: D 677 MET cc_start: 0.8533 (ttp) cc_final: 0.8223 (ttm) outliers start: 8 outliers final: 4 residues processed: 171 average time/residue: 0.5538 time to fit residues: 152.0330 Evaluate side-chains 168 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain C residue 378 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 561 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 189 optimal weight: 1.9990 chunk 204 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 187 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 17060 Z= 0.462 Angle : 0.642 9.037 23204 Z= 0.323 Chirality : 0.039 0.127 2656 Planarity : 0.004 0.057 2844 Dihedral : 15.586 176.415 2952 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.56 % Allowed : 8.08 % Favored : 91.35 % 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: -0.55 (0.18), residues: 2076 helix: 0.29 (0.14), residues: 1296 sheet: -4.09 (0.40), residues: 56 loop : -1.08 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 549 HIS 0.027 0.002 HIS D 378 PHE 0.017 0.002 PHE B 448 TYR 0.012 0.002 TYR C 530 ARG 0.005 0.001 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.7061 (pm20) REVERT: A 677 MET cc_start: 0.8631 (ttp) cc_final: 0.8322 (ttm) REVERT: B 677 MET cc_start: 0.8573 (ttp) cc_final: 0.8361 (ttm) REVERT: C 677 MET cc_start: 0.8618 (ttp) cc_final: 0.8380 (ttm) REVERT: D 561 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: D 677 MET cc_start: 0.8624 (ttp) cc_final: 0.8389 (ttm) outliers start: 9 outliers final: 5 residues processed: 176 average time/residue: 0.5737 time to fit residues: 158.2556 Evaluate side-chains 169 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 320 HIS Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 20 optimal weight: 9.9990 chunk 90 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 54 optimal weight: 40.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN C 498 GLN C 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17060 Z= 0.146 Angle : 0.483 5.770 23204 Z= 0.249 Chirality : 0.033 0.122 2656 Planarity : 0.003 0.058 2844 Dihedral : 14.543 176.482 2952 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.75 % Allowed : 8.58 % Favored : 90.66 % 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: 0.19 (0.18), residues: 2076 helix: 0.94 (0.15), residues: 1296 sheet: -3.55 (0.42), residues: 56 loop : -0.97 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 740 HIS 0.019 0.001 HIS B 378 PHE 0.008 0.001 PHE D 638 TYR 0.011 0.001 TYR B 309 ARG 0.002 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8531 (ttp) cc_final: 0.8300 (ttm) REVERT: C 561 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: C 677 MET cc_start: 0.8533 (ttp) cc_final: 0.8238 (ttm) REVERT: D 677 MET cc_start: 0.8602 (ttp) cc_final: 0.8385 (ttm) outliers start: 12 outliers final: 5 residues processed: 175 average time/residue: 0.4844 time to fit residues: 139.3568 Evaluate side-chains 168 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 102 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN C 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17060 Z= 0.243 Angle : 0.508 6.969 23204 Z= 0.258 Chirality : 0.034 0.165 2656 Planarity : 0.003 0.052 2844 Dihedral : 14.547 179.771 2952 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.69 % Allowed : 9.65 % Favored : 89.66 % 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: 0.27 (0.18), residues: 2076 helix: 1.02 (0.15), residues: 1296 sheet: -3.25 (0.45), residues: 56 loop : -1.01 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 372 HIS 0.009 0.001 HIS B 378 PHE 0.009 0.001 PHE C 439 TYR 0.009 0.001 TYR C 530 ARG 0.002 0.000 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 677 MET cc_start: 0.8560 (ttp) cc_final: 0.8326 (ttm) REVERT: C 561 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: C 677 MET cc_start: 0.8554 (ttp) cc_final: 0.8306 (ttm) REVERT: D 561 GLN cc_start: 0.8018 (mp10) cc_final: 0.7455 (pm20) REVERT: D 677 MET cc_start: 0.8617 (ttp) cc_final: 0.8350 (ttm) outliers start: 11 outliers final: 8 residues processed: 175 average time/residue: 0.5564 time to fit residues: 153.9838 Evaluate side-chains 174 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 320 HIS Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 201 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN C 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17060 Z= 0.255 Angle : 0.506 