Starting phenix.real_space_refine on Sat Mar 23 15:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cg6_16632/03_2024/8cg6_16632_trim_updated.pdb" } resolution = 3.4 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= 0.009 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 85 5.16 5 C 11904 2.51 5 N 3360 2.21 5 O 3626 1.98 5 H 18739 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 951": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 969": "OD1" <-> "OD2" Residue "B ASP 1110": "OD1" <-> "OD2" Residue "B GLU 1250": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1208, 18155 Classifications: {'peptide': 1208} Link IDs: {'PTRANS': 73, 'TRANS': 1134} Chain breaks: 4 Chain: "B" Number of atoms: 18361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 18361 Classifications: {'peptide': 1223} Link IDs: {'PCIS': 1, 'PTRANS': 73, 'TRANS': 1148} Chain breaks: 3 Chain: "C" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1174 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: 14.58, per 1000 atoms: 0.39 Number of scatterers: 37715 At special positions: 0 Unit cell: (167.28, 143.5, 110.7, 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 85 16.00 P 1 15.00 O 3626 8.00 N 3360 7.00 C 11904 6.00 H 18739 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: 32.12 Conformation dependent library (CDL) restraints added in 4.2 seconds 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 41.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 34 through 52 Proline residue: A 43 - end of helix removed outlier: 4.031A pdb=" N ARG A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.801A pdb=" N GLU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.904A pdb=" N VAL A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Proline residue: A 72 - end of helix Processing helix chain 'A' and resid 81 through 101 Processing helix chain 'A' and resid 121 through 130 removed outlier: 3.735A pdb=" N SER A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 162 removed outlier: 3.661A pdb=" N VAL A 138 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 185 through 199 Processing helix chain 'A' and resid 224 through 233 removed outlier: 4.081A pdb=" N THR A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 removed outlier: 4.610A pdb=" N CYS A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.622A pdb=" N GLY A 346 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.759A pdb=" N HIS A 352 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' 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 531 through 539 removed outlier: 3.981A pdb=" N VAL A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 569 removed outlier: 3.741A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'A' and resid 666 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 728 through 731 No H-bonds generated for 'chain 'A' and resid 728 through 731' Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 839 through 855 Processing helix chain 'A' and resid 864 through 873 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 removed outlier: 3.561A pdb=" N GLU A 968 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 975 removed outlier: 3.608A pdb=" N THR A 975 " --> pdb=" O VAL A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 972 through 975' Processing helix chain 'A' and resid 978 through 999 Processing helix chain 'A' and resid 1011 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: 3.981A pdb=" N LYS A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1131 Proline residue: A1122 - end of helix Proline residue: A1125 - end of helix Processing helix chain 'A' and resid 1155 through 1158 Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1174 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 1248 through 1251 removed outlier: 4.248A pdb=" N ASP A1251 " --> pdb=" O TYR A1248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1253 through 1255 No H-bonds generated for 'chain 'A' and resid 1253 through 1255' Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 33 through 52 Proline residue: B 43 - end of helix removed outlier: 3.882A pdb=" N ARG B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 71 through 76 Processing helix chain 'B' and resid 81 through 101 removed outlier: 3.808A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.561A pdb=" N VAL B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 162 removed outlier: 3.589A pdb=" N VAL B 138 " --> pdb=" O THR B 135 " (cutoff:3.500A) 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: 3.682A pdb=" N THR B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 removed outlier: 4.795A pdb=" N CYS B 266 " --> pdb=" O HIS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 Processing helix chain 'B' and resid 313 through 327 removed outlier: 4.606A pdb=" N ALA