Starting phenix.real_space_refine on Fri Feb 16 02:22:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9w_24939/02_2024/7s9w_24939_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9w_24939/02_2024/7s9w_24939.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9w_24939/02_2024/7s9w_24939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9w_24939/02_2024/7s9w_24939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9w_24939/02_2024/7s9w_24939_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9w_24939/02_2024/7s9w_24939_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= 0.045 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 73 5.16 5 C 8825 2.51 5 N 2508 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 247": "OD1" <-> "OD2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 744": "OE1" <-> "OE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A ASP 1016": "OD1" <-> "OD2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A GLU 1152": "OE1" <-> "OE2" Residue "A PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1179": "OD1" <-> "OD2" Residue "A GLU 1244": "OE1" <-> "OE2" Residue "A TYR 1262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1314": "OD1" <-> "OD2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ASP 353": "OD1" <-> "OD2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 427": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B ASP 573": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14052 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9746 Classifications: {'peptide': 1238} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 1172} Chain breaks: 2 Chain: "B" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4139 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 491} Chain breaks: 3 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.63, per 1000 atoms: 0.54 Number of scatterers: 14052 At special positions: 0 Unit cell: (97.9, 123.2, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 73 16.00 P 9 15.00 O 2637 8.00 N 2508 7.00 C 8825 6.00 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=0, symmetry=0 Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.3 seconds 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3284 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 20 sheets defined 31.7% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.791A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'A' and resid 109 through 118 Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.646A pdb=" N GLN A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 471 through 490 removed outlier: 3.594A pdb=" N ASP A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 485 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N SER A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 521 removed outlier: 4.066A pdb=" N ARG A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 550 removed outlier: 4.284A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 566 Processing helix chain 'A' and resid 570 through 584 Proline residue: A 581 - end of helix Processing helix chain 'A' and resid 610 through 627 removed outlier: 3.578A pdb=" N GLY A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG A 626 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N MET A 627 " --> pdb=" O ALA A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 676 removed outlier: 3.731A pdb=" N GLN A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 658 " --> pdb=" O GLN A 654 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.618A pdb=" N ILE A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.521A pdb=" N ALA A 805 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 807 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 808 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 3.770A pdb=" N THR A 815 " --> pdb=" O GLN A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 873 through 889 removed outlier: 3.665A pdb=" N MET A 878 " --> pdb=" O PRO A 874 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 886 " --> pdb=" O TYR A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 964 through 986 removed outlier: 3.643A pdb=" N ARG A 970 " --> pdb=" O ALA A 966 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 Proline residue: A 992 - end of helix Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.778A pdb=" N ARG A1011 " --> pdb=" O GLY A1007 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN A1018 " --> pdb=" O GLU A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Proline residue: A1055 - end of helix Processing helix chain 'A' and resid 1118 through 1126 removed outlier: 3.539A pdb=" N SER A1126 " --> pdb=" O ILE A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1154 through 1157 No H-bonds generated for 'chain 'A' and resid 1154 through 1157' Processing helix chain 'A' and resid 1162 through 1164 No H-bonds generated for 'chain 'A' and resid 1162 through 1164' Processing helix chain 'A' and