Starting phenix.real_space_refine on Sat May 11 05:35:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usx_42522/05_2024/8usx_42522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usx_42522/05_2024/8usx_42522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usx_42522/05_2024/8usx_42522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usx_42522/05_2024/8usx_42522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usx_42522/05_2024/8usx_42522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8usx_42522/05_2024/8usx_42522.pdb" } resolution = 4.1 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= 0.037 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 11048 2.51 5 N 3325 2.21 5 O 3493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "C GLU 751": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 17926 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 4477 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 708} Chain breaks: 2 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1478 Unresolved non-hydrogen angles: 1901 Unresolved non-hydrogen dihedrals: 1245 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 19, 'TYR:plan': 15, 'ASN:plan1': 26, 'TRP:plan': 10, 'HIS:plan': 14, 'PHE:plan': 14, 'GLU:plan': 28, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 791 Chain: "B" Number of atoms: 4500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 4500 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 415} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 708} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1433 Unresolved non-hydrogen angles: 1856 Unresolved non-hydrogen dihedrals: 1186 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 12, 'TYR:plan': 7, 'ASN:plan1': 23, 'TRP:plan': 9, 'ASP:plan': 19, 'PHE:plan': 24, 'GLU:plan': 25, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 739 Chain: "C" Number of atoms: 4495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 4495 Classifications: {'peptide': 738} Incomplete info: {'truncation_to_alanine': 399} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 705} Chain breaks: 2 Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1859 Unresolved non-hydrogen dihedrals: 1212 Unresolved non-hydrogen chiralities: 137 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 19, 'TYR:plan': 15, 'ASN:plan1': 24, 'TRP:plan': 10, 'HIS:plan': 13, 'PHE:plan': 14, 'GLU:plan': 27, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 770 Chain: "D" Number of atoms: 4454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 4454 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 423} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 706} Chain breaks: 4 Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1466 Unresolved non-hydrogen angles: 1899 Unresolved non-hydrogen dihedrals: 1214 Unresolved non-hydrogen chiralities: 160 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 13, 'TYR:plan': 8, 'ASN:plan1': 23, 'TRP:plan': 9, 'ASP:plan': 19, 'PHE:plan': 24, 'GLU:plan': 28, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 762 Time building chain proxies: 10.23, per 1000 atoms: 0.57 Number of scatterers: 17926 At special positions: 0 Unit cell: (146.376, 182.328, 189.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 3493 8.00 N 3325 7.00 C 11048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 575 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 859 " - pdb=" SG CYS B 913 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 537 " - pdb=" SG CYS D 575 " distance=2.03 Simple disulfide: pdb=" SG CYS D 543 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 859 " - pdb=" SG CYS D 913 " distance=2.03 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: 6.83 Conformation dependent library (CDL) restraints added in 4.0 seconds 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 27 sheets defined 41.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 34 through 53 removed outlier: 4.120A pdb=" N HIS A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 4.046A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.649A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.712A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.817A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.858A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.621A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.676A pdb=" N LYS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 469 removed outlier: 3.656A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 561 through 578 Processing helix chain 'A' and resid 604 through 614 Processing helix chain 'A' and resid 629 through 655 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.726A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 724 Processing helix chain 'A' and resid 732 through 743 removed outlier: 3.519A pdb=" N LEU