B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Proline residue: B 347 - end of helix removed outlier: 4.269A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 453 through 456 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 468 through 483 Processing helix chain 'B' and resid 529 through 539 Proline residue: B 533 - end of helix removed outlier: 3.501A pdb=" N PHE B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 661 through 675 Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 694 through 707 removed outlier: 5.041A pdb=" N THR B 700 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 701 " --> pdb=" O SER B 697 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 839 through 855 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'B' and resid 889 through 904 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 972 through 975 Processing helix chain 'B' and resid 978 through 999 Processing helix chain 'B' and resid 1012 through 1020 Processing helix chain 'B' and resid 1025 through 1041 Processing helix chain 'B' and resid 1057 through 1062 Processing helix chain 'B' and resid 1089 through 1102 Processing helix chain 'B' and resid 1118 through 1133 Proline residue: B1122 - end of helix Proline residue: B1125 - end of helix removed outlier: 3.565A pdb=" N ALA B1132 " --> pdb=" O GLN B1129 " (cutoff:3.500A) 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 1161 through 1168 Processing helix chain 'B' and resid 1174 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 1246 through 1248 No H-bonds generated for 'chain 'B' and resid 1246 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 '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 Processing helix chain 'C' and resid 68 through 72 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 177 through 181 removed outlier: 6.729A pdb=" N SER A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A 209 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 625 through 627 removed outlier: 3.510A pdb=" N ILE A 384 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 640 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= E, first strand: chain 'A' and resid 644 through 646 removed outlier: 3.882A pdb=" N GLY A 644 " --> pdb=" O VAL A 811 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 830 through 836 Processing sheet with id= G, first strand: chain 'A' and resid 1106 through 1109 removed outlier: 4.327A pdb=" N MET A1050 " --> pdb=" O LEU A1109 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A1086 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N PHE A1074 " --> pdb=" O GLY A1086 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1143 through 1145 Processing sheet with id= I, first strand: chain 'B' and resid 332 through 337 removed outlier: 6.840A pdb=" N MET B 7 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER B 335 " --> pdb=" O MET B 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 9 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 337 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.225A 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: 3.585A pdb=" N ALA B 211 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU B 209 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 384 through 386 removed outlier: 3.862A pdb=" N ALA B 640 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 811 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE B 645 " --> pdb=" O CYS B 809 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N CYS B 809 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 796 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU B 797 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS B 685 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN B 799 " --> pdb=" O CYS B 685 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 687 " --> pdb=" O ASN B 799 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TYR B 723 " --> pdb=" O CYS B 685 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N MET B 687 " --> pdb=" O TYR B 723 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY B 725 " --> pdb=" O MET B 687 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 546 through 549 removed outlier: 9.030A pdb=" N TYR B 547 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 501 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE B 549 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR B 503 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR B 574 " --> pdb=" O GLY B 500 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N TRP B 502 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 576 " --> pdb=" O TRP B 502 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY B 504 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 830 through 836 removed outlier: 3.878A pdb=" N ALA B 882 " --> pdb=" O