resid 1175 through 1193 removed outlier: 4.022A pdb=" N ARG A1180 " --> pdb=" O ARG A1176 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR A1183 " --> pdb=" O ASP A1179 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLY A1184 " --> pdb=" O ARG A1180 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1192 " --> pdb=" O SER A1188 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1202 No H-bonds generated for 'chain 'A' and resid 1200 through 1202' Processing helix chain 'A' and resid 1211 through 1229 removed outlier: 3.526A pdb=" N LEU A1214 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A1215 " --> pdb=" O SER A1212 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS A1216 " --> pdb=" O GLU A1213 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A1229 " --> pdb=" O GLY A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1253 removed outlier: 3.771A pdb=" N LEU A1237 " --> pdb=" O ALA A1233 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A1252 " --> pdb=" O GLU A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1270 removed outlier: 4.309A pdb=" N ASP A1270 " --> pdb=" O PRO A1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1267 through 1270' Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.748A pdb=" N ALA B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 169 through 174 removed outlier: 3.772A pdb=" N HIS B 174 " --> pdb=" O HIS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.711A pdb=" N GLY B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 222 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 removed outlier: 4.318A pdb=" N GLU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 435 through 443 removed outlier: 4.036A pdb=" N SER B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 465 removed outlier: 3.688A pdb=" N SER B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 496 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 542 through 557 removed outlier: 3.985A pdb=" N GLY B 546 " --> pdb=" O PRO B 542 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 555 " --> pdb=" O GLN B 551 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 601 through 603 No H-bonds generated for 'chain 'B' and resid 601 through 603' Processing sheet with id= A, first strand: chain 'A' and resid 14 through 17 removed outlier: 4.230A pdb=" N ARG A 81 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 35 removed outlier: 3.862A pdb=" N ARG A 67 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 158 through 160 Processing sheet with id= D, first strand: chain 'A' and resid 396 through 399 removed outlier: 3.526A pdb=" N GLY A 239 " --> pdb=" O HIS A 399 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 288 through 293 removed outlier: 5.096A pdb=" N LEU A 353 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 357 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N THR A 415 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU A 406 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 417 " --> pdb=" O HIS A 404 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS A 404 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N THR A 419 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA A 402 " --> pdb=" O THR A 419 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 424 through 427 removed outlier: 3.500A pdb=" N ARG A 952 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A1134 " --> pdb=" O ARG A 953 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LEU A 955 " --> pdb=" O GLY A1134 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A1136 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL A 957 " --> pdb=" O VAL A1136 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR A1138 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET A1109 " --> pdb=" O CYS A1137 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL A1139 " --> pdb=" O MET A1109 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A1111 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 997 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASN A1112 " --> pdb=" O VAL A 997 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N TYR A 999 " --> pdb=" O ASN A1112 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 430 through 432 Processing sheet with id= H, first strand: chain 'A' and resid 924 through 928 removed outlier: 5.261A pdb=" N ILE A 903 " --> pdb=" O TYR A 598 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP A 866 " --> pdb=" O ARG A 645 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 800 " --> pdb=" O TRP A 691 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 743 through 745 Processing sheet with id= J, first strand: chain 'A' and resid 892 through 894 removed outlier: 3.524A pdb=" N TRP A 892 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1068 through 1070 Processing sheet with id= L, first strand: chain 'A' and resid 1259 through 1261 Processing sheet with