A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 783 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 39 through 45 Processing helix chain 'B' and resid 125 through 138 removed outlier: 3.547A pdb=" N VAL B 138 " --> pdb=" O ASN B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 removed outlier: 4.418A pdb=" N PHE B 180 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 245 through 258 removed outlier: 4.039A pdb=" N ASP B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 286 removed outlier: 4.428A pdb=" N ASN B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.517A pdb=" N LEU B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.687A pdb=" N PHE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 407 removed outlier: 3.511A pdb=" N ILE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 428 through 439 Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.779A pdb=" N LEU B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 578 through 591 Processing helix chain 'B' and resid 614 through 621 removed outlier: 3.507A pdb=" N GLY B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 770 removed outlier: 3.743A pdb=" N GLY B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 787 removed outlier: 3.868A pdb=" N HIS B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 787 " --> pdb=" O PRO B 783 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 782 through 787' Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 814 through 820 removed outlier: 3.800A pdb=" N TYR B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 833 removed outlier: 3.555A pdb=" N LYS B 833 " --> pdb=" O VAL B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 854 removed outlier: 3.745A pdb=" N SER B 854 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 897 removed outlier: 3.984A pdb=" N ILE B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 888 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 905 removed outlier: 3.545A pdb=" N MET B 902 " --> pdb=" O GLY B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 955 Processing helix chain 'C' and resid 34 through 53 removed outlier: 4.264A pdb=" N HIS C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.896A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.635A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.641A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.531A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.248A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.755A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.504A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.993A pdb=" N GLN C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR C 526 " --> pdb=" O ARG C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 526' Processing helix chain 'C' and resid 551 through 556 Processing helix chain 'C' and resid 559 through 579 removed outlier: 3.742A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 Processing helix chain 'C' and resid 629 through 657 removed outlier: 3.610A pdb=" N LEU C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.511A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 removed outlier: 3.904A pdb=" N MET C 706 " --> pdb=" O MET C 702 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 707 " --> pdb=" O TYR C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 707' Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.551A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 780 removed outlier: 3.512A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.046A pdb=" N ASN D 145 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 4.027A pdb=" N PHE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 190 " --> pdb=" O HIS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 276 through 286 removed outlier: 4.085A pdb=" N ASN D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 removed outlier: 3.571A pdb=" N LEU D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 384 through 405 Processing helix chain 'D' and resid 407 through 413 removed outlier: 3.562A pdb=" N ILE D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 439 Processing helix chain 'D' and resid 552 through 562 removed outlier: 3.706A pdb=" N SER D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 573 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 614 through 622 Processing helix chain 'D' and resid 635 through 642 removed outlier: 4.083A pdb=" N VAL D 641 " --> pdb=" O ALA D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 769 removed outlier: 3.559A pdb=" N VAL D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 810 Processing helix chain 'D' and resid 810 through 820 removed outlier: 3.911A pdb=" N HIS D 814 " --> pdb=" O PHE D 810 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 815 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR D 820 " --> pdb=" O TYR