LEU B 834 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 919 through 923 removed outlier: 6.636A pdb=" N ILE B1191 " --> pdb=" O VAL B 920 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA B 922 " --> pdb=" O ILE B1191 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B1193 " --> pdb=" O ALA B 922 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 1082 through 1088 Processing sheet with id= P, first strand: chain 'B' and resid 1143 through 1145 removed outlier: 3.552A pdb=" N SER B1145 " --> pdb=" O LYS B1150 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1797 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: 15.95 Time building geometry restraints manager: 33.17 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: 18699 1.03 - 1.23: 53 1.23 - 1.42: 7953 1.42 - 1.62: 11277 1.62 - 1.82: 130 Bond restraints: 38112 Sorted by residual: bond pdb=" CB PRO A 378 " pdb=" CG PRO A 378 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.01e+00 bond pdb=" CB PRO A 709 " pdb=" CG PRO A 709 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 4.00e+00 bond pdb=" CB PRO B 378 " pdb=" CG PRO B 378 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.78e+00 bond pdb=" CB GLN B 376 " pdb=" CG GLN B 376 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CA HIS B 540 " pdb=" C HIS B 540 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.80e-02 3.09e+03 1.39e+00 ... (remaining 38107 not shown) Histogram of bond angle deviations from ideal: 93.54 - 101.63: 34 101.63 - 109.72: 27830 109.72 - 117.81: 23925 117.81 - 125.90: 16636 125.90 - 133.99: 487 Bond angle restraints: 68912 Sorted by residual: angle pdb=" CA PRO A 378 " pdb=" N PRO A 378 " pdb=" CD PRO A 378 " ideal model delta sigma weight residual 112.00 100.70 11.30 1.40e+00 5.10e-01 6.51e+01 angle pdb=" CA PRO A 709 " pdb=" N PRO A 709 " pdb=" CD PRO A 709 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" CA PRO B 709 " pdb=" N PRO B 709 " pdb=" CD PRO B 709 " ideal model delta sigma weight residual 112.00 106.04 5.96 1.40e+00 5.10e-01 1.81e+01 angle pdb=" N PRO B 709 " pdb=" CD PRO B 709 " pdb=" CG PRO B 709 " ideal model delta sigma weight residual 103.20 97.11 6.09 1.50e+00 4.44e-01 1.65e+01 angle pdb=" CA PRO B 709 " pdb=" CB PRO B 709 " pdb=" CG PRO B 709 " ideal model delta sigma weight residual 104.50 96.92 7.58 1.90e+00 2.77e-01 1.59e+01 ... (remaining 68907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 16401 22.09 - 44.18: 1299 44.18 - 66.27: 300 66.27 - 88.36: 43 88.36 - 110.45: 5 Dihedral angle restraints: 18048 sinusoidal: 9895 harmonic: 8153 Sorted by residual: dihedral pdb=" CA THR A 364 " pdb=" C THR A 364 " pdb=" N SER A 365 " pdb=" CA SER A 365 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLY B 121 " pdb=" C GLY B 121 " pdb=" N ALA B 122 " pdb=" CA ALA B 122 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA SER A 340 " pdb=" C SER A 340 " pdb=" N PHE A 341 " pdb=" CA PHE A 341 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 18045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2011 0.032 - 0.064: 693 0.064 - 0.096: 200 0.096 - 0.128: 117 0.128 - 0.160: 10 Chirality restraints: 3031 Sorted by residual: chirality pdb=" CB THR B 196 " pdb=" CA THR B 196 " pdb=" OG1 THR B 196 " pdb=" CG2 THR B 196 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE B 576 " pdb=" N ILE B 576 " pdb=" C ILE B 576 " pdb=" CB ILE B 576 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL A 499 " pdb=" N VAL A 499 " pdb=" C VAL A 499 " pdb=" CB VAL A 499 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 3028 not shown) Planarity restraints: 5803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 377 " -0.091 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO A 378 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 708 " 0.082 5.00e-02 4.00e+02 1.19e-01 2.28e+01 pdb=" N PRO A 709 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 709 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 709 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 377 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO B 378 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 378 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 378 " 0.036 5.00e-02 4.00e+02 ... (remaining 5800 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 452 2.01 - 2.66: 53767 2.66 - 3.31: 110055 3.31 - 3.95: 138052 3.95 - 4.60: 215815 Nonbonded interactions: 518141 Sorted by model distance: nonbonded pdb=" OE2 GLU A 157 " pdb=" HE ARG B 950 " model vdw 1.368 1.850 nonbonded pdb=" O LYS B1102 " pdb=" HZ2 LYS B1102 " model vdw 1.468 1.850 nonbonded pdb=" OE1 GLU B 823 " pdb=" H GLU B 823 " model vdw 1.476 1.850 nonbonded pdb=" O ASP A1138 " pdb="HH21 ARG B 167 " model vdw 1.504 1.850 nonbonded pdb=" O GLY B 121 " pdb=" H ALA B 125 " model vdw 1.513 1.850 ... (remaining 