id= M, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= N, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.669A pdb=" N VAL B 419 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 109 through 111 Processing sheet with id= P, first strand: chain 'B' and resid 117 through 120 Processing sheet with id= Q, first strand: chain 'B' and resid 245 through 248 Processing sheet with id= R, first strand: chain 'B' and resid 184 through 187 removed outlier: 3.673A pdb=" N TRP B 199 " --> pdb=" O PHE B 187 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 421 through 426 removed outlier: 3.950A pdb=" N ASN B 422 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 262 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 258 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 390 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 256 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 503 through 508 removed outlier: 3.789A pdb=" N ARG B 374 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET B 358 " --> pdb=" O GLU B 379 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1170 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: 4.95 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.31: 2357 1.31 - 1.61: 11891 1.61 - 1.91: 119 1.91 - 2.21: 0 2.21 - 2.51: 1 Bond restraints: 14368 Sorted by residual: bond pdb=" CB PRO A 960 " pdb=" CG PRO A 960 " ideal model delta sigma weight residual 1.492 2.510 -1.018 5.00e-02 4.00e+02 4.15e+02 bond pdb=" CG PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 1.503 1.013 0.490 3.40e-02 8.65e+02 2.08e+02 bond pdb=" N PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 1.473 1.597 -0.124 1.40e-02 5.10e+03 7.89e+01 bond pdb=" CG PRO B 74 " pdb=" CD PRO B 74 " ideal model delta sigma weight residual 1.503 1.268 0.235 3.40e-02 8.65e+02 4.78e+01 bond pdb=" N PRO A 960 " pdb=" CA PRO A 960 " ideal model delta sigma weight residual 1.467 1.401 0.066 1.21e-02 6.83e+03 2.95e+01 ... (remaining 14363 not shown) Histogram of bond angle deviations from ideal: 0.07 - 29.57: 1 29.57 - 59.07: 0 59.07 - 88.57: 1 88.57 - 118.07: 10856 118.07 - 147.58: 8647 Bond angle restraints: 19505 Sorted by residual: angle pdb=" CB PRO A 960 " pdb=" CG PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 106.10 0.07 106.03 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CA PRO A 960 " pdb=" N PRO A 960 " pdb=" CD PRO A 960 " ideal model delta sigma weight residual 112.00 87.66 24.34 1.40e+00 5.10e-01 3.02e+02 angle pdb=" N PRO A 960 " pdb=" CA PRO A 960 " pdb=" CB PRO A 960 " ideal model delta sigma weight residual 103.31 91.44 11.87 8.90e-01 1.26e+00 1.78e+02 angle pdb=" CA PRO B 74 " pdb=" N PRO B 74 " pdb=" CD PRO B 74 " ideal model delta sigma weight residual 112.00 96.69 15.31 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO A 960 " pdb=" CB PRO A 960 " pdb=" CG PRO A 960 " ideal model delta sigma weight residual 104.50 88.84 15.66 1.90e+00 2.77e-01 6.79e+01 ... (remaining 19500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.32: 8406 34.32 - 68.64: 258 68.64 - 102.96: 20 102.96 - 137.28: 0 137.28 - 171.60: 1 Dihedral angle restraints: 8685 sinusoidal: 3603 harmonic: 5082 Sorted by residual: dihedral pdb=" CA ASP A 937 " pdb=" C ASP A 937 " pdb=" N ASN A 938 " pdb=" CA ASN A 938 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" N PRO A 960 " pdb=" CG PRO A 960 " pdb=" CD PRO A 960 " pdb=" CB PRO A 960 " ideal model delta sinusoidal sigma weight residual -30.00 -95.63 65.63 1 1.50e+01 4.44e-03 2.51e+01 dihedral pdb=" N PRO A 960 " pdb=" C PRO A 960 " pdb=" CA PRO A 960 " pdb=" CB PRO A 960 " ideal model delta harmonic sigma weight residual 115.10 103.01 12.09 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 8682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1854 0.069 - 0.139: 278 0.139 - 0.208: 18 0.208 - 0.277: 0 0.277 - 0.347: 2 Chirality restraints: 2152 Sorted by residual: chirality pdb=" CA PRO B 74 " pdb=" N PRO B 74 " pdb=" C PRO B 74 " pdb=" CB PRO B 74 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU A 650 " pdb=" CB LEU A 650 " pdb=" CD1 LEU A 650 " pdb=" CD2 LEU A 650 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" P DT C 5 " pdb=" OP1 DT C 5 " pdb=" OP2 DT C 5 " pdb=" O5' DT C 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 2149 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 73 " -0.107 5.00e-02 4.00e+02 1.47e-01 3.48e+01 pdb=" N PRO B 74 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 547 " 0.352 9.50e-02 1.11e+02 1.58e-01 1.53e+01 pdb=" NE ARG B 547 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG B 547 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 547 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 547 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 959 " -0.066 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 960 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 960 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 960 " -0.048 