Starting phenix.real_space_refine on Thu Feb 15 15:45:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uoe_26646/02_2024/7uoe_26646_neut_updated.pdb" } resolution = 2.67 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= 0.072 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 74 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 7595 2.51 5 N 2105 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12705 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7478 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 898} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1426 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 559 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 697 Classifications: {'RNA': 33} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 32} Chain: "T" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 795 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 21, 'rna3p_pyr': 16} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 33 Unusual residues: {' MG': 2, ' ZN': 2, 'CTP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'L2B': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "T" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2462 SG CYS A 301 34.108 95.946 114.728 1.00 24.16 S ATOM 2503 SG CYS A 306 35.877 99.307 115.464 1.00 49.44 S ATOM 2535 SG CYS A 310 35.918 96.443 118.076 1.00 28.70 S ATOM 3943 SG CYS A 487 33.995 92.897 94.633 1.00 43.34 S ATOM 5196 SG CYS A 645 35.198 96.649 94.646 1.00 31.46 S ATOM 5202 SG CYS A 646 32.961 94.804 97.289 1.00 36.67 S Time building chain proxies: 7.08, per 1000 atoms: 0.56 Number of scatterers: 12705 At special positions: 0 Unit cell: (90.64, 125.66, 170.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 74 15.00 Mg 2 11.99 O 2845 8.00 N 2105 7.00 C 7595 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 6 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 10 sheets defined 49.6% alpha, 10.7% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.592A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.779A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.586A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.086A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.039A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 320 removed outlier: 3.665A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.832A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.740A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 580 removed outlier: 3.511A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.518A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.545A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 857 through 869 Proline residue: A 868 - end of helix Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.960A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.797A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 924 removed outlier: 4.007A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 35 through 97 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.580A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.586A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.676A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 23 " --> pdb=" O GLN D 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 81 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.343A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= E, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.570A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 799 through 802 removed outlier: 3.948A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.883A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.050A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 127 through 132 removed outlier: 5.858A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3858 1.35 - 1.49: 3748 1.49 - 1.62: 5091 1.62 - 1.75: 2 1.75 - 1.89: 129 Bond restraints: 12828 Sorted by residual: bond pdb=" C2' L2B P 101 " pdb=" C3' L2B P 101 " ideal model delta sigma weight residual 1.281 1.534 -0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" O5' L2B P 101 " pdb=" P L2B P 101 " ideal model delta sigma weight residual 1.648 1.889 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C4' L2B P 101 " pdb=" C5' L2B P 101 " ideal model delta sigma weight residual 1.418 1.620 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1' L2B P 101 " pdb=" N1 L2B P 101 " ideal model delta