Starting phenix.real_space_refine on Tue Apr 16 15:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg5_16631/04_2024/8cg5_16631_trim_updated.pdb" } resolution = 2.7 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= -0.000 sd= 0.014 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 1 5.49 5 S 86 5.16 5 C 12550 2.51 5 N 3545 2.21 5 O 3834 1.98 5 H 19691 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A PHE 919": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1175": "OD1" <-> "OD2" Residue "A PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 973": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1040": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 83": "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-5288/modules/chem_data/mon_lib" Total number of atoms: 39707 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 19248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 19248 Classifications: {'peptide': 1282} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1204} Chain: "B" Number of atoms: 19249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 19249 Classifications: {'peptide': 1282} Link IDs: {'PCIS': 1, 'PTRANS': 76, 'TRANS': 1204} Chain: "C" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1185 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'42X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 16.12, per 1000 atoms: 0.41 Number of scatterers: 39707 At special positions: 0 Unit cell: (196.8, 109.06, 122.18, 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 86 16.00 P 1 15.00 O 3834 8.00 N 3545 7.00 C 12550 6.00 H 19691 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.33 Conformation dependent library (CDL) restraints added in 4.9 seconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4924 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 111 helices and 15 sheets defined 42.2% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 33 through 52 Proline residue: A 43 - end of helix removed outlier: 4.123A pdb=" N ARG A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.640A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.695A pdb=" N LEU A 123 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 124 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 125 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 162 Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 224 through 233 removed outlier: 4.397A pdb=" N THR A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 295 through 307 Processing helix chain 'A' and resid 313 through 327 removed outlier: 3.736A pdb=" N MET A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 318 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 4.427A pdb=" N GLY A 346 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.612A pdb=" N SER A 351 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 423 through 426 No H-bonds generated for 'chain 'A' and resid 423 through 426' Processing helix chain 'A' and resid 460 through 465 Proline residue: A 464 - end of helix No H-bonds generated for 'chain 'A' and resid 460 through 465' Processing helix chain 'A' and resid 468 through 483 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 529 through 540 Proline residue: A 533 - end of helix removed outlier: 3.605A pdb=" N HIS A 540 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 661 through 675 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 693 through 707 Processing helix chain 'A' and resid 727 through 731 removed outlier: 3.864A pdb=" N VAL A 731 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 839 through 856 Processing helix chain 'A' and resid 863 through 872 Processing helix chain 'A' and resid 889 through 904 Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 942 through 958 Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 978 through 999 Processing helix chain 'A' and resid 1013 through 1019 Processing helix chain 'A' and resid 1025 through 1042 Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1089 through 1102 removed outlier: 3.784A pdb=" N LYS A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1120 No H-bonds generated for 'chain 'A' and resid 1118 through 1120' Processing helix chain 'A' and resid 1124 through 1131 Processing helix chain 'A' and resid 1155 through 1157 No H-bonds generated for 'chain 'A' and resid 1155 through 1157' Processing helix chain 'A' and resid 1160 through 1168 removed outlier: 3.598A pdb=" N THR A1164 " --> pdb=" O PRO A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1183 Processing helix chain 'A' and resid 1201 through 1209 Processing helix chain 'A' and resid 1225 through 1239 Processing helix chain 'A' and resid 1245 through 1248 No H-bonds generated for 'chain 'A' and resid 1245 through 1248' Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'A' and resid 1279 through 1281 No H-bonds generated for 'chain 'A' and resid 1279 through 1281' Processing helix chain 'B' and resid 20 through 28 removed outlier: 3.543A pdb=" N ARG B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 50 Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 55 through 58 No H-bonds generated for 'chain 'B' and resid 55 through 58' Processing helix chain 'B' and resid 67 through 75 removed outlier: 3.746A pdb=" N VAL B 71 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.598A pdb=" N ARG B 75 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 101 Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.672A pdb=" N ALA B 122 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 123 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 124 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 162 Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.925A