D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 826 No H-bonds generated for 'chain 'D' and resid 824 through 826' Processing helix chain 'D' and resid 827 through 832 removed outlier: 3.535A pdb=" N LEU D 832 " --> pdb=" O GLY D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 Processing helix chain 'D' and resid 883 through 898 Processing helix chain 'D' and resid 898 through 908 Processing helix chain 'D' and resid 927 through 954 removed outlier: 3.777A pdb=" N ILE D 954 " --> pdb=" O ILE D 950 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 3.894A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 196 removed outlier: 7.059A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.653A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.618A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 475 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 536 removed outlier: 3.840A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.623A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 152 removed outlier: 6.269A pdb=" N VAL B 48 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 151 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL B 50 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ALA B 195 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B 49 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU B 197 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY B 51 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 196 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA B 198 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL B 457 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN B 239 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER B 459 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N SER B 241 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 296 removed outlier: 6.177A pdb=" N PHE B 265 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER B 293 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 267 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 324 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 375 through 379 removed outlier: 6.505A pdb=" N PHE B 463 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER B 483 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 465 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 593 through 599 removed outlier: 3.966A pdb=" N MET B 627 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 541 through 544 removed outlier: 3.695A pdb=" N GLN B 541 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 576 " --> pdb=" O GLN B 541 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS B 543 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 844 through 845 removed outlier: 4.174A pdb=" N ILE B 655 " --> pdb=" O VAL B 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 59 through 65 removed outlier: 7.297A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR C 88 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASN C 28 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE C 90 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLY C 30 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 92 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 32 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 196 removed outlier: 6.643A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 270 through 271 removed outlier: 3.630A pdb=" N SER C 352 " --> pdb=" O GLN C 270 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 398 Processing sheet with id=AB9, first strand: chain 'C' and resid 434 through 436 Processing sheet with id=AC1, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AC2, first strand: chain 'C' and resid 535 through 537 Processing sheet with id=AC3, first strand: chain 'C' and resid 710 through 711 removed outlier: 9.305A pdb=" N TYR C 711 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR C 683 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 147 through 152 removed outlier: 12.568A pdb=" N ALA D 47 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ALA D 195 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ARG D 49 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N LEU D 197 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY D 51 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE D 221 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU D 196 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA D 198 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL D 457 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLN D 239 " --> pdb=" O VAL D 457 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER D 459 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N SER D 241 " --> pdb=" O SER D 459 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 290 through 296 removed outlier: 6.294A pdb=" N PHE D 265 