sigma weight residual 1.463 1.622 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" C5 L2B P 101 " pdb=" C6 L2B P 101 " ideal model delta sigma weight residual 1.493 1.362 0.131 2.00e-02 2.50e+03 4.26e+01 ... (remaining 12823 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 666 106.85 - 113.65: 7204 113.65 - 120.44: 5005 120.44 - 127.24: 4631 127.24 - 134.03: 231 Bond angle restraints: 17737 Sorted by residual: angle pdb=" OP1 L2B P 101 " pdb=" P L2B P 101 " pdb=" OP2 L2B P 101 " ideal model delta sigma weight residual 109.47 123.66 -14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C1' L2B P 101 " pdb=" O4' L2B P 101 " pdb=" C4' L2B P 101 " ideal model delta sigma weight residual 105.45 115.11 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C2' CTP A1005 " pdb=" C3' CTP A1005 " pdb=" C4' CTP A1005 " ideal model delta sigma weight residual 111.00 104.38 6.62 3.00e+00 1.11e-01 4.87e+00 angle pdb=" C5' L2B P 101 " pdb=" C4' L2B P 101 " pdb=" O4' L2B P 101 " ideal model delta sigma weight residual 110.24 116.78 -6.54 3.00e+00 1.11e-01 4.75e+00 angle pdb=" C TYR A 217 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " ideal model delta sigma weight residual 121.54 125.62 -4.08 1.91e+00 2.74e-01 4.57e+00 ... (remaining 17732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.92: 7383 25.92 - 51.84: 268 51.84 - 77.77: 129 77.77 - 103.69: 5 103.69 - 129.61: 2 Dihedral angle restraints: 7787 sinusoidal: 3697 harmonic: 4090 Sorted by residual: dihedral pdb=" CA ASP A 910 " pdb=" C ASP A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual 180.00 143.33 36.67 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" O3B CTP A1005 " pdb=" O3A CTP A1005 " pdb=" PB CTP A1005 " pdb=" PA CTP A1005 " ideal model delta sinusoidal sigma weight residual -39.29 89.97 -129.26 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" C5' CTP A1005 " pdb=" O5' CTP A1005 " pdb=" PA CTP A1005 " pdb=" O3A CTP A1005 " ideal model delta sinusoidal sigma weight residual 1.42 69.93 -68.50 1 2.00e+01 2.50e-03 1.52e+01 ... (remaining 7784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1635 0.040 - 0.080: 313 0.080 - 0.119: 93 0.119 - 0.159: 15 0.159 - 0.199: 1 Chirality restraints: 2057 Sorted by residual: chirality pdb=" C1' L2B P 101 " pdb=" C2' L2B P 101 " pdb=" N1 L2B P 101 " pdb=" O4' L2B P 101 " both_signs ideal model delta sigma weight residual False 2.38 2.58 -0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" C2' L2B P 101 " pdb=" C1' L2B P 101 " pdb=" C3' L2B P 101 " pdb=" O2' L2B P 101 " both_signs ideal model delta sigma weight residual False -2.42 -2.57 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL D 159 " pdb=" N VAL D 159 " pdb=" C VAL D 159 " pdb=" CB VAL D 159 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 2054 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CTP A1005 " 0.014 2.00e-02 2.50e+03 1.79e-02 4.00e+00 pdb=" C4 CTP A1005 " -0.013 2.00e-02 2.50e+03 pdb=" C5 CTP A1005 " -0.015 2.00e-02 2.50e+03 pdb=" N3 CTP A1005 " -0.014 2.00e-02 2.50e+03 pdb=" N4 CTP A1005 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 190 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.39e+00 pdb=" C VAL A 190 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 190 " 0.008 2.00e-02 2.50e+03 pdb=" N GLN A 191 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 189 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C THR A 189 " -0.020 2.00e-02 2.50e+03 pdb=" O THR A 189 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 190 " 0.007 2.00e-02 2.50e+03 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 226 2.60 - 3.17: 11046 3.17 - 3.75: 21279 3.75 - 4.32: 31506 4.32 - 4.90: 49150 Nonbonded interactions: 113207 Sorted by model distance: nonbonded pdb=" OD2 ASP A 36 " pdb=" O HOH A1101 " model vdw 2.022 2.440 nonbonded pdb=" OD2 ASP A 452 " pdb=" OG1 THR A 556 " model vdw 2.026 2.440 nonbonded pdb=" O HOH A1168 " pdb=" O HOH A1303 " model vdw 2.027 2.440 nonbonded pdb=" O LEU A 247 " pdb=" O HOH A1102 " model vdw 2.036 2.440 nonbonded pdb=" O LYS A 545 " pdb=" O HOH A1103 " model vdw 2.039 2.440 ... (remaining 113202 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 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N \ or name CA or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 11.780 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 44.090 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.006 0.253 12828 