pdb=" N THR B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 313 through 326 removed outlier: 4.380A pdb=" N ALA B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 318 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 removed outlier: 4.085A pdb=" N GLY B 346 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.689A pdb=" N ASN B 350 " --> pdb=" O PRO B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 423 through 426 No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 460 through 465 Proline residue: B 464 - end of helix No H-bonds generated for 'chain 'B' and resid 460 through 465' Processing helix chain 'B' and resid 468 through 483 Processing helix chain 'B' and resid 492 through 494 No H-bonds generated for 'chain 'B' and resid 492 through 494' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 529 through 540 Proline residue: B 533 - end of helix removed outlier: 3.720A pdb=" N HIS B 540 " --> pdb=" O ASN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 569 removed outlier: 3.517A pdb=" N ARG B 569 " --> pdb=" O ASN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 594 Processing helix chain 'B' and resid 628 through 633 Processing helix chain 'B' and resid 661 through 675 Processing helix chain 'B' and resid 693 through 707 Processing helix chain 'B' and resid 727 through 731 removed outlier: 3.607A pdb=" N VAL B 731 " --> pdb=" O LYS B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 772 through 775 No H-bonds generated for 'chain 'B' and resid 772 through 775' Processing helix chain 'B' and resid 839 through 855 Processing helix chain 'B' and resid 863 through 872 Processing helix chain 'B' and resid 889 through 905 Processing helix chain 'B' and resid 935 through 940 Processing helix chain 'B' and resid 942 through 957 Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 973 through 975 No H-bonds generated for 'chain 'B' and resid 973 through 975' Processing helix chain 'B' and resid 978 through 999 Processing helix chain 'B' and resid 1013 through 1020 Processing helix chain 'B' and resid 1025 through 1042 Processing helix chain 'B' and resid 1057 through 1063 removed outlier: 3.965A pdb=" N VAL B1061 " --> pdb=" O GLU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1102 removed outlier: 3.727A pdb=" N ALA B1101 " --> pdb=" O ALA B1097 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS B1102 " --> pdb=" O ALA B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1133 Proline residue: B1125 - end of helix Processing helix chain 'B' and resid 1155 through 1157 No H-bonds generated for 'chain 'B' and resid 1155 through 1157' Processing helix chain 'B' and resid 1160 through 1168 removed outlier: 3.904A pdb=" N THR B1164 " --> pdb=" O PRO B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1173 through 1182 Processing helix chain 'B' and resid 1201 through 1209 Processing helix chain 'B' and resid 1225 through 1239 Processing helix chain 'B' and resid 1245 through 1248 No H-bonds generated for 'chain 'B' and resid 1245 through 1248' Processing helix chain 'B' and resid 1253 through 1255 No H-bonds generated for 'chain 'B' and resid 1253 through 1255' Processing helix chain 'B' and resid 1280 through 1282 No H-bonds generated for 'chain 'B' and resid 1280 through 1282' Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 42 No H-bonds generated for 'chain 'C' and resid 39 through 42' Processing helix chain 'C' and resid 46 through 59 removed outlier: 3.612A pdb=" N VAL C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing sheet with id= A, first strand: chain 'A' and resid 331 through 334 Processing sheet with id= B, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.617A pdb=" N SER A 219 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA A 211 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A 209 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 546 through 549 removed outlier: 9.062A pdb=" N TYR A 547 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 501 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE A 549 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A 503 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 574 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP A 502 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE A 576 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLY A 504 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY A 578 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 388 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LYS A 626 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE A 386 " --> pdb=" O LYS A 626 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 644 through 649 removed outlier: 3.819A pdb=" N GLY A 644 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 796 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU A 797 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS A 685 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASN A 799 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A 723 " --> pdb=" O CYS A 685 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 830 through 836 Processing sheet with id= F, first strand: chain 'A' and resid 919 through 923 removed outlier: 6.922A pdb=" N ILE A1191 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA A 922 " --> pdb=" O ILE A1191 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A1193 " --> pdb=" O ALA A 922 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 1005 through 1007 removed outlier: 3.675A pdb=" N LYS A1150 " --> pdb=" O SER A1145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1106 through 1108 removed outlier: 5.903A pdb=" N GLY A1086 