Starting phenix.real_space_refine on Fri Aug 9 09:41:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orq_17130/08_2024/8orq_17130.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orq_17130/08_2024/8orq_17130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orq_17130/08_2024/8orq_17130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orq_17130/08_2024/8orq_17130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orq_17130/08_2024/8orq_17130.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orq_17130/08_2024/8orq_17130.cif" } resolution = 3.2 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= 0.001 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 Zn 5 6.06 5 Mg 1 5.21 5 S 112 5.16 5 C 16667 2.51 5 N 4549 2.21 5 O 4861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B GLU 948": "OE1" <-> "OE2" Residue "B TYR 969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H ASP 59": "OD1" <-> "OD2" Residue "N ASP 37": "OD1" <-> "OD2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "P GLU 3": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26195 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 7197 Classifications: {'peptide': 901} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 848} Chain: "B" Number of atoms: 8637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8637 Classifications: {'peptide': 1076} Link IDs: {'PTRANS': 59, 'TRANS': 1016} Chain breaks: 2 Chain: "C" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3041 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1496 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 986 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 777 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "H" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "N" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 543 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 6, 'TRANS': 48} Chain: "P" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 393 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 434 SG CYS A 57 84.267 70.420 56.761 1.00 92.06 S ATOM 456 SG CYS A 60 83.637 66.870 58.038 1.00 88.93 S ATOM 499 SG CYS A 67 82.719 69.842 60.215 1.00 83.44 S ATOM 736 SG CYS A 97 126.281 84.310 77.826 1.00 97.30 S ATOM 762 SG CYS A 100 126.308 80.626 77.329 1.00 96.01 S ATOM 1138 SG CYS A 144 128.126 82.078 80.345 1.00 95.76 S ATOM 1161 SG CYS A 147 129.506 82.383 76.791 1.00 95.13 S ATOM 15366 SG CYS B1059 98.704 59.307 65.032 1.00 93.50 S ATOM 15389 SG CYS B1062 99.797 62.795 66.117 1.00 91.72 S ATOM 15519 SG CYS B1077 98.296 62.295 62.686 1.00 91.84 S ATOM 15539 SG CYS B1080 101.781 60.935 63.519 1.00 89.75 S ATOM 24883 SG CYS N 7 30.737 57.923 116.981 1.00 0.59 S ATOM 24907 SG CYS N 10 29.040 54.553 117.774 1.00 30.00 S ATOM 25187 SG CYS N 44 31.593 56.099 120.161 1.00 0.60 S ATOM 25193 SG CYS N 45 27.987 57.309 119.703 1.00 0.60 S ATOM 25853 SG CYS P 8 27.156 92.551 89.764 1.00 86.83 S ATOM 25879 SG CYS P 11 23.616 93.222 90.308 1.00 84.70 S ATOM 26008 SG CYS P 27 25.366 94.689 87.149 1.00 79.74 S ATOM 26033 SG CYS P 30 26.157 96.099 90.564 1.00 82.76 S Time building chain proxies: 13.31, per 1000 atoms: 0.51 Number of scatterers: 26195 At special positions: 0 Unit cell: (140.36, 146.168, 164.56, 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) Zn 5 29.99 S 112 16.00 Mg 1 11.99 O 4861 8.00 N 4549 7.00 C 16667 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: 9.29 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" NE2 HIS A 70 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 60 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 57 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 100 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 147 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 97 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 144 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1062 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1059 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1077 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 10 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 45 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 7 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 8 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 11 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 30 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 27 " Number of angles added : 27 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6070 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 40 sheets defined 43.6% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 123 through 141 removed outlier: 3.554A pdb=" N ARG A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 3.851A pdb=" N LYS A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.732A pdb=" N MET A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 210' Processing helix chain 'A' and resid 236 through 258 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.555A pdb=" N GLY A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.730A pdb=" N TYR A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 482 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.605A pdb=" N ILE A 488 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.838A pdb=" N GLY A 508 " --> pdb=" O HIS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.865A pdb=" N CYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.634A pdb=" N VAL A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.170A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 663 removed outlier: 3.762A pdb=" N GLY A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLU A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 653 " --> pdb=" O ASP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.873A pdb=" N GLU A 671 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 701 Processing helix chain 'A' and resid 711 through 739 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 756 through 765 removed outlier: 3.626A pdb=" N ILE A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 Processing