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N SER D 293 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASN D 264 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL D 326 " --> pdb=" O ASN D 264 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER D 266 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE D 328 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU D 268 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET D 327 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP D 354 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N HIS D 377 " --> pdb=" O TRP D 354 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU D 356 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LYS D 379 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE D 463 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER D 483 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 465 " --> pdb=" O LEU D 481 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 595 through 596 removed outlier: 4.069A pdb=" N ASP D 596 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG D 516 " --> pdb=" O MET D 627 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 527 through 528 removed outlier: 3.676A pdb=" N TYR D 577 " --> pdb=" O PHE D 527 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 650 through 651 removed outlier: 3.517A pdb=" N THR D 651 " --> pdb=" O GLU D 871 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU D 871 " --> pdb=" O THR D 651 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 844 through 845 removed outlier: 3.845A pdb=" N ILE D 655 " --> pdb=" O VAL D 864 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 657 " --> pdb=" O LEU D 862 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 862 " --> pdb=" O VAL D 657 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2643 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: 6.77 Time building geometry restraints manager: 7.43 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: 6518 1.34 - 1.46: 3469 1.46 - 1.58: 8052 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 18132 Sorted by residual: bond pdb=" N LYS B 586 " pdb=" CA LYS B 586 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.33e+00 bond pdb=" CD GLU B 830 " pdb=" OE1 GLU B 830 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.27e+00 bond pdb=" CA PHE B 794 " pdb=" CB PHE B 794 " ideal model delta sigma weight residual 1.530 1.555 -0.024 1.69e-02 3.50e+03 2.10e+00 bond pdb=" N GLU B 830 " pdb=" CA GLU B 830 " ideal model delta sigma weight residual 1.458 1.476 -0.018 1.26e-02 6.30e+03 2.00e+00 bond pdb=" N ARG B 622 " pdb=" CA ARG B 622 " ideal model delta sigma weight residual 1.458 1.477 -0.019 1.42e-02 4.96e+03 1.85e+00 ... (remaining 18127 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.62: 312 105.62 - 112.71: 9660 112.71 - 119.81: 5308 119.81 - 126.91: 9489 126.91 - 134.00: 124 Bond angle restraints: 24893 Sorted by residual: angle pdb=" N PRO C 447 " pdb=" CA PRO C 447 " pdb=" CB PRO C 447 " ideal model delta sigma weight residual 103.25 110.91 -7.66 1.05e+00 9.07e-01 5.33e+01 angle pdb=" C ARG B 793 " pdb=" N PHE B 794 " pdb=" CA PHE B 794 " ideal model delta sigma weight residual 121.54 133.29 -11.75 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C GLU A 545 " pdb=" CA GLU A 545 " pdb=" CB GLU A 545 " ideal model delta sigma weight residual 115.79 110.08 5.71 1.19e+00 7.06e-01 2.30e+01 angle pdb=" C GLU B 830 " pdb=" CA GLU B 830 " pdb=" CB GLU B 830 " ideal model delta sigma weight residual 110.70 119.21 -8.51 1.83e+00 2.99e-01 2.16e+01 angle pdb=" N GLU B 830 " pdb=" CA GLU B 830 " pdb=" C GLU B 830 " ideal model delta sigma weight residual 111.69 106.08 5.61 1.23e+00 6.61e-01 2.08e+01 ... (remaining 24888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10170 17.87 - 35.74: 419 35.74 - 53.61: 90 53.61 - 71.48: 16 71.48 - 89.35: 8 Dihedral angle restraints: 10703 sinusoidal: 2155 harmonic: 8548 Sorted by residual: dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 454 " pdb=" CB CYS A 454 " ideal model delta sinusoidal sigma weight residual 93.00 -179.36 -87.64 1 1.00e+01 1.00e-02 9.20e+01 dihedral pdb=" CB CYS B 543 " pdb=" SG CYS B 543 " pdb=" SG CYS B 576 " pdb=" CB CYS B 576 " ideal model delta sinusoidal sigma weight residual -86.00 -170.10 84.10 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -165.28 79.28 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 10700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2424 0.051 - 0.102: 502 0.102 - 0.153: 135 0.153 - 0.204: 9 0.204 - 0.256: 4 Chirality restraints: 3074 Sorted by residual: chirality pdb=" CA LYS B 586 " pdb=" N LYS B 586 " pdb=" C LYS B 586 " pdb=" CB LYS B 586 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO C 447 " pdb=" N PRO C 447 " pdb=" C PRO C 447 " pdb=" CB PRO C 447 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL B 629 " pdb=" CA VAL B 629 " pdb=" CG1 VAL B 629 " pdb=" CG2 VAL B 629 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3071 not shown) Planarity restraints: 3410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 523 " -0.090 5.00e-02 4.00e+02 1.36e-01 2.97e+01 pdb=" N PRO D 524 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO D 524 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO D 524 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 793 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C ARG B 793 " -0.073 2.00e-02 2.50e+03 pdb=" O ARG B 793 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE B 794 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 515 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO C 516 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.029 5.00e-02 4.00e+02 ... (remaining 3407 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 615 2.71 - 3.26: 18351 3.26 - 3.81: 27105 3.81 - 4.35: 28257 4.35 - 4.90: 48936 Nonbonded interactions: 123264 Sorted by model distance: nonbonded pdb=" OG SER A 507 " pdb=" OE1 GLN A 509 " model vdw 2.167 2.440 nonbonded pdb=" OG SER D 551 " pdb=" OG1 THR D 624 " model vdw 2.204 2.440 nonbonded pdb=" OG1 THR D 519 " pdb=" OG1 THR D 630 " model vdw 2.212 2.440 nonbonded pdb=" OD1 ASP B 533 " pdb=" N GLU B 534 " model vdw 2.224 2.520 nonbonded pdb=" O GLY C 485 " pdb=" NH2 ARG C 523 " model vdw 2.230 2.520 ... (remaining 123259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 439 or (resid 440 through 444 and (name N or na \ me CA or name C or name O or name CB )) or (resid 445 through 448 and (name N or \ name CA or name C or name O or name CB )) or resid 449 through 452 or (resid 45 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 454 through \ 546 or (resid 547 through 566 and (name N or name CA or name C or name O or name \ CB )) or resid 567 through 614 or resid 628 through 731 or (resid 732 and (name \ N or name CA or name C or name O or name CB )) or resid 733 through 745 or (res \ id 746 and (name N or name CA or name C or name O or name CB )) or resid 747 thr \ ough 798)) selection = (chain 'C' and ((resid 25 through 394 and (name N or name CA or name C or name O \ or name CB )) or resid 395 through 397 or (resid 398 and (name N or name CA or \ name C or name O or name CB )) or resid 399 through 431 or (resid 432 through 43 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 434 through \ 487 or (resid 488 through 489 and (name N or name CA or name C or name O or name \ CB )) or resid 490 or (resid 491 through 496 and (name N or name CA or name C o \ r name O or name CB )) or resid 497 through 510 or (resid 511 and (name N or nam \ e CA or name C or name O or name CB )) or resid 512 through 543 or (resid 544 th \ rough 566 and (name N or name CA or name C or name O or name CB )) or resid 567 \ through 693 or (resid 694 through 695 and (name N or name CA or name C or name O \ or name CB )) or resid 696 through 708 or (resid 709 and (name N or name CA or \ name C or name O or name CB )) or resid 710 through 787 or (resid 788 and (name \ N or name CA or name C or name O or name CB )) or resid 789 through 798)) } ncs_group { reference = (chain 'B' and (resid 38 through 529 or (resid 530 through 532 and (name N or na \ me CA or name C or name O or name CB )) or resid 533 through 541 or (resid 542 a \ nd (name N or name CA or name C or name O or name CB )) or resid 543 or (resid 5 \ 44 through 545 and (name N or name CA or name C or name O or name CB )) or resid \ 546 through 549 or (resid 550 and (name N or name CA or name C or name O or nam \ e CB )) or resid 551 through 579 or (resid 580 and (name N or name CA or name C \ or name O or name CB )) or resid 581 through 596 or (resid 597 and (name N or na \ me CA or name C or name O or name CB )) or resid 598 through 625 or (resid 626 a \ nd (name N or name CA or name C or name O or name CB )) or resid 627 through 660 \ or (resid 740 through 776 and (name N or name CA or name C or name O or name CB \ )) or resid 777 through 784 or (resid 785 and (name N or name CA or name C or n \ ame O or name CB )) or resid 786 through 829 or (resid 830 and (name N or name C \ A or name C or name O or name CB )) or resid 831 through 855 or (resid 856 throu \ gh 857 and (name N or name CA or name C or name O or name CB )) or resid 858 thr \ ough 892 or (resid 893 through 894 and (name N or name CA or name C or name O or \ name CB )) or resid 895 through 955)) selection = (chain 'D' and (resid 38 through 565 or (resid 566 and (name N or name CA or nam \ e C or name O or name CB )) or resid 567 through 642 or (resid 643 and (name N o \ r name CA or name C or name O or name CB )) or resid 644 through 659 or (resid 6 \ 60 through 741 and (name N or name CA or name C or name O or name CB )) or (resi \ d 742 through 769 and (name N or name CA or