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE A1074 " --> pdb=" O GLY A1086 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 332 through 337 removed outlier: 6.625A pdb=" N MET B 7 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER B 335 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 9 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE B 337 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 11 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 239 through 242 removed outlier: 3.616A pdb=" N ALA B 211 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU B 209 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 546 through 549 removed outlier: 9.076A pdb=" N TYR B 547 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 501 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE B 549 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR B 503 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 574 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N TRP B 502 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE B 576 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLY B 504 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY B 578 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 388 " --> pdb=" O ILE B 624 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS B 626 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE B 386 " --> pdb=" O LYS B 626 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 640 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 641 " --> pdb=" O GLU B 813 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 811 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 645 " --> pdb=" O CYS B 809 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N CYS B 809 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR B 647 " --> pdb=" O ASN B 807 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN B 807 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 684 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASN B 799 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU B 686 " --> pdb=" O ASN B 799 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N PHE B 801 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR B 723 " --> pdb=" O CYS B 685 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 830 through 836 Processing sheet with id= M, first strand: chain 'B' and resid 1191 through 1195 removed outlier: 7.544A pdb=" N LEU B 921 " --> pdb=" O LYS B1004 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B1006 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE B 923 " --> pdb=" O VAL B1006 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1106 through 1108 removed outlier: 3.509A pdb=" N GLN B1107 " --> pdb=" O ALA B1052 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY B1086 " --> pdb=" O PHE B1074 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE B1074 " --> pdb=" O GLY B1086 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1143 through 1145 removed outlier: 3.509A pdb=" N LYS B1150 " --> pdb=" O SER B1145 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2049 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: 16.88 Time building geometry restraints manager: 32.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19653 1.03 - 1.23: 81 1.23 - 1.42: 8417 1.42 - 1.62: 11858 1.62 - 1.81: 134 Bond restraints: 40143 Sorted by residual: bond pdb=" CG PRO B 334 " pdb=" CD PRO B 334 " ideal model delta sigma weight residual 1.503 1.408 0.095 3.40e-02 8.65e+02 7.86e+00 bond pdb=" CB PRO A 269 " pdb=" CG PRO A 269 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.70e+00 bond pdb=" CG PRO B 961 " pdb=" CD PRO B 961 " ideal model delta sigma weight residual 1.503 1.433 0.070 3.40e-02 8.65e+02 4.19e+00 bond pdb=" CB PRO B 334 " pdb=" CG PRO B 334 " ideal model delta sigma weight residual 1.492 1.593 -0.101 5.00e-02 4.00e+02 4.04e+00 bond pdb=" CB PRO A 334 " pdb=" CG PRO A 334 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.33e+00 ... (remaining 40138 not shown) Histogram of bond angle deviations from ideal: 95.00 - 102.79: 89 102.79 - 110.59: 41727 110.59 - 118.38: 13052 118.38 - 126.18: 17169 126.18 - 133.97: 524 Bond angle restraints: 72561 Sorted by residual: angle pdb=" CA PRO B 334 " pdb=" N PRO B 334 " pdb=" CD PRO B 334 " ideal model delta sigma weight residual 112.00 101.56 10.44 1.40e+00 5.10e-01 5.56e+01 angle pdb=" CA PRO B 961 " pdb=" N PRO B 961 " pdb=" CD PRO B 961 " ideal model delta sigma weight residual 112.00 102.46 9.54 1.40e+00 5.10e-01 4.65e+01 angle pdb=" N PRO B 334 " pdb=" CD PRO B 334 " pdb=" CG PRO B 334 " ideal model delta sigma weight residual 103.20 95.00 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N PRO B 961 " pdb=" CD PRO B 961 " pdb=" CG PRO B 961 " ideal model delta sigma weight residual 103.20 95.59 7.61 1.50e+00 4.44e-01 2.57e+01 angle pdb=" CA PRO A 269 " pdb=" N PRO A 269 " pdb=" CD PRO A 269 " ideal model delta sigma weight residual 112.00 106.31 5.69 1.40e+00 5.10e-01 1.65e+01 ... (remaining 72556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.16: 17998 30.16 - 60.32: 971 60.32 - 90.48: 56 90.48 - 120.63: 0 120.63 - 150.79: 2 Dihedral angle restraints: 19027 sinusoidal: 10403 harmonic: 8624 Sorted by residual: dihedral pdb=" CA VAL B 118 " pdb=" C VAL B 118 " pdb=" N ALA B 119 " pdb=" CA ALA B 119 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLU B 735 " pdb=" C GLU B 735 " pdb=" N SER B 736 " pdb=" CA SER B 736 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" C26 42X C2000 " pdb=" C29 42X C2000 " pdb=" C32 42X C2000 " pdb=" O33 42X C2000 " ideal model delta sinusoidal sigma weight residual 12.53 -138.26 150.79 