helix chain 'A' and resid 811 through 848 removed outlier: 3.804A pdb=" N THR A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.941A pdb=" N ASP A 873 " --> pdb=" O TYR A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 901 Processing helix chain 'B' and resid 10 through 25 removed outlier: 4.028A pdb=" N ILE B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 20 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 51 removed outlier: 4.138A pdb=" N SER B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 262 Processing helix chain 'B' and resid 269 through 278 Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 308 through 329 removed outlier: 4.366A pdb=" N LYS B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 347 through 377 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.847A pdb=" N THR B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 393 removed outlier: 3.620A pdb=" N PHE B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 428 through 436 Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.608A pdb=" N ASP B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 460 removed outlier: 3.577A pdb=" N TRP B 460 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 503 removed outlier: 3.680A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 544 Processing helix chain 'B' and resid 587 through 596 Processing helix chain 'B' and resid 600 through 607 Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 626 through 630 removed outlier: 3.946A pdb=" N VAL B 630 " --> pdb=" O PRO B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.934A pdb=" N LEU B 645 " --> pdb=" O ALA B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 652 removed outlier: 3.508A pdb=" N VAL B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.619A pdb=" N ASN B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 672 Processing helix chain 'B' and resid 678 through 683 removed outlier: 4.255A pdb=" N ARG B 682 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 709 removed outlier: 4.179A pdb=" N LYS B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 707 " --> pdb=" O ARG B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 713 Processing helix chain 'B' and resid 739 through 745 Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.669A pdb=" N GLY B 765 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 766 " --> pdb=" O LEU B 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 766' Processing helix chain 'B' and resid 782 through 787 Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 909 through 913 Processing helix chain 'B' and resid 918 through 935 removed outlier: 3.975A pdb=" N LEU B 922 " --> pdb=" O THR B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 removed outlier: 3.537A pdb=" N GLY B 945 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 994 through 999 removed outlier: 3.739A pdb=" N LYS B 998 " --> pdb=" O MET B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1038 removed outlier: 3.613A pdb=" N ARG B1031 " --> pdb=" O GLY B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1048 Processing helix chain 'B' and resid 1093 through 1105 Processing helix chain 'C' and resid 2 through 14 Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 39 through 58 Processing helix chain 'C' and resid 64 through 80 Proline residue: C 76 - end of helix removed outlier: 3.917A pdb=" N GLN C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.492A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 140 Processing helix chain 'C' and resid 144 through 147 No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 154 through 158 removed outlier: 4.217A pdb=" N ASN C 157 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 158 " --> pdb=" O LEU C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 158' Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.758A pdb=" N LEU C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 278 Processing helix chain 'C' and resid 278 through 297 removed outlier: 3.615A pdb=" N ALA C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 314 removed outlier: 4.051A pdb=" N ILE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 331 Processing helix chain 'C' and resid 333 through 339 Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.583A pdb=" N PHE C 348 " --> pdb=" O VAL C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'D' and resid 24 through 38 Processing helix chain 'D' and resid 57 through 68 removed outlier: 3.515A pdb=" N ILE D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.820A pdb=" N LEU D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 209 removed outlier: 4.634A pdb=" N GLU D 207 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 260 removed outlier: 3.742A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 23 through 37 removed outlier: 3.598A pdb=" N GLU E 37 " --> pdb=" O ARG E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 174 through 187 removed outlier: 4.309A pdb=" N GLU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 31 removed outlier: 3.608A pdb=" N ALA F 17 " --> pdb=" O THR F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 74 through 85 Processing helix chain 'F' and resid 88 through 96 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.557A pdb=" N MET F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 33 removed outlier: 3.812A pdb=" N LEU L 27 " --> pdb=" O THR L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 94 removed outlier: 3.849A pdb=" N LYS L 94 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 22 through 33 Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.534A pdb=" N LEU H 40 " --> pdb=" O LEU H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 53 Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 17 through 27 Processing helix chain 'N' and resid 30 through 39 Processing helix chain 'N' and resid 42 through 51 removed outlier: 3.893A pdb=" N MET N 48 " --> pdb=" O CYS N 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU N 49 " --> pdb=" O CYS N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 23 