name C or name O or name CB )) or re \ sid 770 through 844 or (resid 845 and (name N or name CA or name C or name O or \ name CB )) or resid 846 through 955)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.690 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: 0.010 Extract box with map and model: 14.360 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.500 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.090 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18132 Z= 0.189 Angle : 0.617 11.749 24893 Z= 0.351 Chirality : 0.045 0.256 3074 Planarity : 0.004 0.136 3410 Dihedral : 11.314 89.352 5119 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.85 % Favored : 92.61 % Rotamer: Outliers : 0.21 % Allowed : 0.42 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: 0.07 (0.17), residues: 2935 helix: 2.05 (0.16), residues: 1128 sheet: -0.08 (0.28), residues: 398 loop : -1.68 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 613 HIS 0.003 0.001 HIS D 787 PHE 0.028 0.002 PHE A 754 TYR 0.018 0.001 TYR B 831 ARG 0.008 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 664 ILE cc_start: 0.7535 (mm) cc_final: 0.6994 (mm) REVERT: C 424 PHE cc_start: 0.7408 (m-80) cc_final: 0.7068 (m-80) outliers start: 2 outliers final: 2 residues processed: 204 average time/residue: 0.2225 time to fit residues: 78.0431 Evaluate side-chains 176 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 40.0000 chunk 223 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 chunk 140 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN C 696 GLN ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 18132 Z= 0.461 Angle : 0.695 11.859 24893 Z= 0.374 Chirality : 0.047 0.214 3074 Planarity : 0.005 0.136 3410 Dihedral : 4.797 35.649 3039 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.55 % Favored : 90.87 % Rotamer: Outliers : 0.42 % Allowed : 9.25 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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: -0.20 (0.16), residues: 2935 helix: 1.79 (0.16), residues: 1162 sheet: -0.17 (0.27), residues: 399 loop : -1.92 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 498 HIS 0.012 0.002 HIS C 780 PHE 0.056 0.003 PHE B 794 TYR 0.047 0.003 TYR B 579 ARG 0.008 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.8622 (tpp) cc_final: 0.8091 (mmt) outliers start: 4 outliers final: 4 residues processed: 184 average time/residue: 0.2193 time to fit residues: 70.6223 Evaluate side-chains 165 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 80.0000 chunk 83 optimal weight: 40.0000 chunk 222 optimal weight: 50.0000 chunk 182 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 289 optimal weight: 0.0070 chunk 239 optimal weight: 50.0000 chunk 266 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 215 optimal weight: 0.7980 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18132 Z= 0.335 Angle : 0.612 9.332 24893 Z= 0.331 Chirality : 0.045 0.225 3074 Planarity : 0.005 0.135 3410 Dihedral : 4.595 33.802 3039 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.36 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -0.07 (0.17), residues: 2935 helix: 1.99 (0.16), residues: 1155 sheet: -0.30 (0.27), residues: 412 loop : -1.86 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 608 HIS 0.006 0.001 HIS C 780 PHE 0.024 0.002 PHE B 649 TYR 0.025 0.002 TYR B 579 ARG 0.004 0.000 ARG C 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 PHE cc_start: 0.6629 (m-80) cc_final: 0.6404 (m-80) REVERT: A 501 MET cc_start: 0.8463 (tpp) cc_final: 0.7932 (mmt) REVERT: A 664 ILE cc_start: 0.7778 (mm) cc_final: 0.7558 (mm) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2199 time to fit residues: 73.6158 Evaluate side-chains 160 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 30.0000 chunk 201 optimal weight: 30.0000 chunk 139 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 180 optimal weight: 50.0000 chunk 269 optimal weight: 9.9990 chunk 285 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 255 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 HIS ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 18132 Z= 0.581 Angle : 0.796 16.065 24893 Z= 0.425 Chirality : 0.050 0.245 3074 Planarity : 0.006 0.135 3410 Dihedral : 5.236 35.422 3039 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.54 % Favored : 89.85 % Rotamer: Outliers : 0.42 % Allowed : 11.12 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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: -0.34 (0.16), residues: 2935 helix: 1.75 (0.16), residues: 1142 sheet: -0.31 (0.27), residues: 389 loop : -1.98 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 498 HIS 0.013 0.002 HIS C 727 PHE 0.040 0.004 PHE B 899 TYR 0.038 0.003 TYR B 579 ARG 0.005 0.001 ARG D 793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8775 (mpp) cc_final: 0.8476 (mpp) REVERT: A 664 