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 19024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1907 0.028 - 0.056: 841 0.056 - 0.083: 216 0.083 - 0.111: 159 0.111 - 0.139: 59 Chirality restraints: 3182 Sorted by residual: chirality pdb=" CB VAL A1120 " pdb=" CA VAL A1120 " pdb=" CG1 VAL A1120 " pdb=" CG2 VAL A1120 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 755 " pdb=" N ILE A 755 " pdb=" C ILE A 755 " pdb=" CB ILE A 755 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL A 416 " pdb=" N VAL A 416 " pdb=" C VAL A 416 " pdb=" CB VAL A 416 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 3179 not shown) Planarity restraints: 6140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 960 " -0.072 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO B 961 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 961 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 961 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 333 " 0.059 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO B 334 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 325 " 0.228 9.50e-02 1.11e+02 7.64e-02 7.12e+00 pdb=" NE ARG A 325 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 325 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 325 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 325 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 325 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 325 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 325 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 325 " 0.001 2.00e-02 2.50e+03 ... (remaining 6137 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1681 2.16 - 2.77: 75358 2.77 - 3.38: 111841 3.38 - 3.99: 147124 3.99 - 4.60: 231607 Nonbonded interactions: 567611 Sorted by model distance: nonbonded pdb=" OE1 GLU B 21 " pdb=" H GLU B 21 " model vdw 1.545 1.850 nonbonded pdb=" OE1 GLN A1137 " pdb="HH21 ARG B 167 " model vdw 1.554 1.850 nonbonded pdb=" HG SER A 184 " pdb=" OD2 ASP A 187 " model vdw 1.556 1.850 nonbonded pdb=" O HIS A1165 " pdb=" H SER A1169 " model vdw 1.561 1.850 nonbonded pdb=" O ILE A 831 " pdb=" HG SER A 868 " model vdw 1.563 1.850 ... (remaining 567606 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' selection = (chain 'B' and (resid 5 through 552 or (resid 553 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 554 through 1286)) } 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=1.00 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: 3.470 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: 0.610 Extract box with map and model: 13.790 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 124.300 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.004 0.108 20452 Z= 0.241 Angle : 0.571 10.440 27862 Z= 0.293 Chirality : 0.040 0.139 3182 Planarity : 0.006 0.104 3658 Dihedral : 17.704 150.794 7409 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.06 % Allowed : 29.85 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.78 (0.17), residues: 2634 helix: 1.63 (0.16), residues: 1132 sheet: 0.51 (0.32), residues: 288 loop : -0.54 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1226 HIS 0.010 0.001 HIS B1165 PHE 0.017 0.001 PHE A 973 TYR 0.013 0.001 TYR A1018 ARG 0.016 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 908 ARG cc_start: 0.8131 (mmp80) cc_final: 0.7914 (mmm160) outliers start: 44 outliers final: 43 residues processed: 176 average time/residue: 2.3003 time to fit residues: 477.3690 Evaluate side-chains 167 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 124 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 553 CYS Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1076 CYS Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 106 optimal weight: 20.0000 chunk 206 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 508 ASN A 897 GLN A1178 GLN A1214 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 348 GLN B 632 GLN B 680 ASN B1083 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 GLN B1231 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20452 Z= 0.251 Angle : 0.528 6.360 27862 Z= 0.270 Chirality : 0.041 0.145 3182 Planarity : 0.004 0.053 3658 Dihedral : 7.327 140.651 2897 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.94 % Allowed : 27.17 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.65 (0.17), residues: 2634 helix: 1.38 (0.16), residues: 1141 sheet: 0.55 (0.32), residues: 290 loop : -0.48 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1226 HIS 0.004 0.001 HIS A1166 PHE 0.011 0.001 PHE B 973 TYR 0.013 0.001 TYR B1018 ARG 0.009 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 126 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: B 686 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: B 924 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8599 (p) outliers start: 84 outliers final: 48 residues processed: 202 average time/residue: 2.1893 time to fit residues: 525.5986 Evaluate side-chains 176 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 125 time to evaluate : 3.