518136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 420 or resid 440 through 508 or resid 530 throug \ h 1272)) selection = (chain 'B' and (resid 5 through 118 or (resid 119 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 120 through 508 or (resid 530 and (name N or name CA or name C or nam \ e O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid 531 thr \ ough 586 or resid 600 through 650 or (resid 651 and (name N or name CA or name C \ or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resid \ 664 through 1272)) } 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.550 Extract box with map and model: 13.750 Check model and map are aligned: 0.610 Set scattering table: 0.360 Process input model: 119.470 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.003 0.123 19373 Z= 0.191 Angle : 0.584 12.559 26376 Z= 0.295 Chirality : 0.039 0.160 3031 Planarity : 0.005 0.130 3455 Dihedral : 16.921 110.454 7031 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 0.20 % Allowed : 22.45 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.06 (0.18), residues: 2486 helix: 1.56 (0.17), residues: 1081 sheet: -1.57 (0.31), residues: 263 loop : -1.25 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 156 HIS 0.006 0.001 HIS A 540 PHE 0.022 0.001 PHE A 607 TYR 0.012 0.001 TYR B 951 ARG 0.005 0.000 ARG A 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1054 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8523 (mtp85) outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 0.7204 time to fit residues: 172.6612 Evaluate side-chains 147 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 705 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 195 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 ASN A1140 GLN ** A1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1227 GLN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19373 Z= 0.213 Angle : 0.539 6.103 26376 Z= 0.276 Chirality : 0.039 0.145 3031 Planarity : 0.005 0.069 3455 Dihedral : 5.133 97.151 2708 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.28 % Favored : 93.68 % Rotamer: Outliers : 1.43 % Allowed : 21.51 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.35 (0.18), residues: 2486 helix: 1.14 (0.17), residues: 1089 sheet: -1.58 (0.30), residues: 281 loop : -1.24 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1226 HIS 0.004 0.001 HIS A1048 PHE 0.018 0.001 PHE A 607 TYR 0.008 0.001 TYR B1018 ARG 0.003 0.000 ARG A 950 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 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 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1054 ARG cc_start: 0.8803 (mtp-110) cc_final: 0.8548 (mtp85) outliers start: 29 outliers final: 15 residues processed: 169 average time/residue: 0.6393 time to fit residues: 171.8675 Evaluate side-chains 150 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1140 GLN Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 201 optimal weight: 0.6980 chunk 224 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 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 495 GLN A1078 ASN ** A1166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19373 Z= 0.318 Angle : 0.559 6.309 26376 Z= 0.290 Chirality : 0.040 0.157 3031 Planarity : 0.005 0.051 3455 Dihedral : 4.904 75.441 2706 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.48 % Favored : 92.48 % Rotamer: Outliers : 2.03 % Allowed : 21.46 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 2486 helix: 0.88 (0.16), residues: 1072 sheet: -1.72 (0.30), residues: 288 loop : -1.33 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 15 HIS 0.004 0.001 HIS A 413 PHE 0.019 0.001 PHE A 607 TYR 0.010 0.001 TYR A1248 ARG 0.006 0.001 ARG A1168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 140 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1042 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7499 (m-70) REVERT: A 1054 ARG cc_start: 0.8800 (mtp-110) cc_final: 0.8585 (mtp85) REVERT: A 1140 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8119 (mm110) REVERT: B 157 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 497 ASN cc_start: 0.9460 (OUTLIER) cc_final: 0.9187 (p0) REVERT: B 550 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6055 (p0) REVERT: B 1154 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8776 (p) outliers start: 41 outliers final: 25 residues processed: 168 average time/residue: 0.7020 time to fit residues: 184.4061 Evaluate side-chains 166 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1042 HIS Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 497 ASN Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 1154 SER Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 ASN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19373 Z= 0.187 Angle : 0.507 6.183 26376 Z= 0.258 