7.218 23204 Z= 0.257 Chirality : 0.034 0.116 2656 Planarity : 0.003 0.051 2844 Dihedral : 14.468 178.768 2952 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.94 % Allowed : 9.84 % Favored : 89.22 % 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 (0.18), residues: 2076 helix: 1.06 (0.15), residues: 1292 sheet: -3.17 (0.47), residues: 56 loop : -1.01 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 372 HIS 0.005 0.001 HIS B 378 PHE 0.010 0.001 PHE D 655 TYR 0.010 0.001 TYR C 530 ARG 0.003 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.5987 (OUTLIER) cc_final: 0.5398 (tt0) REVERT: A 677 MET cc_start: 0.8575 (ttp) cc_final: 0.8322 (ttm) REVERT: C 561 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: C 677 MET cc_start: 0.8591 (ttp) cc_final: 0.8306 (ttm) REVERT: D 478 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5423 (tt0) REVERT: D 677 MET cc_start: 0.8608 (ttp) cc_final: 0.8314 (ttm) outliers start: 15 outliers final: 7 residues processed: 181 average time/residue: 0.5825 time to fit residues: 168.9085 Evaluate side-chains 175 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 561 GLN Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN D 206 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17060 Z= 0.172 Angle : 0.471 6.329 23204 Z= 0.240 Chirality : 0.033 0.177 2656 Planarity : 0.003 0.051 2844 Dihedral : 14.207 177.900 2952 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.75 % Allowed : 10.09 % Favored : 89.16 % 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: 0.53 (0.18), residues: 2076 helix: 1.26 (0.15), residues: 1292 sheet: -2.98 (0.49), residues: 56 loop : -0.97 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 372 HIS 0.004 0.001 HIS D 206 PHE 0.008 0.001 PHE C 439 TYR 0.009 0.001 TYR B 309 ARG 0.002 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 2.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5566 (tt0) REVERT: A 677 MET cc_start: 0.8545 (ttp) cc_final: 0.8316 (ttm) REVERT: C 561 GLN cc_start: 0.7423 (mp10) cc_final: 0.7131 (pm20) REVERT: C 677 MET cc_start: 0.8568 (ttp) cc_final: 0.8329 (ttm) REVERT: D 478 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5549 (tt0) REVERT: D 677 MET cc_start: 0.8582 (ttp) cc_final: 0.8334 (ttm) outliers start: 12 outliers final: 6 residues processed: 177 average time/residue: 0.5116 time to fit residues: 145.2800 Evaluate side-chains 172 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17060 Z= 0.261 Angle : 0.506 7.389 23204 Z= 0.255 Chirality : 0.034 0.124 2656 Planarity : 0.003 0.048 2844 Dihedral : 14.263 177.638 2952 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.13 % Allowed : 10.09 % Favored : 88.78 % 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: 0.45 (0.18), residues: 2076 helix: 1.21 (0.15), residues: 1292 sheet: -2.98 (0.51), residues: 56 loop : -1.04 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 372 HIS 0.002 0.001 HIS C 410 PHE 0.010 0.001 PHE A 439 TYR 0.014 0.001 TYR C 309 ARG 0.002 0.000 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5423 (tt0) REVERT: B 478 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5434 (tt0) REVERT: C 259 ASN cc_start: 0.4965 (t0) cc_final: 0.4514 (m-40) REVERT: C 561 GLN cc_start: 0.7615 (mp10) cc_final: 0.7297 (pm20) REVERT: C 677 MET cc_start: 0.8605 (ttp) cc_final: 0.8337 (ttm) REVERT: D 478 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5404 (tt0) REVERT: D 523 MET cc_start: 0.7430 (ttp) cc_final: 0.6932 (ttp) outliers start: 18 outliers final: 7 residues processed: 186 average time/residue: 0.5342 time to fit residues: 157.3424 Evaluate side-chains 178 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 646 ASP Chi-restraints excluded: chain D residue 689 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 176 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS C 498 GLN D 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17060 Z= 0.194 Angle : 0.471 6.456 23204 Z= 0.239 Chirality : 0.033 0.116 2656 Planarity : 0.003 0.049 2844 Dihedral : 13.994 176.765 2952 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.50 % Allowed : 10.96 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2076 helix: 1.38 (0.15), residues: 1292 sheet: -2.86 (0.52), residues: 56 loop : -1.03 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 372 HIS 0.002 0.001 HIS C 410 PHE 0.008 0.001 PHE D 439 TYR 0.015 0.001 TYR A 309 ARG 