ILE cc_start: 0.7916 (mm) cc_final: 0.7623 (mm) REVERT: C 470 MET cc_start: 0.7467 (mmt) cc_final: 0.7062 (mmt) outliers start: 4 outliers final: 3 residues processed: 190 average time/residue: 0.2167 time to fit residues: 73.6891 Evaluate side-chains 161 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 50.0000 chunk 161 optimal weight: 0.0000 chunk 4 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 243 optimal weight: 50.0000 chunk 197 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 145 optimal weight: 0.0040 chunk 255 optimal weight: 40.0000 chunk 71 optimal weight: 0.7980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 ASN ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18132 Z= 0.189 Angle : 0.570 8.981 24893 Z= 0.306 Chirality : 0.044 0.222 3074 Planarity : 0.005 0.135 3410 Dihedral : 4.504 32.214 3039 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.30 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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 (0.17), residues: 2935 helix: 2.12 (0.16), residues: 1158 sheet: -0.35 (0.27), residues: 411 loop : -1.84 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 731 HIS 0.004 0.001 HIS C 477 PHE 0.027 0.002 PHE A 754 TYR 0.014 0.002 TYR B 605 ARG 0.004 0.001 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.164 Fit side-chains revert: symmetry clash REVERT: A 501 MET cc_start: 0.8329 (tpp) cc_final: 0.7895 (mmt) REVERT: B 608 TRP cc_start: 0.7832 (t-100) cc_final: 0.7334 (t60) REVERT: C 470 MET cc_start: 0.7078 (mmt) cc_final: 0.6687 (mmt) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2275 time to fit residues: 78.6821 Evaluate side-chains 163 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.9990 chunk 256 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 167 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 236 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 50.0000 chunk 94 optimal weight: 9.9990 chunk 149 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 18132 Z= 0.475 Angle : 0.707 11.361 24893 Z= 0.379 Chirality : 0.047 0.223 3074 Planarity : 0.005 0.136 3410 Dihedral : 4.907 34.679 3039 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.13 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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: -0.13 (0.17), residues: 2935 helix: 1.98 (0.16), residues: 1155 sheet: -0.30 (0.27), residues: 389 loop : -1.93 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 608 HIS 0.009 0.002 HIS C 780 PHE 0.032 0.003 PHE B 649 TYR 0.029 0.003 TYR B 873 ARG 0.005 0.001 ARG D 793 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8774 (mpp) cc_final: 0.8431 (mpp) REVERT: C 470 MET cc_start: 0.7420 (mmt) cc_final: 0.6996 (mmt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2256 time to fit residues: 71.4312 Evaluate side-chains 157 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 162 optimal weight: 50.0000 chunk 208 optimal weight: 3.9990 chunk 161 optimal weight: 0.0470 chunk 240 optimal weight: 5.9990 chunk 159 optimal weight: 40.0000 chunk 284 optimal weight: 4.9990 chunk 177 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 18132 Z= 0.469 Angle : 0.698 11.212 24893 Z= 0.375 Chirality : 0.047 0.234 3074 Planarity : 0.005 0.135 3410 Dihedral : 5.016 34.877 3039 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.69 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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: -0.20 (0.16), residues: 2935 helix: 1.94 (0.16), residues: 1154 sheet: -0.39 (0.27), residues: 386 loop : -1.96 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 608 HIS 0.011 0.002 HIS C 780 PHE 0.035 0.003 PHE B 899 TYR 0.028 0.003 TYR B 873 ARG 0.005 0.001 ARG B 793 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.049 Fit side-chains REVERT: A 470 MET cc_start: 0.8820 (mpp) cc_final: 0.8541 (mpp) REVERT: A 501 MET cc_start: 0.8672 (tpp) cc_final: 0.8106 (mmt) REVERT: C 470 MET cc_start: 0.7345 (mmt) cc_final: 0.6936 (mmt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2215 time to fit residues: 68.6724 Evaluate side-chains 152 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 8.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 55 optimal weight: 30.0000 chunk 180 optimal weight: 40.0000 chunk 193 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 223 optimal weight: 50.0000 chunk 258 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN ** A 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 886 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.167 18132 Z= 1.130 Angle : 1.182 18.569 24893 Z= 0.628 Chirality : 0.062 0.385 3074 Planarity : 0.008 0.148 3410 Dihedral : 6.675 43.212 3039 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.89 % Allowed : 11.86 % Favored : 87.26 % Rotamer: Outliers : 0.21 % Allowed : 4.68 % Favored : 95.