Chirality : 0.039 0.160 3031 Planarity : 0.004 0.042 3455 Dihedral : 4.658 73.370 2703 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.34 % Allowed : 21.36 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2486 helix: 1.06 (0.17), residues: 1081 sheet: -1.48 (0.31), residues: 267 loop : -1.29 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1226 HIS 0.003 0.001 HIS A 250 PHE 0.017 0.001 PHE A 607 TYR 0.008 0.001 TYR B1018 ARG 0.003 0.000 ARG A 950 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 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 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6954 (OUTLIER) cc_final: 0.6732 (p) REVERT: A 1054 ARG cc_start: 0.8796 (mtp-110) cc_final: 0.8540 (mtp85) REVERT: B 157 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8482 (tm-30) outliers start: 27 outliers final: 19 residues processed: 159 average time/residue: 0.6826 time to fit residues: 172.1517 Evaluate side-chains 157 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN B1093 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19373 Z= 0.319 Angle : 0.548 6.368 26376 Z= 0.283 Chirality : 0.040 0.145 3031 Planarity : 0.004 0.039 3455 Dihedral : 4.824 74.532 2703 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.73 % Allowed : 21.12 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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 (0.18), residues: 2486 helix: 0.83 (0.17), residues: 1079 sheet: -1.62 (0.30), residues: 281 loop : -1.35 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1226 HIS 0.004 0.001 HIS A 413 PHE 0.019 0.001 PHE A 607 TYR 0.010 0.001 TYR B1018 ARG 0.004 0.000 ARG A1168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6628 (p) REVERT: A 1054 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8552 (mtp85) REVERT: B 379 MET cc_start: 0.8516 (ptp) cc_final: 0.8264 (ttp) REVERT: B 550 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.6060 (p0) outliers start: 35 outliers final: 30 residues processed: 162 average time/residue: 0.6703 time to fit residues: 169.8459 Evaluate side-chains 165 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 240 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19373 Z= 0.181 Angle : 0.503 6.206 26376 Z= 0.254 Chirality : 0.039 0.146 3031 Planarity : 0.004 0.038 3455 Dihedral : 4.673 72.869 2703 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.68 % Allowed : 21.71 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2486 helix: 1.04 (0.17), residues: 1081 sheet: -1.48 (0.32), residues: 253 loop : -1.26 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1226 HIS 0.004 0.001 HIS A1042 PHE 0.018 0.001 PHE A 607 TYR 0.008 0.001 TYR B1018 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 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 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6907 (OUTLIER) cc_final: 0.6700 (p) REVERT: A 823 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 1054 ARG cc_start: 0.8789 (mtp-110) cc_final: 0.8537 (mtp85) REVERT: B 550 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.6053 (p0) REVERT: B 822 GLN cc_start: 0.9071 (mm110) cc_final: 0.8746 (mp10) outliers start: 34 outliers final: 28 residues processed: 167 average time/residue: 0.6716 time to fit residues: 176.7051 Evaluate side-chains 169 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19373 Z= 0.345 Angle : 0.567 6.415 26376 Z= 0.293 Chirality : 0.040 0.142 3031 Planarity : 0.004 0.039 3455 Dihedral : 4.776 73.563 2703 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 1.98 % Allowed : 21.46 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.75 (0.17), residues: 2486 helix: 0.71 (0.16), residues: 1073 sheet: -1.52 (0.31), residues: 278 loop : -1.39 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1226 HIS 0.006 0.001 HIS B 253 PHE 0.019 0.002 PHE A 607 TYR 0.012 0.001 TYR B1018 ARG 0.005 0.000 ARG A1168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6530 (p) REVERT: A 823 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 1054 ARG cc_start: 0.8801 (mtp-110) cc_final: 0.8548 (mtp85) REVERT: B 550 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6088 (p0) REVERT: B 822 GLN cc_start: 0.9144 (mm110) cc_final: 0.8853 (mp10) outliers start: 40 outliers final: 33 residues processed: 170 average time/residue: 0.7071 time to fit residues: 190.5804 Evaluate side-chains 173 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 188 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19373 Z= 0.205 Angle : 0.515 6.270 26376 Z= 0.261 Chirality : 0.039 0.146 3031 Planarity : 0.004 0.055 3455 Dihedral : 4.692 72.636 2703 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.78 % Allowed : 21.36 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2486 helix: 0.94 (0.17), residues: 1072 sheet: -1.45 (0.32), residues: 271 loop : -1.30 