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4136 2.83 - 3.34: 11443 3.34 - 3.86: 20695 3.86 - 4.38: 23185 4.38 - 4.90: 41837 Nonbonded interactions: 101296 Sorted by model distance: nonbonded pdb=" O ILE A 969 " pdb=" OG1 THR A 973 " model vdw 2.308 2.440 nonbonded pdb=" O ASP A1015 " pdb=" OG1 THR A1019 " model vdw 2.311 2.440 nonbonded pdb=" O ASP A 111 " pdb=" OG1 THR A 115 " model vdw 2.324 2.440 nonbonded pdb=" O ASP A1268 " pdb=" OG1 THR A1272 " model vdw 2.325 2.440 nonbonded pdb=" OE1 GLN B 235 " pdb=" NH2 ARG B 413 " model vdw 2.330 2.520 ... (remaining 101291 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.700 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.720 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.018 14368 Z= 0.775 Angle : 1.155 106.034 19505 Z= 0.545 Chirality : 0.049 0.347 2152 Planarity : 0.008 0.158 2529 Dihedral : 15.908 171.599 5401 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.66 % Rotamer: Outliers : 0.47 % Allowed : 14.86 % Favored : 84.67 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.97 % 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: -0.94 (0.18), residues: 1753 helix: -0.44 (0.22), residues: 497 sheet: 0.17 (0.31), residues: 288 loop : -0.94 (0.17), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 568 HIS 0.021 0.001 HIS B 170 PHE 0.051 0.002 PHE A 620 TYR 0.055 0.002 TYR A 614 ARG 0.008 0.000 ARG A1301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 232 average time/residue: 0.2905 time to fit residues: 95.4345 Evaluate side-chains 231 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 226 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 528 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 137 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 14368 Z= 0.188 Angle : 0.561 11.480 19505 Z= 0.289 Chirality : 0.043 0.149 2152 Planarity : 0.005 0.086 2529 Dihedral : 8.521 167.061 2017 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.81 % Allowed : 14.59 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1753 helix: 0.47 (0.24), residues: 501 sheet: 0.59 (0.31), residues: 301 loop : -0.80 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.007 0.001 HIS B 170 PHE 0.013 0.001 PHE A 529 TYR 0.009 0.001 TYR A 614 ARG 0.003 0.000 ARG A1037 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 563 LEU cc_start: 0.8640 (tt) cc_final: 0.8435 (tt) REVERT: A 1023 ARG cc_start: 0.6698 (mtp180) cc_final: 0.6285 (mtp85) outliers start: 27 outliers final: 18 residues processed: 250 average time/residue: 0.2825 time to fit residues: 102.2347 Evaluate side-chains 239 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 221 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 132 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 827 HIS A1164 HIS B 69 ASN B 89 ASN B 170 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 14368 Z= 0.364 Angle : 0.658 9.051 19505 Z= 0.341 Chirality : 0.046 0.175 2152 Planarity : 0.006 0.051 2529 Dihedral : 8.711 165.493 2012 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.82 % Allowed : 15.39 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1753 helix: 0.29 (0.24), residues: 500 sheet: 0.60 (0.32), residues: 290 loop : -0.95 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 281 HIS 0.005 0.001 HIS B 482 PHE 0.021 0.002 PHE A 529 TYR 0.018 0.002 TYR B 171 ARG 0.006 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 230 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 563 LEU cc_start: 0.8728 (tt) cc_final: 0.8453 (tt) REVERT: A 1023 ARG cc_start: 0.6887 (mtp180) cc_final: 0.6372 (mtp85) REVERT: A 1211 GLN cc_start: 0.8125 (mt0) cc_final: 0.7761 (mt0) REVERT: B 547 ARG cc_start: 0.6979 (tpp-160) cc_final: 0.6663 (tpp-160) outliers start: 57 outliers final: 39 residues processed: 262 average time/residue: 0.2878 time to fit residues: 107.9294 Evaluate side-chains 260 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 HIS A1164 HIS B 69 ASN B 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14368 Z= 0.197 Angle : 0.552 6.481 19505 Z= 0.284 Chirality : 0.043 0.146 2152 Planarity : 0.004 0.046 2529 Dihedral : 8.490 167.251 2012 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.88 % Allowed : 16.80 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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 (0.20), residues: 1753 helix: 0.71 (0.24), residues: 497 sheet: 0.56 (0.31), residues: 300 loop : -0.90 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.006 0.001 HIS B 133 PHE 0.014 0.001 PHE A 529 TYR 0.011 0.001 TYR A1157 ARG 0.002 0.000 ARG A 970 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 1.874 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7039 (mtp-110) cc_final: 0.6720 (mpp80) REVERT: A 1211 GLN cc_start: 0.8088 (mt0) cc_final: 0.7818 (mt0) REVERT: A 1301 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6443 (mtp85) outliers start: 43 outliers final: 33 residues processed: 257 average