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.14 % 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: -1.23 (0.16), residues: 2935 helix: 0.92 (0.16), residues: 1141 sheet: -0.91 (0.27), residues: 372 loop : -2.35 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.005 TRP B 608 HIS 0.025 0.004 HIS C 780 PHE 0.073 0.006 PHE C 472 TYR 0.078 0.006 TYR B 605 ARG 0.012 0.002 ARG B 807 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.933 Fit side-chains REVERT: A 470 MET cc_start: 0.8725 (mpp) cc_final: 0.8253 (mpp) REVERT: A 484 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: C 424 PHE cc_start: 0.8194 (m-80) cc_final: 0.7557 (m-80) REVERT: C 470 MET cc_start: 0.7718 (mmt) cc_final: 0.7406 (mmt) outliers start: 2 outliers final: 1 residues processed: 167 average time/residue: 0.2123 time to fit residues: 63.1024 Evaluate side-chains 151 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 2.9990 chunk 248 optimal weight: 50.0000 chunk 264 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 239 optimal weight: 50.0000 chunk 250 optimal weight: 50.0000 chunk 173 optimal weight: 40.0000 chunk 280 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 18132 Z= 0.520 Angle : 0.792 12.471 24893 Z= 0.423 Chirality : 0.049 0.238 3074 Planarity : 0.006 0.136 3410 Dihedral : 5.810 40.210 3039 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.20 % Favored : 90.26 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.11 % 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: -0.95 (0.16), residues: 2935 helix: 1.29 (0.16), residues: 1158 sheet: -0.80 (0.27), residues: 362 loop : -2.35 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 608 HIS 0.012 0.002 HIS C 780 PHE 0.037 0.003 PHE C 458 TYR 0.031 0.003 TYR B 908 ARG 0.005 0.001 ARG D 793 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.945 Fit side-chains revert: symmetry clash REVERT: A 470 MET cc_start: 0.8615 (mpp) cc_final: 0.8317 (mpp) REVERT: C 470 MET cc_start: 0.7425 (mmt) cc_final: 0.7055 (mmt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2227 time to fit residues: 67.3932 Evaluate side-chains 152 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 50.0000 chunk 132 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 293 optimal weight: 40.0000 chunk 270 optimal weight: 1.9990 chunk 234 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 chunk 180 optimal weight: 50.0000 chunk 143 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 249 optimal weight: 50.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18132 Z= 0.223 Angle : 0.613 10.211 24893 Z= 0.326 Chirality : 0.045 0.209 3074 Planarity : 0.005 0.138 3410 Dihedral : 4.920 33.062 3039 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.14 % Favored : 91.35 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.04 % 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 (0.16), residues: 2935 helix: 1.93 (0.16), residues: 1156 sheet: -0.55 (0.28), residues: 370 loop : -2.04 (0.17), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 608 HIS 0.005 0.001 HIS B 814 PHE 0.019 0.002 PHE B 558 TYR 0.018 0.002 TYR B 908 ARG 0.003 0.000 ARG D 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5870 Ramachandran restraints generated. 2935 Oldfield, 0 Emsley, 2935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.093 Fit side-chains revert: symmetry clash REVERT: C 470 MET cc_start: 0.7179 (mmt) cc_final: 0.6811 (mmt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2247 time to fit residues: 72.3125 Evaluate side-chains 156 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 234 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 chunk 240 optimal weight: 0.0000 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 205 optimal weight: 20.0000 chunk 13 optimal weight: 0.0670 overall best weight: 1.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 886 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.174685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.152033 restraints weight = 55418.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.147794 restraints weight = 81986.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.146798 restraints weight = 65319.720| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18132 Z= 0.207 Angle : 0.585 8.764 24893 Z= 0.311 Chirality : 0.044 0.215 3074 Planarity : 0.005 0.138 3410 Dihedral : 4.597 33.174 3039 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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 (0.17), residues: 2935 helix: 2.16 (0.16), residues: 1155 sheet: -0.53 (0.28), residues: 382 loop : -1.89 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 768 HIS 0.005 0.001 HIS C 780 PHE 0.017 0.002 PHE B 558 TYR 0.017 0.002 TYR B 908 ARG 0.006 0.000 ARG B 793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3018.11 seconds wall clock time: 55 minutes 57.38 seconds (3357.38 seconds total)