0.002 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.5470 (tt0) REVERT: A 523 MET cc_start: 0.7360 (ttp) cc_final: 0.6868 (ttp) REVERT: C 259 ASN cc_start: 0.4858 (t0) cc_final: 0.4374 (m-40) REVERT: C 561 GLN cc_start: 0.7710 (mp10) cc_final: 0.7360 (pm20) REVERT: D 478 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5408 (tt0) REVERT: D 523 MET cc_start: 0.7384 (ttp) cc_final: 0.6893 (ttp) outliers start: 8 outliers final: 5 residues processed: 179 average time/residue: 0.5421 time to fit residues: 156.2626 Evaluate side-chains 173 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 378 HIS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 chunk 131 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN C 410 HIS C 498 GLN D 378 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17060 Z= 0.283 Angle : 0.513 7.469 23204 Z= 0.259 Chirality : 0.035 0.116 2656 Planarity : 0.003 0.051 2844 Dihedral : 14.010 177.504 2952 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.63 % Allowed : 10.90 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2076 helix: 1.27 (0.15), residues: 1288 sheet: -2.99 (0.52), residues: 56 loop : -1.04 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 372 HIS 0.017 0.001 HIS B 378 PHE 0.010 0.001 PHE D 655 TYR 0.010 0.001 TYR D 530 ARG 0.002 0.000 ARG B 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Residue TYR 199 is missing expected H atoms. Skipping. Residue LYS 200 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 LEU 219 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue SER 282 is missing expected H atoms. Skipping. Residue THR 286 is missing expected H atoms. Skipping. Residue LYS 303 is missing expected H atoms. Skipping. Residue MET 308 is missing expected H atoms. Skipping. Residue LEU 323 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 SER 394 is missing expected H atoms. Skipping. Residue LYS 464 is missing expected H atoms. Skipping. Residue LYS 688 is missing expected H atoms. Skipping. Residue LYS 694 is missing expected H atoms. Skipping. Residue LYS 710 is missing expected H atoms. Skipping. Residue LEU 713 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 SER 722 is missing expected H atoms. Skipping. Residue LYS 724 is missing expected H atoms. Skipping. Residue LEU 725 is missing expected H atoms. Skipping. Residue LEU 726 is missing expected H atoms. Skipping. Residue THR 731 is missing expected H atoms. Skipping. Residue LYS 735 is missing expected H atoms. Skipping. Residue TYR 738 is missing expected H atoms. Skipping. Residue VAL 744 is missing expected H atoms. Skipping. Residue THR 750 is missing expected H atoms. Skipping. Residue THR 751 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5415 (tt0) REVERT: A 523 MET cc_start: 0.7407 (ttp) cc_final: 0.6902 (ttp) REVERT: B 478 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5418 (tt0) REVERT: C 561 GLN cc_start: 0.7776 (mp10) cc_final: 0.7424 (pm20) REVERT: D 478 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5395 (tt0) REVERT: D 523 MET cc_start: 0.7431 (ttp) cc_final: 0.6932 (ttp) outliers start: 10 outliers final: 5 residues processed: 177 average time/residue: 0.5237 time to fit residues: 148.7819 Evaluate side-chains 174 residues out of total 1860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 166 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 646 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN C 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.215685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138723 restraints weight = 47177.422| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.89 r_work: 0.3303 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17060 Z= 0.263 Angle : 0.507 7.362 23204 Z= 0.256 Chirality : 0.034 0.164 2656 Planarity : 0.003 0.053 2844 Dihedral : 13.934 176.980 2952 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.50 % Allowed : 11.09 % Favored : 88.41 % 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: 0.51 (0.18), residues: 2076 helix: 1.28 (0.15), residues: 1288 sheet: -3.03 (0.52), residues: 56 loop : -1.04 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 372 HIS 0.025 0.001 HIS D 378 PHE 0.009 0.001 PHE D 655 TYR 0.011 0.001 TYR B 401 ARG 0.002 0.000 ARG C 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6296.93 seconds wall clock time: 114 minutes 11.06 seconds (6851.06 seconds total)