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 132 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 162 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN A1140 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20452 Z= 0.382 Angle : 0.545 5.278 27862 Z= 0.280 Chirality : 0.042 0.141 3182 Planarity : 0.004 0.060 3658 Dihedral : 7.103 129.230 2890 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.61 % Allowed : 26.79 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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 (0.17), residues: 2634 helix: 1.20 (0.16), residues: 1145 sheet: 0.52 (0.32), residues: 290 loop : -0.51 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1226 HIS 0.004 0.001 HIS B1249 PHE 0.008 0.001 PHE B 451 TYR 0.016 0.002 TYR B1018 ARG 0.004 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 125 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 686 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: B 924 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 1082 ARG cc_start: 0.7973 (mpt-90) cc_final: 0.7355 (mpp80) REVERT: B 1107 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7913 (pt0) outliers start: 77 outliers final: 56 residues processed: 193 average time/residue: 2.4033 time to fit residues: 541.1032 Evaluate side-chains 181 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 918 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1107 GLN Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1280 SER Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 236 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20452 Z= 0.264 Angle : 0.508 5.101 27862 Z= 0.259 Chirality : 0.041 0.139 3182 Planarity : 0.004 0.040 3658 Dihedral : 6.858 127.524 2890 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.38 % Allowed : 26.28 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2634 helix: 1.27 (0.16), residues: 1145 sheet: 0.60 (0.32), residues: 290 loop : -0.47 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1226 HIS 0.002 0.001 HIS A 100 PHE 0.009 0.001 PHE C 83 TYR 0.014 0.001 TYR B1018 ARG 0.004 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 127 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: A 971 LYS cc_start: 0.8797 (mppt) cc_final: 0.8550 (mptp) REVERT: A 1002 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7359 (pp30) REVERT: B 686 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: B 924 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8707 (p) REVERT: B 1082 ARG cc_start: 0.7958 (mpt-90) cc_final: 0.7368 (mpp80) outliers start: 72 outliers final: 50 residues processed: 190 average time/residue: 2.2857 time to fit residues: 515.1914 Evaluate side-chains 178 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 211 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 216 optimal weight: 0.0980 chunk 175 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20452 Z= 0.253 Angle : 0.502 5.162 27862 Z= 0.255 Chirality : 0.040 0.139 3182 Planarity : 0.004 0.039 3658 Dihedral : 6.627 127.483 2885 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.38 % Allowed : 26.09 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.64 (0.17), residues: 2634 helix: 1.32 (0.16), residues: 1145 sheet: 0.58 (0.32), residues: 290 loop : -0.44 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1226 HIS 0.003 0.001 HIS B 100 PHE 0.012 0.001 PHE C 83 TYR 0.014 0.001 TYR B1018 ARG 0.006 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 124 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: A 479 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: A 512 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: A 1002 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7347 (pp30) REVERT: B 686 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: B 1082 ARG cc_start: 0.7952 (mpt-90) cc_final: 0.7391 (mpp80) outliers start: 72 outliers final: 53 residues processed: 186 average time/residue: 2.3784 time to fit residues: 519.6279 Evaluate side-chains 178 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 121 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1285 ASP Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 840 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 85 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 254 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 0.0470 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20452 Z= 0.187 Angle : 0.485 5.127 27862 Z= 0.245 Chirality : 0.039 0.138 3182 Planarity : 0.004 0.038 3658 Dihedral : 6.365 128.660 2884 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.77 % Allowed : 26.61 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.77 (0.17), residues: 2634 helix: 1.43 (0.16), residues: 1143 sheet: 0.67 (0.32), residues: 290 loop : -0.37 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1226 HIS 0.003 0.001 HIS B1165 PHE 0.012 0.001 PHE B 973 TYR 0.012 0.001 TYR B1018 ARG 0.009 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 130 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: A 512 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 1002 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7353 (pp30) REVERT: B 363 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7240 (pt) REVERT: B 1082 ARG cc_start: 0.7926 (mpt-90) cc_final: 0.7378 (mpp80) outliers start: 59 outliers final: 45 residues processed: 181 average time/residue: 2.4681 time to fit residues: 524.0933 Evaluate side-chains 175 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 127 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 245 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20452 Z= 0.167 Angle : 0.479 5.317 27862 Z= 0.240 Chirality : 0.039 0.137 3182 Planarity : 0.004 0.097 3658 Dihedral : 6.081 128.010 2878 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.67 % Allowed : 26.51 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2634 helix: 1.54 (0.16), residues: 1143 sheet: 0.73 (0.32), residues: 290 loop : -0.29 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1226 HIS 0.003 0.001 HIS B 100 PHE 0.008 0.001 PHE A 973 TYR 0.011 0.001 TYR B1018 ARG 0.013 0.000 ARG B 908 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 128 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: A 971 LYS cc_start: 0.8715 (mppt) cc_final: 0.8463 (mptp) REVERT: A 1002 