Z= 0.340 Angle : 0.522 14.193 17737 Z= 0.276 Chirality : 0.037 0.199 2057 Planarity : 0.003 0.027 2003 Dihedral : 15.617 129.609 5139 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.41 % Favored : 97.37 % Rotamer: Outliers : 1.18 % Allowed : 5.47 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.41 (0.23), residues: 1368 helix: 1.30 (0.20), residues: 696 sheet: -0.98 (0.40), residues: 138 loop : -0.69 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.015 0.001 PHE A 741 TYR 0.012 0.001 TYR A 515 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7605 (t70) cc_final: 0.7098 (t0) REVERT: A 64 ASN cc_start: 0.7787 (m-40) cc_final: 0.7202 (m110) REVERT: C 18 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8392 (tm-30) outliers start: 14 outliers final: 2 residues processed: 144 average time/residue: 1.6291 time to fit residues: 251.2420 Evaluate side-chains 114 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 82 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 613 HIS A 650 HIS A 722 ASN D 176 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12828 Z= 0.250 Angle : 0.508 8.644 17737 Z= 0.263 Chirality : 0.038 0.172 2057 Planarity : 0.003 0.036 2003 Dihedral : 15.173 134.018 2614 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.56 % Favored : 97.22 % Rotamer: Outliers : 1.43 % Allowed : 10.01 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.68 (0.23), residues: 1368 helix: 1.53 (0.20), residues: 686 sheet: -0.81 (0.40), residues: 137 loop : -0.53 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.018 0.001 PHE D 92 TYR 0.011 0.001 TYR A 80 ARG 0.005 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7950 (m-40) cc_final: 0.7519 (m-40) REVERT: A 110 MET cc_start: 0.8658 (mmm) cc_final: 0.8294 (mmm) REVERT: B 69 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 23 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: C 44 ASP cc_start: 0.7075 (t0) cc_final: 0.5160 (t0) REVERT: D 50 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: D 57 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7895 (mtm110) outliers start: 17 outliers final: 7 residues processed: 124 average time/residue: 1.6589 time to fit residues: 220.2941 Evaluate side-chains 118 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 127 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12828 Z= 0.270 Angle : 0.498 8.651 17737 Z= 0.258 Chirality : 0.038 0.180 2057 Planarity : 0.003 0.034 2003 Dihedral : 15.253 135.662 2614 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.19 % Favored : 97.59 % Rotamer: Outliers : 2.19 % Allowed : 10.18 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.76 (0.23), residues: 1368 helix: 1.59 (0.20), residues: 689 sheet: -0.86 (0.38), residues: 139 loop : -0.46 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.012 0.001 TYR A 80 ARG 0.008 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7963 (m-40) cc_final: 0.7537 (m-40) REVERT: A 110 MET cc_start: 0.8641 (mmm) cc_final: 0.8255 (mmm) REVERT: B 19 GLN cc_start: 0.8305 (tp40) cc_final: 0.7852 (pt0) REVERT: B 55 MET cc_start: 0.7788 (ppp) cc_final: 0.7542 (ppp) REVERT: B 69 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8248 (tm-30) REVERT: D 50 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: D 57 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7674 (mtm110) outliers start: 26 outliers final: 8 residues processed: 129 average time/residue: 1.6808 time to fit residues: 232.3156 Evaluate side-chains 118 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 791 ASN D 65 GLN D 157 GLN D 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12828 Z= 0.235 Angle : 0.491 9.560 17737 Z= 0.252 Chirality : 0.037 0.181 2057 Planarity : 0.003 0.033 2003 Dihedral : 15.260 135.816 2613 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.97 % Favored : 97.81 % Rotamer: Outliers : 1.68 % Allowed : 11.44 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.82 (0.23), residues: 1368 helix: 1.61 (0.20), residues: 690 sheet: -0.62 (0.38), residues: 143 loop : -0.48 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.019 0.001 PHE B 49 TYR 0.011 0.001 TYR A 80 ARG 0.004 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7927 (m-40) cc_final: 0.7430 (m-40) REVERT: B 69 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 50 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: D 57 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7568 (mtm110) outliers start: 20 outliers final: 9 residues processed: 127 average time/residue: 1.6419 time to fit residues: 223.5037 Evaluate side-chains 117 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 40.0000 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12828 Z= 0.301 Angle : 0.511 9.620 17737 Z= 0.262 Chirality : 0.038 0.185 2057 Planarity : 0.003 0.036 2003 Dihedral : 15.309 135.961 2613 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.27 % Favored : 97.51 % Rotamer: Outliers : 2.19 % Allowed : 11.52 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1368 helix: 1.60 (0.20), residues: 693 sheet: -0.79 (0.38), residues: 143 loop : -0.48 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.018 0.001 PHE A 741 TYR 0.012 0.001 TYR A 80 ARG 0.007 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7899 (m-40) cc_final: 0.7381 (m-40) REVERT: A 110 MET cc_start: 0.8614 (mmm) cc_final: 0.8170 (mmm) REVERT: B 55 MET cc_start: 0.7776 (ppp) cc_final: 0.7530 (ppp) REVERT: B 67 MET cc_start: 0.8315 (tmm) cc_final: 0.8083 (tmm) REVERT: B 69 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8275 (tm-30) REVERT: D 50 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8308 (m-30) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 1.6193 time to fit residues: 224.4839 Evaluate side-chains 119 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 chunk 80 optimal weight: 0.3980 chunk 33 optimal weight: 0.0970 chunk 136 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12828 Z= 0.160 Angle : 0.488 12.602 17737 Z= 0.248 Chirality : 0.036 0.181 2057 Planarity : 0.003 0.033 2003 Dihedral : 15.264 135.348 2613 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 1.90 % Favored : 97.88 % Rotamer: Outliers : 1.68 % Allowed : 12.62 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.95 (0.23), residues: 1368 helix: 1.71 (0.20), residues: 684 sheet: -0.44 (0.38), residues: 143 loop : -0.42 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.003 0.000 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.009 0.001 TYR A 80 ARG 0.006 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7816 (m-40) cc_final: 0.7297 (m-40) REVERT: B 55 MET cc_start: 0.7784 (ppp) cc_final: 0.7548 (ppp) REVERT: B 67 MET cc_start: 0.8315 (tmm) cc_final: 0.8047 (tmm) REVERT: B 69 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8263 (tm-30) REVERT: D 50 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: D 57 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7567 (mtm-85) outliers start: 20 outliers final: 9 residues processed: 124 average time/residue: 1.5948 time to fit residues: 212.5023 Evaluate side-chains 117 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.0040 chunk 77 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12828 Z= 0.261 Angle : 0.512 11.928 17737 Z= 0.261 Chirality : 0.038 0.187 2057 Planarity : 0.003 0.034 2003 Dihedral : 15.290 135.475 2613 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.12 % Favored : 97.66 % Rotamer: Outliers : 1.51 % Allowed : 13.12 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.97 (0.23), residues: 1368 helix: 1.72 (0.20), residues: 693 sheet: -0.42 (0.40), residues: 133 loop : -0.43 (0.28), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.018 0.001 PHE A 741 TYR 0.011 0.001 TYR A 80 ARG 0.010 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7822 (m-40) cc_final: 0.7296 (m-40) REVERT: A 110 MET cc_start: 0.8591 (mmm) cc_final: 0.8155 (mmm) REVERT: B 55 MET cc_start: 0.7871 (ppp) cc_final: 0.7588 (ppp) REVERT: B 57 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7870 (mtm110) REVERT: B 67 MET cc_start: 0.8345 (tmm) cc_final: 0.8071 (tmm) REVERT: B 69 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 57 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7644 (mtm110) REVERT: D 70 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8172 (tmm) outliers start: 18 outliers final: 11 residues processed: 120 average time/residue: 1.6801 time to fit residues: 216.1762 Evaluate side-chains 118 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12828 Z= 0.238 Angle : 0.519 12.303 17737 Z= 0.264 Chirality : 0.037 0.187 2057 Planarity : 0.003 0.033 2003 Dihedral : 15.313 135.450 2613 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.19 % Favored : 97.59 % Rotamer: Outliers : 1.51 % Allowed : 13.79 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1368 helix: 1.70 (0.20), residues: 688 sheet: -0.27 (0.39), residues: 143 loop : -0.49 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.018 0.001 PHE A 741 TYR 0.010 0.001 TYR A 80 ARG 0.009 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7815 (m-40) cc_final: 0.7299 (m-40) REVERT: A 110 MET cc_start: 0.8580 (mmm) cc_final: 0.8143 (mmm) REVERT: B 55 MET cc_start: 0.7878 (ppp) cc_final: 0.7649 (ppp) REVERT: B 67 MET cc_start: 0.8308 (tmm) cc_final: 0.8067 (tmm) REVERT: B 69 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8264 (tm-30) REVERT: D 70 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8210 (tmm) outliers start: 18 outliers final: 11 residues processed: 123 average time/residue: 1.6277 time to fit residues: 214.9061 Evaluate side-chains 117 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0670 chunk 130 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12828 Z= 0.270 Angle : 0.529 12.581 17737 Z= 0.271 Chirality : 0.038 0.189 2057 Planarity : 0.003 0.034 2003 Dihedral : 15.344 135.410 2613 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.12 % Favored : 97.66 % Rotamer: Outliers : 1.51 % Allowed : 13.79 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.96 (0.23), residues: 1368 helix: 1.69 (0.20), residues: 693 sheet: -0.24 (0.39), residues: 143 loop : -0.47 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 75 PHE 0.023 0.001 PHE D 49 TYR 0.011 0.001 TYR A 80 ARG 0.006 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7816 (m-40) cc_final: 0.7310 (m-40) REVERT: A 110 MET cc_start: 0.8557 (mmm) cc_final: 0.8122 (mmm) REVERT: B 55 MET cc_start: 0.7936 (ppp) cc_final: 0.7710 (ppp) REVERT: B 67 MET cc_start: 0.8308 (tmm) cc_final: 0.8035 (tmm) REVERT: B 69 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 67 ASP cc_start: 0.7735 (t0) cc_final: 0.7476 (p0) REVERT: C 73 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: D 70 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8232 (tmm) outliers start: 18 outliers final: 11 residues processed: 123 average time/residue: 1.5779 time to fit residues: 208.3400 Evaluate side-chains 119 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 119 optimal weight: 30.0000 chunk 34 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12828 Z= 0.285 Angle : 0.559 13.299 17737 Z= 0.283 Chirality : 0.038 0.190 2057 Planarity : 0.003 0.033 2003 Dihedral : 15.375 135.375 2613 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.34 % Favored : 97.44 % Rotamer: Outliers : 1.26 % Allowed : 14.21 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.92 (0.23), residues: 1368 helix: 1.65 (0.20), residues: 692 sheet: -0.24 (0.39), residues: 143 loop : -0.48 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.024 0.001 PHE B 49 TYR 0.011 0.001 TYR A 80 ARG 0.009 0.000 ARG B 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.7825 (m-40) cc_final: 0.7320 (m-40) REVERT: A 110 MET cc_start: 0.8579 (mmm) cc_final: 0.8138 (mmm) REVERT: B 67 MET cc_start: 0.8324 (tmm) cc_final: 0.8053 (tmm) REVERT: B 69 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 73 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: D 57 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7783 (mtm-85) REVERT: D 70 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8217 (tmm) outliers start: 15 outliers final: 11 residues processed: 119 average time/residue: 1.6611 time to fit residues: 212.4488 Evaluate side-chains 117 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 80 optimal weight: 0.0010 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.087789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.056882 restraints weight = 26554.553| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.35 r_work: 0.2758 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12828 Z= 0.161 Angle : 0.499 9.971 17737 Z= 0.259 Chirality : 0.036 0.185 2057 Planarity : 0.003 0.056 2003 Dihedral : 15.285 134.426 2613 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.05 % Favored : 97.73 % Rotamer: Outliers : 1.01 % Allowed : 14.72 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.00 (0.23), residues: 1368 helix: 1.64 (0.20), residues: 694 sheet: 0.03 (0.42), residues: 133 loop : -0.40 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.003 0.000 HIS A 75 PHE 0.018 0.001 PHE A 741 TYR 0.009 0.001 TYR A 748 ARG 0.009 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4815.94 seconds wall clock time: 86 minutes 55.17 seconds (5215.17 seconds total)