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1226 HIS 0.005 0.001 HIS A1042 PHE 0.018 0.001 PHE A 607 TYR 0.009 0.001 TYR B1018 ARG 0.004 0.000 ARG B1054 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6814 (OUTLIER) cc_final: 0.6597 (p) REVERT: A 823 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 1054 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8539 (mtp85) REVERT: B 550 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.6077 (p0) REVERT: B 822 GLN cc_start: 0.9070 (mm110) cc_final: 0.8776 (mp10) outliers start: 36 outliers final: 30 residues processed: 168 average time/residue: 0.6542 time to fit residues: 174.3642 Evaluate side-chains 168 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 175 optimal weight: 0.0870 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19373 Z= 0.247 Angle : 0.525 6.316 26376 Z= 0.267 Chirality : 0.039 0.144 3031 Planarity : 0.004 0.038 3455 Dihedral : 4.659 72.123 2703 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.73 % Allowed : 21.51 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.57 (0.18), residues: 2486 helix: 0.91 (0.17), residues: 1075 sheet: -1.58 (0.31), residues: 282 loop : -1.30 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1226 HIS 0.004 0.001 HIS A1042 PHE 0.018 0.001 PHE A 607 TYR 0.010 0.001 TYR B1018 ARG 0.003 0.000 ARG A1168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6737 (OUTLIER) cc_final: 0.6527 (p) REVERT: A 823 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 1054 ARG cc_start: 0.8780 (mtp-110) cc_final: 0.8530 (mtp85) REVERT: B 550 ASP cc_start: 0.6531 (OUTLIER) cc_final: 0.6105 (p0) REVERT: B 822 GLN cc_start: 0.9089 (mm110) cc_final: 0.8808 (mp10) outliers start: 35 outliers final: 31 residues processed: 165 average time/residue: 0.6607 time to fit residues: 172.2175 Evaluate side-chains 169 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 1039 MET Chi-restraints excluded: chain B residue 1169 SER Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.2980 chunk 236 optimal weight: 2.9990 chunk 144 optimal weight: 0.0030 chunk 112 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 228 optimal weight: 0.6980 chunk 197 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19373 Z= 0.139 Angle : 0.497 6.779 26376 Z= 0.247 Chirality : 0.039 0.147 3031 Planarity : 0.004 0.039 3455 Dihedral : 4.445 70.045 2701 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.24 % Allowed : 21.96 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2486 helix: 1.20 (0.17), residues: 1082 sheet: -1.47 (0.31), residues: 275 loop : -1.18 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1226 HIS 0.003 0.001 HIS B 100 PHE 0.018 0.001 PHE A 607 TYR 0.007 0.001 TYR B 993 ARG 0.002 0.000 ARG B 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4972 Ramachandran restraints generated. 2486 Oldfield, 0 Emsley, 2486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6597 (p) REVERT: A 503 TYR cc_start: 0.8184 (m-80) cc_final: 0.7928 (m-80) REVERT: A 823 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 1054 ARG cc_start: 0.8765 (mtp-110) cc_final: 0.8514 (mtp85) REVERT: B 85 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7932 (mm-40) REVERT: B 379 MET cc_start: 0.8659 (ptp) cc_final: 0.8439 (ttp) REVERT: B 550 ASP cc_start: 0.6283 (OUTLIER) cc_final: 0.6029 (p0) REVERT: B 634 ASP cc_start: 0.8614 (t0) cc_final: 0.8240 (t0) REVERT: B 822 GLN cc_start: 0.9007 (mm110) cc_final: 0.8698 (mp10) outliers start: 25 outliers final: 18 residues processed: 167 average time/residue: 0.6758 time to fit residues: 177.5600 Evaluate side-chains 164 residues out of total 2022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1179 SER Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1251 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain C residue 70 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 ASN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 807 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069338 restraints weight = 161808.427| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.02 r_work: 0.3098 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19373 Z= 0.229 Angle : 0.517 6.714 26376 Z= 0.261 Chirality : 0.039 0.142 3031 Planarity : 0.004 0.038 3455 Dihedral : 4.439 70.787 2701 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 1.29 % Allowed : 22.11 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -0.37 (0.18), residues: 2486 helix: 1.10 (0.17), residues: 1083 sheet: -1.60 (0.31), residues: 278 loop : -1.20 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1226 HIS 0.005 0.001 HIS A1042 PHE 0.026 0.001 PHE B 668 TYR 0.009 0.001 TYR B1018 ARG 0.003 0.000 ARG A1168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6718.08 seconds wall clock time: 121 minutes 44.42 seconds (7304.42 seconds total)