Processing helix chain 'K' and resid 35 through 46 Processing sheet with id=AA1, first strand: chain 'B' and resid 1107 through 1114 removed outlier: 6.432A pdb=" N ARG B1108 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE A 10 " --> pdb=" O ARG B1108 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS B1110 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE A 8 " --> pdb=" O LYS B1110 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN B1112 " --> pdb=" O GLY A 6 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A 4 " --> pdb=" O SER B1114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 81 removed outlier: 7.049A pdb=" N THR A 213 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N ARG A 78 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N VAL A 211 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 157 Processing sheet with id=AA4, first strand: chain 'B' and resid 1000 through 1002 removed outlier: 8.131A pdb=" N PHE A 445 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 328 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU A 447 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 330 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 4.047A pdb=" N TYR A 380 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 517 through 519 Processing sheet with id=AA7, first strand: chain 'A' and resid 567 through 570 removed outlier: 6.658A pdb=" N TYR A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 769 removed outlier: 3.508A pdb=" N GLY A 768 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 802 " --> pdb=" O GLY A 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB1, first strand: chain 'A' and resid 858 through 859 Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 53 removed outlier: 5.497A pdb=" N VAL B 62 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 107 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE B 64 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 105 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS B 66 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 52 through 53 removed outlier: 5.497A pdb=" N VAL B 62 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 107 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE B 64 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE B 105 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS B 66 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA B 98 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 122 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU B 100 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 75 Processing sheet with id=AB5, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.727A pdb=" N SER B 167 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 177 through 180 removed outlier: 3.734A pdb=" N TYR B 187 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 203 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 485 through 486 Processing sheet with id=AB9, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC1, first strand: chain 'B' and resid 505 through 506 removed outlier: 5.545A pdb=" N LEU B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 521 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 527 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.760A pdb=" N SER B 749 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 847 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU B 867 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY B 843 " --> pdb=" O LEU B 867 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 688 through 692 removed outlier: 3.760A pdb=" N SER B 749 " --> pdb=" O ARG B 868 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 847 " --> pdb=" O THR B 863 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ARG B 865 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 845 " --> pdb=" O ARG B 865 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU B 867 " --> pdb=" O GLY B 843 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY B 843 " --> pdb=" O LEU B 867 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA P 4 " --> pdb=" O LEU P 17 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU P 17 " --> pdb=" O ALA P 4 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AC5, first strand: chain 'B' and resid 965 through 966 removed outlier: 7.311A pdb=" N ILE B 735 " --> pdb=" O GLY B 887 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 889 " --> pdb=" O ILE B 735 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 737 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE B 982 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AC7, first strand: chain 'B' and resid 806 through 808 removed outlier: 6.867A pdb=" N VAL B 835 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 897 through 898 Processing sheet with id=AC9, first strand: chain 'B' and resid 1053 through 1058 Processing sheet with id=AD1, first strand: chain 'B' and resid 1067 through 1069 Processing sheet with id=AD2, first strand: chain 'C' and resid 233 through 238 removed outlier: 7.505A pdb=" N TYR C 242 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C 121 " --> pdb=" O TYR C 242 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR C 120 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARG C 264 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 142 through 143 removed outlier: 6.924A pdb=" N THR C 142 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 148 through 152 removed outlier: 3.595A pdb=" N ILE C 161 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.657A pdb=" N LEU E 77 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE E 50 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP E 75 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU E 52 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL E 73 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N LYS E 54 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N GLU E 71 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 10.535A pdb=" N ILE E 56 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N