time/residue: 0.2793 time to fit residues: 102.4398 Evaluate side-chains 253 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 7.9990 chunk 96 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 125 optimal weight: 0.0570 chunk 69 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 151 optimal weight: 0.0050 chunk 42 optimal weight: 2.9990 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14368 Z= 0.125 Angle : 0.505 8.456 19505 Z= 0.256 Chirality : 0.042 0.140 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.227 171.180 2010 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.61 % Allowed : 16.80 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 0.01 (0.20), residues: 1753 helix: 1.05 (0.25), residues: 502 sheet: 0.64 (0.31), residues: 300 loop : -0.77 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 603 HIS 0.007 0.001 HIS B 133 PHE 0.009 0.001 PHE A 656 TYR 0.036 0.001 TYR A 614 ARG 0.003 0.000 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8791 (mt) cc_final: 0.8544 (mm) REVERT: A 176 ARG cc_start: 0.7014 (mtp-110) cc_final: 0.6748 (mpp80) REVERT: A 564 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8608 (ptpt) REVERT: A 1301 ARG cc_start: 0.6809 (mtm-85) cc_final: 0.6373 (mtp85) REVERT: B 215 PHE cc_start: 0.7467 (m-80) cc_final: 0.7257 (m-80) REVERT: B 547 ARG cc_start: 0.6765 (tpp-160) cc_final: 0.6336 (tpp-160) outliers start: 39 outliers final: 28 residues processed: 258 average time/residue: 0.2956 time to fit residues: 109.0361 Evaluate side-chains 258 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 0.0370 chunk 99 optimal weight: 0.0010 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 0.0030 chunk 163 optimal weight: 3.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14368 Z= 0.154 Angle : 0.505 6.838 19505 Z= 0.257 Chirality : 0.042 0.139 2152 Planarity : 0.004 0.042 2529 Dihedral : 8.204 171.727 2010 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.41 % Allowed : 16.53 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1753 helix: 1.19 (0.25), residues: 495 sheet: 0.65 (0.32), residues: 285 loop : -0.69 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 568 HIS 0.005 0.001 HIS B 133 PHE 0.015 0.001 PHE A 620 TYR 0.009 0.001 TYR A1157 ARG 0.003 0.000 ARG A1130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 236 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8802 (mt) cc_final: 0.8554 (mm) REVERT: A 176 ARG cc_start: 0.7045 (mtp-110) cc_final: 0.6762 (mpp80) REVERT: A 564 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8532 (ptpt) REVERT: A 1301 ARG cc_start: 0.6661 (mtm-85) cc_final: 0.6336 (mtp85) outliers start: 51 outliers final: 42 residues processed: 267 average time/residue: 0.2852 time to fit residues: 108.7338 Evaluate side-chains 270 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1088 ILE Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14368 Z= 0.188 Angle : 0.536 9.680 19505 Z= 0.270 Chirality : 0.043 0.140 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.234 170.992 2010 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.68 % Allowed : 16.40 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 0.05 (0.20), residues: 1753 helix: 1.11 (0.25), residues: 502 sheet: 0.60 (0.32), residues: 285 loop : -0.71 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.005 0.001 HIS B 133 PHE 0.015 0.001 PHE A 620 TYR 0.031 0.001 TYR A 614 ARG 0.009 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 234 time to evaluate : 1.674 Fit side-chains revert: symmetry clash REVERT: A 65 ILE cc_start: 0.8864 (mt) cc_final: 0.8613 (mm) REVERT: A 176 ARG cc_start: 0.7081 (mtp-110) cc_final: 0.6791 (mpp80) REVERT: A 564 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8489 (ptpt) REVERT: A 1301 ARG cc_start: 0.6780 (mtm-85) cc_final: 0.6404 (mtp85) REVERT: B 166 ASP cc_start: 0.8527 (m-30) cc_final: 0.7918 (m-30) REVERT: B 547 ARG cc_start: 0.6815 (tpp-160) cc_final: 0.6425 (tpp-160) outliers start: 55 outliers final: 45 residues processed: 269 average time/residue: 0.2775 time to fit residues: 107.8379 Evaluate side-chains 277 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain A residue 1292 SER Chi-restraints excluded: chain A residue 1311 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.0060 chunk 32 optimal weight: 0.0010 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 153 optimal weight: 0.8980 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14368 Z= 0.128 Angle : 0.512 10.450 19505 Z= 0.257 Chirality : 0.042 0.174 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.129 172.469 2010 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.95 % Allowed : 17.74 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1753 helix: 1.31 (0.25), residues: 494 sheet: 0.71 (0.32), residues: 298 loop : -0.69 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 603 HIS 0.005 0.001 HIS B 232 PHE 0.014 0.001 PHE A 620 TYR 0.009 0.001 TYR A1157 ARG 0.008 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7039 (mtp-110) cc_final: 0.6784 (mpp80) REVERT: A 564 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8480 (ptpt) REVERT: A 654 GLN cc_start: 0.7776 (mp10) cc_final: 0.7523 (mp10) REVERT: B 166 ASP cc_start: 0.8480 (m-30) cc_final: 0.8003 (m-30) outliers start: 44 outliers final: 37 residues processed: 262 average time/residue: 0.2878 time to fit residues: 107.3638 Evaluate side-chains 269 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 231 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 647 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1094 THR Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 148 optimal weight: 0.4980 chunk 156 optimal weight: 0.6980 chunk 103 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14368 Z= 0.167 Angle : 0.533 9.467 19505 Z= 0.265 Chirality : 0.042 0.174 2152 Planarity : 0.004 0.047 2529 Dihedral : 8.148 172.675 2010 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.81 % Allowed : 17.74 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 0.16 (0.20), residues: 1753 helix: 1.27 (0.25), residues: 496 sheet: 0.68 (0.32), residues: 288 loop : -0.69 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.006 0.001 HIS A 840 PHE 0.015 0.001 PHE A 620 TYR 0.029 0.001 TYR A 614 ARG 0.007 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 233 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7067 (mtp-110) cc_final: 0.6800 (mpp80) REVERT: A 446 MET cc_start: 0.8617 (ttm) cc_final: 0.8134 (ttp) REVERT: A 564 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8542 (ptpt) REVERT: A 654 GLN cc_start: 0.7788 (mp10) cc_final: 0.7516 (mp10) REVERT: A 964 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.7540 (mtm180) REVERT: B 547 ARG cc_start: 0.6776 (tpp-160) cc_final: 0.6374 (tpp-160) outliers start: 42 outliers final: 37 residues processed: 258 average time/residue: 0.2943 time to fit residues: 108.6413 Evaluate side-chains 268 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 174 optimal weight: 0.0470 chunk 160 optimal weight: 0.0870 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14368 Z= 0.142 Angle : 0.534 13.463 19505 Z= 0.263 Chirality : 0.042 0.162 2152 Planarity : 0.004 0.043 2529 Dihedral : 8.119 173.217 2010 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.61 % Allowed : 17.94 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1753 helix: 1.31 (0.25), residues: 494 sheet: 0.76 (0.32), residues: 290 loop : -0.70 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 603 HIS 0.006 0.001 HIS B 232 PHE 0.015 0.001 PHE A 620 TYR 0.009 0.001 TYR A1157 ARG 0.007 0.000 ARG A1144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7062 (mtp-110) cc_final: 0.6795 (mpp80) REVERT: A 446 MET cc_start: 0.8615 (ttm) cc_final: 0.8148 (ttp) REVERT: A 564 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (ptpt) REVERT: A 654 GLN cc_start: 0.7786 (mp10) cc_final: 0.7509 (mp10) REVERT: B 72 MET cc_start: 0.8322 (ttp) cc_final: 0.8097 (ttm) REVERT: B 166 ASP cc_start: 0.8495 (m-30) cc_final: 0.8015 (m-30) REVERT: B 547 ARG cc_start: 0.6787 (tpp-160) cc_final: 0.6383 (tpp-160) outliers start: 39 outliers final: 37 residues processed: 259 average time/residue: 0.3147 time to fit residues: 117.0986 Evaluate side-chains 271 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 564 LYS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 603 TRP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 802 ASP Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 910 VAL Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1015 ASP Chi-restraints excluded: chain A residue 1057 TYR Chi-restraints excluded: chain A residue 1091 VAL Chi-restraints excluded: chain A residue 1096 MET Chi-restraints excluded: chain A residue 1161 PHE Chi-restraints excluded: chain A residue 1166 GLU Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 609 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 142 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN B 554 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.173961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.138694 restraints weight = 15671.728| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.40 r_work: 0.3309 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14368 Z= 0.223 Angle : 0.571 15.838 19505 Z= 0.282 Chirality : 0.043 0.160 2152 Planarity : 0.004 0.048 2529 Dihedral : 8.197 172.229 2010 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.21 % Allowed : 17.54 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 0.02 (0.20), residues: 1753 helix: 1.09 (0.25), residues: 505 sheet: 0.58 (0.33), residues: 283 loop : -0.74 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.006 0.001 HIS B 232 PHE 0.016 0.001 PHE A 620 TYR 0.027 0.001 TYR A 614 ARG 0.007 0.000 ARG A1144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.83 seconds wall clock time: 59 minutes 24.47 seconds (3564.47 seconds total)