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7372 (pp30) REVERT: B 363 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7192 (pt) REVERT: B 1082 ARG cc_start: 0.7916 (mpt-90) cc_final: 0.7378 (mpp80) outliers start: 57 outliers final: 43 residues processed: 181 average time/residue: 2.4088 time to fit residues: 511.0028 Evaluate side-chains 171 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 76 optimal weight: 0.0870 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20452 Z= 0.220 Angle : 0.488 5.259 27862 Z= 0.245 Chirality : 0.040 0.138 3182 Planarity : 0.004 0.040 3658 Dihedral : 5.961 127.791 2876 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.49 % Allowed : 26.61 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 0.90 (0.17), residues: 2634 helix: 1.53 (0.16), residues: 1143 sheet: 0.71 (0.32), residues: 290 loop : -0.29 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 421 HIS 0.002 0.001 HIS A 877 PHE 0.013 0.001 PHE B 973 TYR 0.013 0.001 TYR B1018 ARG 0.010 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 971 LYS cc_start: 0.8738 (mppt) cc_final: 0.8480 (mptp) REVERT: A 1002 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7339 (pp30) REVERT: B 363 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7164 (pt) REVERT: B 686 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: B 1082 ARG cc_start: 0.7902 (mpt-90) cc_final: 0.7364 (mpp80) outliers start: 53 outliers final: 42 residues processed: 177 average time/residue: 2.3964 time to fit residues: 496.6633 Evaluate side-chains 172 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 3.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 242 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 155 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20452 Z= 0.168 Angle : 0.476 5.381 27862 Z= 0.238 Chirality : 0.039 0.136 3182 Planarity : 0.003 0.041 3658 Dihedral : 5.795 127.965 2874 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.25 % Allowed : 26.79 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.01 (0.17), residues: 2634 helix: 1.62 (0.16), residues: 1143 sheet: 0.72 (0.32), residues: 292 loop : -0.21 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1226 HIS 0.002 0.000 HIS B 253 PHE 0.010 0.001 PHE C 83 TYR 0.011 0.001 TYR B1018 ARG 0.011 0.000 ARG C 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 128 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: A 490 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7074 (ttp-110) REVERT: A 971 LYS cc_start: 0.8751 (mppt) cc_final: 0.8486 (mptp) REVERT: A 1002 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7280 (pp30) REVERT: B 686 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: B 1082 ARG cc_start: 0.7891 (mpt-90) cc_final: 0.7357 (mpp80) outliers start: 48 outliers final: 37 residues processed: 171 average time/residue: 2.6604 time to fit residues: 534.6987 Evaluate side-chains 166 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B1083 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20452 Z= 0.168 Angle : 0.477 5.648 27862 Z= 0.239 Chirality : 0.039 0.137 3182 Planarity : 0.003 0.043 3658 Dihedral : 5.588 126.420 2870 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.92 % Allowed : 27.12 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.06 (0.17), residues: 2634 helix: 1.68 (0.16), residues: 1141 sheet: 0.73 (0.32), residues: 292 loop : -0.20 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 15 HIS 0.002 0.001 HIS B 100 PHE 0.015 0.001 PHE B 973 TYR 0.011 0.001 TYR B1018 ARG 0.011 0.000 ARG C 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 129 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8234 (mt-10) REVERT: A 971 LYS cc_start: 0.8775 (mppt) cc_final: 0.8515 (mptp) REVERT: A 1002 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7274 (pp30) REVERT: B 1082 ARG cc_start: 0.7864 (mpt-90) cc_final: 0.7330 (mpp80) outliers start: 41 outliers final: 35 residues processed: 166 average time/residue: 2.6980 time to fit residues: 519.5650 Evaluate side-chains 162 residues out of total 2131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 556 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 924 THR Chi-restraints excluded: chain B residue 1115 PHE Chi-restraints excluded: chain B residue 1157 ASP Chi-restraints excluded: chain B residue 1164 THR Chi-restraints excluded: chain B residue 1171 VAL Chi-restraints excluded: chain B residue 1211 THR Chi-restraints excluded: chain B residue 1222 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 208 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 214 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 183 optimal weight: 0.5980 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 680 ASN B 981 GLN B1083 ASN ** B1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.064992 restraints weight = 110912.388| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.67 r_work: 0.2768 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20452 Z= 0.149 Angle : 0.472 5.330 27862 Z= 0.235 Chirality : 0.039 0.136 3182 Planarity : 0.003 0.042 3658 Dihedral : 5.374 124.579 2868 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.74 % Allowed : 27.17 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.29 % 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: 1.14 (0.17), residues: 2634 helix: 1.74 (0.17), residues: 1141 sheet: 0.80 (0.32), residues: 292 loop : -0.15 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1226 HIS 0.003 0.000 HIS B 253 PHE 0.008 0.001 PHE C 83 TYR 0.010 0.001 TYR B1018 ARG 0.013 0.000 ARG C 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11045.00 seconds wall clock time: 222 minutes 18.95 seconds (13338.95 seconds total)