TYR E 69 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY F 8 " --> pdb=" O THR E 8 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS E 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS F 6 " --> pdb=" O LYS E 10 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.657A pdb=" N LEU E 77 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE E 50 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP E 75 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU E 52 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL E 73 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N LYS E 54 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 11.353A pdb=" N GLU E 71 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 10.535A pdb=" N ILE E 56 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 11.558A pdb=" N TYR E 69 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 59 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 383 " --> pdb=" O GLY E 59 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU C 381 " --> pdb=" O ILE E 61 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 5 through 11 removed outlier: 3.562A pdb=" N GLU D 5 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS D 17 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS D 11 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 18 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR D 158 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N ASN D 220 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 11.135A pdb=" N LYS D 156 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 9.611A pdb=" N TYR D 222 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N TYR D 154 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N PHE D 224 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 11.472A pdb=" N PHE D 152 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 107 through 108 removed outlier: 6.316A pdb=" N ARG D 130 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU D 51 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL D 132 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE D 49 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN D 134 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 47 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR D 136 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 99 through 102 removed outlier: 7.032A pdb=" N GLY D 99 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LYS D 124 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL D 101 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 85 through 95 removed outlier: 5.969A pdb=" N VAL E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG E 102 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP E 93 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA E 99 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE E 163 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 109 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E 165 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N HIS E 111 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N THR E 166 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ILE E 148 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 89 " --> pdb=" O VAL E 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 121 through 123 Processing sheet with id=AE3, first strand: chain 'L' and resid 2 through 7 removed outlier: 6.882A pdb=" N GLU L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.920A pdb=" N GLU H 17 " --> pdb=" O LYS H 64 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3372 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: 12.06 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8744 1.34 - 1.46: 5336 1.46 - 1.58: 12409 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 26687 Sorted by residual: bond pdb=" CD LYS E 134 " pdb=" CE LYS E 134 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.21e+00 bond pdb=" C GLU A 705 " pdb=" N PRO A 706 " ideal model delta sigma weight residual 1.335 1.323 0.012 8.70e-03 1.32e+04 2.01e+00 bond pdb=" CA ASP C 154 " pdb=" CB ASP C 154 " ideal model delta sigma weight residual 1.525 1.539 -0.014 1.29e-02 6.01e+03 1.14e+00 bond pdb=" CB THR A 655 " pdb=" CG2 THR A 655 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" C ARG A 423 " pdb=" N GLN A 424 " ideal model delta sigma weight residual 1.339 1.281 0.058 5.57e-02 3.22e+02 1.08e+00 ... (remaining 26682 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.27: 785 106.27 - 113.21: 14497 113.21 - 120.15: 9643 120.15 - 127.09: 10820 127.09 - 134.03: 281 Bond angle restraints: 36026 Sorted by residual: angle pdb=" CA MET E 167 " pdb=" CB MET E 167 " pdb=" CG MET E 167 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 angle pdb=" C LYS A 590 " pdb=" N LEU A 591 " pdb=" CA LEU A 591 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" CB MET K 22 " pdb=" CG MET K 22 " pdb=" SD MET K 22 " ideal model delta sigma weight residual 112.70 123.15 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CA GLY A 49 " pdb=" C GLY A 49 " pdb=" O GLY A 49 " ideal model delta sigma weight residual 122.22 120.02 2.20 6.50e-01 2.37e+00 1.14e+01 angle pdb=" CB MET A 142 " pdb=" CG MET A 142 " pdb=" SD MET A 142 " ideal model delta sigma weight residual 112.70 122.69 -9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 36021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14304 17.95 - 35.90: 1615 35.90 - 53.84: 413 53.84 - 71.79: 74 71.79 - 89.74: 37 Dihedral angle restraints: 16443 sinusoidal: 6996 harmonic: 9447 Sorted by residual: dihedral pdb=" CA MET E 3 " pdb=" C MET E 3 " pdb=" N TYR E 4 " pdb=" CA TYR E 4 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA THR F 104 " pdb=" C THR F 104 " pdb=" N GLN F 105 " pdb=" CA GLN F 105 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASP B 569 " pdb=" C ASP B 569 " pdb=" N GLY B 570 " pdb=" CA GLY B 570 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 16440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3330 0.057 - 0.115: 622 0.115 - 0.172: 42 0.172 - 0.230: 0 0.230 - 0.287: 2 Chirality restraints: 3996 Sorted by residual: chirality pdb=" CG LEU B 499 " pdb=" CB LEU B 499 " pdb=" CD1 LEU B 499 " pdb=" CD2 LEU B 499 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CG LEU B 277 " pdb=" CB LEU B 277 " pdb=" CD1 LEU B 277 " pdb=" CD2 LEU B 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CG LEU C 82 " pdb=" CB LEU C 82 " pdb=" CD1 LEU C 82 " pdb=" CD2 LEU C 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 3993 not shown) Planarity restraints: 4667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 95 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO E 96 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 10 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO B 11 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 11 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 11 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 177 " -0.013 2.00e-02 2.50e+03 1.12e-02 3.13e+00 pdb=" CG TRP E 177 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP E 177 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 177 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 177 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 177 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 177 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 177 " -0.001 2.00e-02 2.50e+03 ... (remaining 4664 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 285 2.62 - 3.19: 23659 3.19 - 3.76: 40576 3.76 - 4.33: 55922 4.33 - 4.90: 93667 Nonbonded interactions: 214109 Sorted by model distance: nonbonded pdb=" OD1 ASP A 458 " pdb="MG MG A1001 " model vdw 2.050 2.170 nonbonded pdb=" OG1 THR C 39 " pdb=" OE1 GLU C 42 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR C 175 " pdb=" OE2 GLU C 177 " model vdw 2.173 3.040 nonbonded pdb=" OG SER H 8 " pdb=" OD1 ASP H 11 " model vdw 2.195 3.040 nonbonded pdb=" N GLU H 24 " pdb=" OE1 GLU H 24 " model vdw 2.215 3.120 ... (remaining 214104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.240 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 76.000 Find NCS groups from input model: 0.240 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.005 0.058 26687 Z= 0.297 Angle : 0.546 10.447 36026 Z= 0.281 Chirality : 0.043 0.287 3996 Planarity : 0.004 0.053 4667 Dihedral : 16.414 89.741 10373 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.18 % Allowed : 21.33 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.79 (0.15), residues: 3240 helix: 1.60 (0.15), residues: 1225 sheet: -0.32 (0.24), residues: 497 loop : 0.04 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 177 HIS 0.004 0.001 HIS B 992 PHE 0.024 0.001 PHE C 215 TYR 0.018 0.001 TYR E 4 ARG 0.005 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 3.022 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: B 1107 ILE cc_start: 0.8758 (mp) cc_final: 0.8547 (mp) outliers start: 5 outliers final: 1 residues processed: 189 average time/residue: 0.4615 time to fit residues: 133.9672 Evaluate side-chains 182 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 187 optimal weight: 0.3980 chunk 291 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: A 273 GLN A 788 HIS B 590 HIS ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26687 Z= 0.169 Angle : 0.509 8.967 36026 Z= 0.267 Chirality : 0.043 0.237 3996 Planarity : 0.004 0.068 4667 Dihedral : 3.937 31.071 3618 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 1.90 % Allowed : 19.42 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 3240 helix: 1.68 (0.15), residues: 1245 sheet: -0.17 (0.24), residues: 464 loop : 0.06 (0.17), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 177 HIS 0.003 0.001 HIS A 70 PHE 0.023 0.001 PHE C 215 TYR 0.013 0.001 TYR E 4 ARG 0.007 0.000 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 194 time to evaluate : 3.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 MET cc_start: 0.7441 (tpp) cc_final: 0.7003 (tpt) REVERT: D 67 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6957 (mmp) outliers start: 54 outliers final: 22 residues processed: 232 average time/residue: 0.4102 time to fit residues: 148.0603 Evaluate side-chains 209 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 500 MET Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 144 VAL Chi-restraints excluded: chain E residue 150 ASN Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain H residue 25 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 292 optimal weight: 1.9990 chunk 315 optimal weight: 0.1980 chunk 260 optimal weight: 30.0000 chunk 289 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26687 Z= 0.177 Angle : 0.489 9.262 36026 Z= 0.252 Chirality : 0.043 0.247 3996 Planarity : 0.004 0.053 4667 Dihedral : 3.820 31.197 3617 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 19.56 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 3240 helix: 1.78 (0.15), residues: 1231 sheet: -0.01 (0.24), residues: 465 loop : 0.10 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 897 HIS 0.003 0.001 HIS B1000 PHE 0.020 0.001 PHE C 215 TYR 0.011 0.001 TYR E 4 ARG 0.006 0.000 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6480 Ramachandran restraints generated. 3240 Oldfield, 0 Emsley, 3240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 194 time to evaluate : 3.206 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: B 18 MET cc_start: 0.7441 (tpp) cc_final: 0.7000 (tpt) REVERT: C 156 ILE cc_start: 0.5255 (OUTLIER) cc_final: 0.4877 (tp) outliers start: 62 outliers final: 29 residues processed: 242 average time/residue: 0.3629 time to fit residues: 137.9215 Evaluate side-chains 216 residues out of total 2837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 505 VAL Chi-restraints excluded: chain B residue 890 VAL Chi-restraints excluded: chain B residue 1037 HIS Chi-restraints excluded: chain B residue 1043 LEU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain H residue 25 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 20.0000 chunk 219 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: