Starting phenix.real_space_refine on Sat Sep 12 12:20:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.map" model { file = "/net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7at8_11910/09_2026/7at8_11910.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 310 5.49 5 S 55 5.16 5 C 9053 2.51 5 N 2945 2.21 5 O 3581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15951 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 619 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 4 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1851 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 13, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1024 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "F" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "I" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "T" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3176 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "U" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3214 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 33 Unusual residues: {' ZN': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 222 SG CYS A 286 42.792 44.930 98.704 1.00172.70 S ATOM 250 SG CYS A 289 39.019 44.911 98.087 0.99172.87 S ATOM 296 SG CYS A 294 41.047 41.721 97.546 0.87165.55 S ATOM 815 SG CYS A 548 59.081 55.951 95.973 1.00224.51 S ATOM 908 SG CYS A 561 56.647 54.817 93.302 1.00185.75 S ATOM 958 SG CYS A 567 55.456 57.195 95.986 1.00196.50 S ATOM 985 SG CYS A 571 57.977 58.482 93.473 1.00189.83 S ATOM 760 SG CYS A 541 56.817 52.987 96.687 1.00200.99 S ATOM 815 SG CYS A 548 59.081 55.951 95.973 1.00224.51 S ATOM 841 SG CYS A 552 60.285 52.403 95.140 1.00211.70 S ATOM 760 SG CYS A 541 56.817 52.987 96.687 1.00200.99 S ATOM 854 SG CYS A 554 56.701 51.050 93.445 0.93198.28 S ATOM 908 SG CYS A 561 56.647 54.817 93.302 1.00185.75 S ATOM 943 SG CYS A 565 53.618 52.936 94.782 1.00180.30 S ATOM 1087 SG CYS A 584 42.028 59.705 77.412 1.00141.94 S ATOM 1197 SG CYS A 598 42.846 57.761 80.573 1.00148.79 S ATOM 1255 SG CYS A 606 40.534 60.860 80.840 1.00151.54 S ATOM 1351 SG CYS A 619 39.256 57.835 79.458 1.00148.68 S ATOM 1041 SG CYS A 578 44.356 61.108 80.066 1.00152.37 S ATOM 1139 SG CYS A 591 46.636 58.342 81.480 1.00155.72 S ATOM 1197 SG CYS A 598 42.846 57.761 80.573 1.00148.79 S ATOM 1234 SG CYS A 603 44.045 59.728 83.596 1.00143.87 S ATOM 1041 SG CYS A 578 44.356 61.108 80.066 1.00152.37 S ATOM 1058 SG CYS A 580 44.717 62.660 76.821 1.00142.11 S ATOM 1087 SG CYS A 584 42.028 59.705 77.412 1.00141.94 S ATOM 1126 SG CYS A 589 45.819 59.144 77.101 1.00147.49 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA D 31 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA D 31 " occ=0.00 residue: pdb=" N THR D 32 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR D 32 " occ=0.00 Time building chain proxies: 3.33, per 1000 atoms: 0.21 Number of scatterers: 15951 At special positions: 0 Unit cell: (130.95, 171.108, 144.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 55 16.00 P 310 15.00 O 3581 8.00 N 2945 7.00 C 9053 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 - 3.00 Amino acid : True - 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: 1.32 Conformation dependent library (CDL) restraints added in 497.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 289 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 286 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 294 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 548 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 567 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 571 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 561 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 543 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 548 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 541 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 552 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 541 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 565 " pdb=" ZN A1005 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 619 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 606 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 598 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 584 " pdb=" ZN A1006 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 603 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 598 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 578 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 591 " pdb=" ZN A1007 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 578 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 589 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 580 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 584 " Number of angles added : 36 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 61.0% alpha, 4.7% beta 150 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.521A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.736A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 462 removed outlier: 3.673A pdb=" N ARG A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 493 through 504 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 666 through 679 removed outlier: 3.545A pdb=" N ASP A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'C' and resid 589 through 602 removed outlier: 4.055A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 removed outlier: 4.377A pdb=" N MET C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 650 removed outlier: 4.426A pdb=" N HIS C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 640 " --> pdb=" O CYS C 636 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.920A pdb=" N ASP C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.878A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.693A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.479A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.950A pdb=" N VAL E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.685A pdb=" N VAL F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 73 removed outlier: 4.538A pdb=" N VAL F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.553A pdb=" N ASP F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 Processing helix chain 'G' and resid 34 through 46 Processing helix chain 'G' and resid 52 through 81 Processing helix chain 'G' and resid 87 through 99 removed outlier: 3.563A pdb=" N ILE G 91 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 121 removed outlier: 3.863A pdb=" N ALA G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 57 Processing helix chain 'H' and resid 63 through 79 removed outlier: 3.943A pdb=" N PHE H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 114 Processing helix chain 'H' and resid 120 through 131 Processing helix chain 'I' and resid 25 through 29 removed outlier: 3.704A pdb=" N ILE I 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 42 Processing helix chain 'I' and resid 49 through 76 removed outlier: 4.390A pdb=" N GLU I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 3.920A pdb=" N VAL I 86 " --> pdb=" O THR I 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 22 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.623A pdb=" N VAL J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 73 Processing helix chain 'J' and resid 79 through 90 removed outlier: 3.669A pdb=" N ASP J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 52 through 81 Processing helix chain 'K' and resid 87 through 99 removed outlier: 3.591A pdb=" N ILE K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 121 removed outlier: 3.817A pdb=" N ALA K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.761A pdb=" N SER A 114 " --> pdb=" O GLY A 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.204A pdb=" N PHE A 120 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N SER A 665 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 636 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 removed outlier: 6.780A pdb=" N PHE A 655 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 730 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.991A pdb=" N ARG D 83 " --> pdb=" O VAL E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'F' and resid 42 through 43 removed outlier: 7.645A pdb=" N ARG F 42 " --> pdb=" O ILE G 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.648A pdb=" N ILE F 78 " --> pdb=" O GLY G 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 100 through 102 removed outlier: 6.782A pdb=" N THR F 101 " --> pdb=" O TYR I 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 83 through 84 removed outlier: 7.563A pdb=" N ARG H 83 " --> pdb=" O VAL I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 42 through 43 removed outlier: 7.602A pdb=" N ARG J 42 " --> pdb=" O ILE K 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 77 through 78 removed outlier: 3.616A pdb=" N ILE J 78 " --> pdb=" O GLY K 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 517 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 766 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3729 1.33 - 1.45: 4551 1.45 - 1.57: 7896 1.57 - 1.69: 620 1.69 - 1.81: 80 Bond restraints: 16876 Sorted by residual: bond pdb=" C1' DC U -58 " pdb=" N1 DC U -58 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C1' DC T 7 " pdb=" N1 DC T 7 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.33e+01 bond pdb=" C1' DT U 15 " pdb=" N1 DT U 15 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C1' DC T 6 " pdb=" N1 DC T 6 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C3' DA U -38 " pdb=" C2' DA U -38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 ... (remaining 16871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 23148 2.01 - 4.01: 934 4.01 - 6.02: 27 6.02 - 8.03: 6 8.03 - 10.04: 4 Bond angle restraints: 24119 Sorted by residual: angle pdb=" O4' DT U 67 " pdb=" C1' DT U 67 " pdb=" N1 DT U 67 " ideal model delta sigma weight residual 108.00 112.17 -4.17 7.00e-01 2.04e+00 3.55e+01 angle pdb=" O4' DC T 7 " pdb=" C4' DC T 7 " pdb=" C3' DC T 7 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DT U -46 " pdb=" C1' DT U -46 " pdb=" N1 DT U -46 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" O4' DG T -68 " pdb=" C1' DG T -68 " pdb=" N9 DG T -68 " ideal model delta sigma weight residual 108.00 111.30 -3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" O4' DC U 52 " pdb=" C4' DC U 52 " pdb=" C3' DC U 52 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 ... (remaining 24114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 6869 18.23 - 36.46: 1167 36.46 - 54.69: 1069 54.69 - 72.91: 240 72.91 - 91.14: 12 Dihedral angle restraints: 9357 sinusoidal: 5864 harmonic: 3493 Sorted by residual: dihedral pdb=" CA PHE C 603 " pdb=" C PHE C 603 " pdb=" N SER C 604 " pdb=" CA SER C 604 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN C 562 " pdb=" C ASN C 562 " pdb=" N ARG C 563 " pdb=" CA ARG C 563 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE C 627 " pdb=" C ILE C 627 " pdb=" N ALA C 628 " pdb=" CA ALA C 628 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 9354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2040 0.047 - 0.095: 324 0.095 - 0.142: 293 0.142 - 0.189: 47 0.189 - 0.237: 2 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CA VAL C 606 " pdb=" N VAL C 606 " pdb=" C VAL C 606 " pdb=" CB VAL C 606 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 745 " pdb=" N ARG A 745 " pdb=" C ARG A 745 " pdb=" CB ARG A 745 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" C3' SAH A1008 " pdb=" C2' SAH A1008 " pdb=" C4' SAH A1008 " pdb=" O3' SAH A1008 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2703 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC U -27 " -0.032 2.00e-02 2.50e+03 2.96e-02 1.97e+01 pdb=" N1 DC U -27 " 0.072 2.00e-02 2.50e+03 pdb=" C2 DC U -27 " -0.038 2.00e-02 2.50e+03 pdb=" O2 DC U -27 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC U -27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC U -27 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC U -27 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DC U -27 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC U -27 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC U 41 " 0.028 2.00e-02 2.50e+03 2.82e-02 1.79e+01 pdb=" N1 DC U 41 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DC U 41 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC U 41 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC U 41 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC U 41 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC U 41 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC U 41 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC U 41 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT U 14 " 0.032 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT U 14 " -0.070 2.00e-02 2.50e+03 pdb=" C2 DT U 14 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DT U 14 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT U 14 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT U 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT U 14 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT U 14 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT U 14 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT U 14 " 0.001 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 27 2.39 - 3.02: 8377 3.02 - 3.65: 26442 3.65 - 4.27: 38411 4.27 - 4.90: 57802 Nonbonded interactions: 131059 Sorted by model distance: nonbonded pdb=" O LYS A 615 " pdb=" NH1 ARG A 626 " model vdw 1.763 3.120 nonbonded pdb=" OG1 THR G 29 " pdb=" OP1 DT T 30 " model vdw 2.036 3.040 nonbonded pdb=" C LYS A 615 " pdb=" NH1 ARG A 626 " model vdw 2.068 3.350 nonbonded pdb=" OD1 ASP C 675 " pdb=" N LYS C 676 " model vdw 2.123 3.120 nonbonded pdb=" OE2 GLU A 658 " pdb=" NE ARG A 725 " model vdw 2.209 3.120 ... (remaining 131054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and resid 25 through 102) selection = chain 'I' } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 16 through 118) } ncs_group { reference = (chain 'G' and resid 29 through 121) selection = chain 'K' } 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=0.00 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.930 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 0.066 16904 Z= 0.498 Angle : 0.790 10.036 24155 Z= 0.664 Chirality : 0.053 0.237 2706 Planarity : 0.004 0.030 1989 Dihedral : 24.584 91.143 7093 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.25 % Favored : 97.40 % Rotamer: Outliers : 0.40 % Allowed : 1.29 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.23), residues: 1155 helix: 0.52 (0.19), residues: 677 sheet: -2.90 (1.27), residues: 14 loop : -2.36 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 593 TYR 0.011 0.001 TYR K 37 PHE 0.006 0.001 PHE C 603 TRP 0.006 0.001 TRP C 617 HIS 0.008 0.001 HIS I 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.50 (16876) covalent geometry : angle 0.77705 / 0.66 (24119) hydrogen bonds : bond 0.10391 / 6.30 ( 900) hydrogen bonds : angle 4.21913 / 2.76 ( 2290) metal coordination : bond 0.00551 / 0.40 ( 28) metal coordination : angle 3.76391 / 2.78 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 THR cc_start: 0.6129 (m) cc_final: 0.5890 (p) REVERT: A 719 MET cc_start: 0.7885 (tpp) cc_final: 0.7678 (tpp) REVERT: C 632 MET cc_start: 0.8165 (mmp) cc_final: 0.7863 (mmp) REVERT: C 649 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8414 (mmtm) REVERT: D 45 THR cc_start: 0.7940 (m) cc_final: 0.7605 (m) REVERT: D 50 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8684 (pt0) REVERT: D 86 SER cc_start: 0.8499 (p) cc_final: 0.7909 (m) REVERT: D 90 MET cc_start: 0.8481 (mmt) cc_final: 0.8182 (mmp) REVERT: D 93 GLN cc_start: 0.9194 (tt0) cc_final: 0.8710 (tt0) REVERT: D 97 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8823 (mt-10) REVERT: D 99 TYR cc_start: 0.8382 (t80) cc_final: 0.7240 (t80) REVERT: D 103 LEU cc_start: 0.9100 (tp) cc_final: 0.8842 (tt) REVERT: D 107 THR cc_start: 0.9501 (m) cc_final: 0.9078 (m) REVERT: D 125 GLN cc_start: 0.9183 (mt0) cc_final: 0.8559 (mm110) REVERT: E 74 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8414 (tp30) REVERT: E 79 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8202 (mmtm) REVERT: F 61 GLU cc_start: 0.8943 (tp30) cc_final: 0.8502 (tp30) REVERT: F 90 ASP cc_start: 0.8123 (t0) cc_final: 0.7470 (t70) REVERT: F 95 LYS cc_start: 0.9273 (ttmt) cc_final: 0.9056 (tmtt) REVERT: F 97 LEU cc_start: 0.9398 (mt) cc_final: 0.9050 (mp) REVERT: G 37 TYR cc_start: 0.8042 (m-80) cc_final: 0.7091 (m-80) REVERT: G 40 LYS cc_start: 0.9065 (mttt) cc_final: 0.8827 (mmtp) REVERT: G 64 ASN cc_start: 0.8973 (m-40) cc_final: 0.8572 (t0) REVERT: G 91 ILE cc_start: 0.9486 (mm) cc_final: 0.9160 (tt) REVERT: G 102 GLU cc_start: 0.7164 (tp30) cc_final: 0.6755 (tp30) REVERT: H 79 LYS cc_start: 0.7791 (tttm) cc_final: 0.7550 (mptt) REVERT: H 80 THR cc_start: 0.7915 (t) cc_final: 0.7157 (t) REVERT: H 120 MET cc_start: 0.7660 (mtt) cc_final: 0.7054 (mtt) REVERT: I 37 LEU cc_start: 0.9183 (mt) cc_final: 0.8977 (mt) REVERT: I 49 LEU cc_start: 0.9027 (mt) cc_final: 0.8386 (mm) REVERT: I 55 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8627 (mtm180) REVERT: I 68 ASP cc_start: 0.8528 (m-30) cc_final: 0.8282 (m-30) REVERT: J 39 TYR cc_start: 0.8113 (m-80) cc_final: 0.7383 (m-80) REVERT: J 56 GLU cc_start: 0.8599 (tt0) cc_final: 0.8377 (tt0) REVERT: J 68 ASN cc_start: 0.7348 (m-40) cc_final: 0.6954 (m-40) REVERT: J 89 ASN cc_start: 0.8737 (m-40) cc_final: 0.8402 (t0) REVERT: J 92 GLU cc_start: 0.7144 (mt-10) cc_final: 0.5802 (mt-10) REVERT: J 94 ASN cc_start: 0.8746 (t0) cc_final: 0.7879 (m-40) REVERT: J 95 LYS cc_start: 0.8987 (tttt) cc_final: 0.8631 (ttpt) REVERT: K 92 GLN cc_start: 0.8800 (tt0) cc_final: 0.8327 (tm-30) outliers start: 4 outliers final: 1 residues processed: 453 average time/residue: 0.1632 time to fit residues: 102.2540 Evaluate side-chains 242 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.0060 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 624 HIS D 68 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN H 68 GLN H 125 GLN K 79 HIS ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.059035 restraints weight = 92138.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.060409 restraints weight = 53013.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061362 restraints weight = 36267.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061973 restraints weight = 28033.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.062316 restraints weight = 23724.683| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.173 16904 Z= 0.164 Angle : 0.717 37.053 24155 Z= 0.385 Chirality : 0.043 0.201 2706 Planarity : 0.005 0.046 1989 Dihedral : 28.771 88.445 4740 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.68 % Favored : 97.23 % Rotamer: Outliers : 0.30 % Allowed : 3.26 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.24), residues: 1155 helix: 0.99 (0.19), residues: 689 sheet: -1.73 (1.50), residues: 10 loop : -1.84 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 42 TYR 0.029 0.002 TYR F 39 PHE 0.013 0.002 PHE A 456 TRP 0.022 0.002 TRP C 591 HIS 0.012 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (16876) covalent geometry : angle 0.65126 / 0.38 (24119) hydrogen bonds : bond 0.05103 / 3.29 ( 900) hydrogen bonds : angle 3.60858 / 2.43 ( 2290) metal coordination : bond 0.03352 / 1.69 ( 28) metal coordination : angle 7.76747 / 4.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 297 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 687 LEU cc_start: 0.8974 (tp) cc_final: 0.8448 (tp) REVERT: A 696 THR cc_start: 0.6424 (m) cc_final: 0.6146 (p) REVERT: A 719 MET cc_start: 0.7630 (tpp) cc_final: 0.7363 (tpp) REVERT: C 593 ARG cc_start: 0.8805 (mpp80) cc_final: 0.8472 (ptp90) REVERT: C 594 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7324 (tp30) REVERT: C 598 THR cc_start: 0.7774 (t) cc_final: 0.7534 (p) REVERT: C 603 PHE cc_start: 0.6720 (m-80) cc_final: 0.5994 (m-10) REVERT: C 630 ASN cc_start: 0.6998 (p0) cc_final: 0.6200 (p0) REVERT: C 637 MET cc_start: 0.8569 (mmt) cc_final: 0.8050 (ppp) REVERT: C 657 MET cc_start: 0.4859 (tpp) cc_final: 0.4175 (tpp) REVERT: D 54 TYR cc_start: 0.8425 (m-10) cc_final: 0.8130 (m-10) REVERT: D 86 SER cc_start: 0.8788 (p) cc_final: 0.8068 (m) REVERT: D 97 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8361 (mt-10) REVERT: D 99 TYR cc_start: 0.8741 (t80) cc_final: 0.7604 (t80) REVERT: D 107 THR cc_start: 0.9459 (m) cc_final: 0.9231 (m) REVERT: D 110 CYS cc_start: 0.8191 (t) cc_final: 0.7974 (t) REVERT: E 63 GLU cc_start: 0.8720 (tp30) cc_final: 0.8467 (tp30) REVERT: E 74 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8397 (tp30) REVERT: E 79 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8027 (mmtm) REVERT: E 88 TYR cc_start: 0.8424 (m-10) cc_final: 0.7444 (m-10) REVERT: F 29 ARG cc_start: 0.6890 (mtp85) cc_final: 0.5268 (ttm170) REVERT: F 38 ASN cc_start: 0.7739 (t0) cc_final: 0.7221 (t0) REVERT: F 61 GLU cc_start: 0.9105 (tp30) cc_final: 0.8596 (tp30) REVERT: F 90 ASP cc_start: 0.8368 (t0) cc_final: 0.7768 (t70) REVERT: G 40 LYS cc_start: 0.9323 (mttt) cc_final: 0.9014 (mmtp) REVERT: G 64 ASN cc_start: 0.8925 (m-40) cc_final: 0.8476 (t0) REVERT: G 81 ASN cc_start: 0.8815 (t0) cc_final: 0.8523 (t0) REVERT: H 46 VAL cc_start: 0.9368 (t) cc_final: 0.8966 (t) REVERT: H 82 LEU cc_start: 0.7968 (tp) cc_final: 0.6979 (tp) REVERT: H 120 MET cc_start: 0.7924 (mtt) cc_final: 0.7027 (mmm) REVERT: I 37 LEU cc_start: 0.9332 (mt) cc_final: 0.8925 (mt) REVERT: I 63 GLU cc_start: 0.8345 (tp30) cc_final: 0.8011 (tm-30) REVERT: J 56 GLU cc_start: 0.8686 (tt0) cc_final: 0.8328 (tt0) REVERT: J 64 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7638 (tp30) REVERT: J 68 ASN cc_start: 0.8312 (m-40) cc_final: 0.7823 (m-40) REVERT: J 82 HIS cc_start: 0.8903 (m170) cc_final: 0.8562 (m90) REVERT: J 87 VAL cc_start: 0.9446 (m) cc_final: 0.9190 (m) REVERT: J 89 ASN cc_start: 0.8694 (m-40) cc_final: 0.8326 (t0) REVERT: J 94 ASN cc_start: 0.8815 (t0) cc_final: 0.7672 (m-40) REVERT: J 95 LYS cc_start: 0.8946 (tttt) cc_final: 0.8595 (ttpt) REVERT: K 70 ILE cc_start: 0.9527 (mm) cc_final: 0.9207 (mm) REVERT: K 90 GLU cc_start: 0.9570 (mp0) cc_final: 0.8983 (mp0) REVERT: K 92 GLN cc_start: 0.9160 (tt0) cc_final: 0.8284 (tm-30) REVERT: K 99 LEU cc_start: 0.8323 (mt) cc_final: 0.8061 (mp) outliers start: 3 outliers final: 1 residues processed: 298 average time/residue: 0.1408 time to fit residues: 60.6783 Evaluate side-chains 230 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 144 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 624 HIS ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.070365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056193 restraints weight = 93954.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057578 restraints weight = 52974.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058510 restraints weight = 35892.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.059068 restraints weight = 27647.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.059518 restraints weight = 23499.940| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.309 16904 Z= 0.192 Angle : 0.719 33.399 24155 Z= 0.384 Chirality : 0.042 0.212 2706 Planarity : 0.005 0.111 1989 Dihedral : 29.159 89.143 4740 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1155 helix: 1.29 (0.20), residues: 696 sheet: -1.48 (1.52), residues: 10 loop : -1.65 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 29 TYR 0.012 0.001 TYR K 39 PHE 0.023 0.002 PHE F 25 TRP 0.019 0.002 TRP C 617 HIS 0.017 0.002 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (16876) covalent geometry : angle 0.65873 / 0.38 (24119) hydrogen bonds : bond 0.05123 / 3.28 ( 900) hydrogen bonds : angle 3.61203 / 2.48 ( 2290) metal coordination : bond 0.05921 / 2.97 ( 28) metal coordination : angle 7.47231 / 4.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9450 (pt0) cc_final: 0.9188 (mm-30) REVERT: A 537 ASN cc_start: 0.8558 (t0) cc_final: 0.8354 (t0) REVERT: A 687 LEU cc_start: 0.8985 (tp) cc_final: 0.8493 (tp) REVERT: A 696 THR cc_start: 0.7809 (m) cc_final: 0.7539 (p) REVERT: A 719 MET cc_start: 0.7771 (tpp) cc_final: 0.7554 (tpp) REVERT: C 590 GLU cc_start: 0.8996 (pm20) cc_final: 0.8490 (tp30) REVERT: C 598 THR cc_start: 0.8108 (t) cc_final: 0.7857 (p) REVERT: C 600 ILE cc_start: 0.6259 (tp) cc_final: 0.6015 (tp) REVERT: C 603 PHE cc_start: 0.6050 (m-80) cc_final: 0.5368 (m-80) REVERT: C 614 MET cc_start: 0.6266 (mtp) cc_final: 0.5972 (mtm) REVERT: C 616 LEU cc_start: 0.8384 (mt) cc_final: 0.7977 (mt) REVERT: C 630 ASN cc_start: 0.6653 (p0) cc_final: 0.5871 (p0) REVERT: C 637 MET cc_start: 0.8219 (mmt) cc_final: 0.7910 (ppp) REVERT: C 657 MET cc_start: 0.4852 (tpp) cc_final: 0.4576 (mmm) REVERT: D 93 GLN cc_start: 0.9582 (tt0) cc_final: 0.8926 (tm-30) REVERT: D 99 TYR cc_start: 0.8734 (t80) cc_final: 0.7809 (t80) REVERT: D 110 CYS cc_start: 0.8259 (t) cc_final: 0.7966 (t) REVERT: E 49 LEU cc_start: 0.9214 (mt) cc_final: 0.8194 (mt) REVERT: E 53 GLU cc_start: 0.8688 (mp0) cc_final: 0.8283 (mp0) REVERT: E 74 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8519 (tp30) REVERT: E 79 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8097 (mmtm) REVERT: E 88 TYR cc_start: 0.8380 (m-10) cc_final: 0.7371 (m-10) REVERT: F 56 GLU cc_start: 0.9440 (tt0) cc_final: 0.9042 (mt-10) REVERT: F 57 TYR cc_start: 0.9023 (t80) cc_final: 0.8540 (t80) REVERT: F 61 GLU cc_start: 0.9155 (tp30) cc_final: 0.8651 (tp30) REVERT: F 90 ASP cc_start: 0.8359 (t0) cc_final: 0.7780 (t70) REVERT: F 97 LEU cc_start: 0.9241 (mp) cc_final: 0.8997 (mp) REVERT: G 37 TYR cc_start: 0.7911 (m-80) cc_final: 0.7105 (m-80) REVERT: G 40 LYS cc_start: 0.9338 (mttt) cc_final: 0.9007 (mmtp) REVERT: G 64 ASN cc_start: 0.8992 (m-40) cc_final: 0.8603 (t0) REVERT: G 81 ASN cc_start: 0.8847 (t0) cc_final: 0.8609 (t0) REVERT: G 102 GLU cc_start: 0.7980 (tp30) cc_final: 0.7776 (tp30) REVERT: H 76 GLN cc_start: 0.7223 (mt0) cc_final: 0.6973 (mt0) REVERT: H 80 THR cc_start: 0.7953 (t) cc_final: 0.7064 (p) REVERT: H 82 LEU cc_start: 0.8344 (tp) cc_final: 0.8038 (tp) REVERT: H 120 MET cc_start: 0.7946 (mtt) cc_final: 0.6573 (mmm) REVERT: H 123 ASP cc_start: 0.8715 (m-30) cc_final: 0.8344 (m-30) REVERT: I 37 LEU cc_start: 0.9377 (mt) cc_final: 0.8923 (mt) REVERT: I 40 ARG cc_start: 0.9000 (tpt-90) cc_final: 0.8741 (ttm-80) REVERT: I 43 VAL cc_start: 0.9331 (t) cc_final: 0.9075 (p) REVERT: I 55 ARG cc_start: 0.9047 (mtt90) cc_final: 0.8653 (mtm180) REVERT: J 56 GLU cc_start: 0.8593 (tt0) cc_final: 0.8213 (mt-10) REVERT: J 64 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7746 (tp30) REVERT: J 68 ASN cc_start: 0.7936 (m-40) cc_final: 0.7333 (m-40) REVERT: J 94 ASN cc_start: 0.8557 (t0) cc_final: 0.7839 (m-40) REVERT: J 95 LYS cc_start: 0.9020 (tttt) cc_final: 0.8668 (ttpt) REVERT: K 70 ILE cc_start: 0.9571 (mm) cc_final: 0.9366 (mm) REVERT: K 79 HIS cc_start: 0.7600 (m90) cc_final: 0.7301 (m170) REVERT: K 90 GLU cc_start: 0.9414 (mp0) cc_final: 0.8962 (mp0) REVERT: K 92 GLN cc_start: 0.9157 (tt0) cc_final: 0.8490 (tm-30) REVERT: K 96 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8114 (tpp80) REVERT: K 99 LEU cc_start: 0.8499 (mt) cc_final: 0.8286 (mp) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1326 time to fit residues: 53.5896 Evaluate side-chains 217 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 132 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 73 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 631 GLN ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN H 68 GLN ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.070213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056235 restraints weight = 93490.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057605 restraints weight = 53832.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.058535 restraints weight = 36928.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059143 restraints weight = 28549.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059478 restraints weight = 24194.834| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 16904 Z= 0.166 Angle : 0.684 35.080 24155 Z= 0.364 Chirality : 0.041 0.205 2706 Planarity : 0.004 0.060 1989 Dihedral : 29.275 89.761 4740 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1155 helix: 1.42 (0.20), residues: 693 sheet: -1.12 (1.61), residues: 10 loop : -1.54 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 593 TYR 0.014 0.001 TYR J 39 PHE 0.014 0.001 PHE A 295 TRP 0.019 0.002 TRP C 617 HIS 0.019 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (16876) covalent geometry : angle 0.62506 / 0.36 (24119) hydrogen bonds : bond 0.04569 / 2.95 ( 900) hydrogen bonds : angle 3.47843 / 2.37 ( 2290) metal coordination : bond 0.04549 / 2.28 ( 28) metal coordination : angle 7.23300 / 4.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9471 (pt0) cc_final: 0.9217 (mm-30) REVERT: A 537 ASN cc_start: 0.8621 (t0) cc_final: 0.8356 (t0) REVERT: A 687 LEU cc_start: 0.8982 (tp) cc_final: 0.8491 (tp) REVERT: A 696 THR cc_start: 0.7794 (m) cc_final: 0.7528 (p) REVERT: A 719 MET cc_start: 0.7690 (tpp) cc_final: 0.7445 (tpp) REVERT: C 590 GLU cc_start: 0.8796 (pm20) cc_final: 0.8514 (tp30) REVERT: C 603 PHE cc_start: 0.5802 (m-80) cc_final: 0.5013 (m-80) REVERT: C 622 MET cc_start: 0.7756 (tpt) cc_final: 0.7549 (tpt) REVERT: C 630 ASN cc_start: 0.6967 (p0) cc_final: 0.6336 (p0) REVERT: C 637 MET cc_start: 0.8261 (mmt) cc_final: 0.7949 (ppp) REVERT: D 86 SER cc_start: 0.8941 (p) cc_final: 0.8622 (p) REVERT: D 93 GLN cc_start: 0.9463 (tt0) cc_final: 0.9122 (tm-30) REVERT: D 99 TYR cc_start: 0.8892 (t80) cc_final: 0.7982 (t80) REVERT: E 49 LEU cc_start: 0.9364 (mt) cc_final: 0.8302 (mt) REVERT: E 68 ASP cc_start: 0.8013 (m-30) cc_final: 0.7800 (m-30) REVERT: E 74 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8509 (tp30) REVERT: E 79 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8237 (mmtm) REVERT: F 56 GLU cc_start: 0.9413 (tt0) cc_final: 0.8941 (mt-10) REVERT: F 57 TYR cc_start: 0.9102 (t80) cc_final: 0.8576 (t80) REVERT: F 61 GLU cc_start: 0.9049 (tp30) cc_final: 0.8554 (tp30) REVERT: F 90 ASP cc_start: 0.8416 (t0) cc_final: 0.7852 (t70) REVERT: G 40 LYS cc_start: 0.9346 (mttt) cc_final: 0.9056 (mmtp) REVERT: G 64 ASN cc_start: 0.8971 (m-40) cc_final: 0.8676 (t0) REVERT: G 80 TYR cc_start: 0.8603 (m-10) cc_final: 0.8216 (m-10) REVERT: G 81 ASN cc_start: 0.8860 (t0) cc_final: 0.8522 (t0) REVERT: H 120 MET cc_start: 0.7970 (mtt) cc_final: 0.6966 (mmm) REVERT: I 37 LEU cc_start: 0.9309 (mt) cc_final: 0.8881 (mt) REVERT: I 43 VAL cc_start: 0.9369 (t) cc_final: 0.9084 (p) REVERT: I 53 GLU cc_start: 0.9014 (pp20) cc_final: 0.8776 (tm-30) REVERT: I 58 LEU cc_start: 0.9168 (tp) cc_final: 0.8916 (tp) REVERT: I 63 GLU cc_start: 0.9092 (tp30) cc_final: 0.8892 (tp30) REVERT: J 56 GLU cc_start: 0.8565 (tt0) cc_final: 0.8333 (tt0) REVERT: J 64 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7997 (tp30) REVERT: J 68 ASN cc_start: 0.8007 (m-40) cc_final: 0.7468 (m-40) REVERT: J 94 ASN cc_start: 0.8653 (t0) cc_final: 0.7541 (m-40) REVERT: J 95 LYS cc_start: 0.9003 (tttt) cc_final: 0.8611 (ttpt) REVERT: K 70 ILE cc_start: 0.9580 (mm) cc_final: 0.9368 (mm) REVERT: K 90 GLU cc_start: 0.9529 (mp0) cc_final: 0.8912 (mp0) REVERT: K 99 LEU cc_start: 0.8468 (mt) cc_final: 0.8150 (mp) REVERT: K 103 LEU cc_start: 0.8371 (mm) cc_final: 0.8002 (mm) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1368 time to fit residues: 54.6355 Evaluate side-chains 212 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 31 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 133 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN E 93 GLN F 38 ASN H 68 GLN H 125 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.067426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053269 restraints weight = 92442.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.054589 restraints weight = 53511.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055419 restraints weight = 36899.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.056029 restraints weight = 28933.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056365 restraints weight = 24593.436| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 16904 Z= 0.231 Angle : 0.753 32.124 24155 Z= 0.398 Chirality : 0.043 0.206 2706 Planarity : 0.005 0.052 1989 Dihedral : 29.537 88.345 4740 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1155 helix: 1.25 (0.20), residues: 688 sheet: -0.84 (1.62), residues: 10 loop : -1.57 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 92 TYR 0.013 0.002 TYR F 39 PHE 0.016 0.002 PHE C 626 TRP 0.029 0.004 TRP A 612 HIS 0.014 0.002 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 (16876) covalent geometry : angle 0.69840 / 0.39 (24119) hydrogen bonds : bond 0.05674 / 3.65 ( 900) hydrogen bonds : angle 3.83531 / 2.63 ( 2290) metal coordination : bond 0.03932 / 1.99 ( 28) metal coordination : angle 7.33638 / 4.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.3067 (ptm) cc_final: 0.2748 (tmm) REVERT: A 473 GLU cc_start: 0.9490 (pt0) cc_final: 0.9233 (mm-30) REVERT: A 537 ASN cc_start: 0.8839 (t0) cc_final: 0.8622 (t0) REVERT: A 687 LEU cc_start: 0.9034 (tp) cc_final: 0.8570 (tp) REVERT: A 696 THR cc_start: 0.7957 (m) cc_final: 0.7703 (p) REVERT: C 590 GLU cc_start: 0.9040 (pm20) cc_final: 0.8461 (tp30) REVERT: C 603 PHE cc_start: 0.5558 (m-80) cc_final: 0.4893 (m-80) REVERT: C 614 MET cc_start: 0.6251 (mtp) cc_final: 0.6016 (mtm) REVERT: C 616 LEU cc_start: 0.8558 (mt) cc_final: 0.8303 (mt) REVERT: C 637 MET cc_start: 0.8279 (mmt) cc_final: 0.7940 (ppp) REVERT: C 646 LYS cc_start: 0.9358 (mmpt) cc_final: 0.8855 (tttm) REVERT: D 90 MET cc_start: 0.8681 (mmp) cc_final: 0.8339 (mmm) REVERT: D 93 GLN cc_start: 0.9398 (tt0) cc_final: 0.9127 (tm-30) REVERT: D 99 TYR cc_start: 0.9080 (t80) cc_final: 0.8345 (t80) REVERT: E 70 VAL cc_start: 0.9660 (m) cc_final: 0.8751 (p) REVERT: E 79 LYS cc_start: 0.8468 (mtpp) cc_final: 0.7906 (mmtm) REVERT: E 88 TYR cc_start: 0.8479 (m-10) cc_final: 0.7653 (m-10) REVERT: F 38 ASN cc_start: 0.8649 (m-40) cc_final: 0.8341 (m110) REVERT: F 61 GLU cc_start: 0.9062 (tp30) cc_final: 0.8595 (tp30) REVERT: F 90 ASP cc_start: 0.8542 (t0) cc_final: 0.7723 (t70) REVERT: G 40 LYS cc_start: 0.9336 (mttt) cc_final: 0.8996 (mmtp) REVERT: G 64 ASN cc_start: 0.9151 (m-40) cc_final: 0.8712 (t0) REVERT: G 81 ASN cc_start: 0.8816 (t0) cc_final: 0.8503 (t0) REVERT: H 80 THR cc_start: 0.7170 (t) cc_final: 0.6701 (t) REVERT: H 120 MET cc_start: 0.8187 (mtt) cc_final: 0.7626 (mmm) REVERT: I 37 LEU cc_start: 0.9395 (mt) cc_final: 0.9052 (mt) REVERT: I 43 VAL cc_start: 0.9452 (t) cc_final: 0.9132 (p) REVERT: I 63 GLU cc_start: 0.9125 (tp30) cc_final: 0.8879 (tp30) REVERT: J 56 GLU cc_start: 0.8533 (tt0) cc_final: 0.8277 (tt0) REVERT: J 64 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8335 (tp30) REVERT: J 68 ASN cc_start: 0.8022 (m-40) cc_final: 0.7715 (m-40) REVERT: J 94 ASN cc_start: 0.8639 (t0) cc_final: 0.8055 (m-40) REVERT: J 95 LYS cc_start: 0.9173 (tttt) cc_final: 0.8815 (ttpt) REVERT: J 99 ARG cc_start: 0.8025 (mpt180) cc_final: 0.7644 (mmt180) REVERT: K 61 SER cc_start: 0.9273 (t) cc_final: 0.8882 (t) REVERT: K 90 GLU cc_start: 0.9416 (mp0) cc_final: 0.8955 (mp0) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1344 time to fit residues: 50.5246 Evaluate side-chains 199 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN H 68 GLN K 79 HIS ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.068323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054153 restraints weight = 91541.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055456 restraints weight = 52751.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056336 restraints weight = 36436.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056921 restraints weight = 28514.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057257 restraints weight = 24272.300| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.259 16904 Z= 0.162 Angle : 0.675 32.966 24155 Z= 0.363 Chirality : 0.041 0.209 2706 Planarity : 0.004 0.048 1989 Dihedral : 29.559 89.534 4740 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1155 helix: 1.39 (0.20), residues: 688 sheet: -0.73 (1.65), residues: 10 loop : -1.38 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 288 TYR 0.018 0.001 TYR J 39 PHE 0.014 0.001 PHE A 290 TRP 0.019 0.002 TRP A 612 HIS 0.011 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (16876) covalent geometry : angle 0.62073 / 0.36 (24119) hydrogen bonds : bond 0.04563 / 2.95 ( 900) hydrogen bonds : angle 3.55054 / 2.43 ( 2290) metal coordination : bond 0.04933 / 2.47 ( 28) metal coordination : angle 6.87076 / 4.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.3154 (ptm) cc_final: 0.2591 (tmm) REVERT: A 473 GLU cc_start: 0.9479 (pt0) cc_final: 0.9217 (mm-30) REVERT: A 537 ASN cc_start: 0.8868 (t0) cc_final: 0.7897 (t0) REVERT: A 687 LEU cc_start: 0.9041 (tp) cc_final: 0.8480 (tp) REVERT: A 696 THR cc_start: 0.7896 (m) cc_final: 0.7638 (p) REVERT: C 590 GLU cc_start: 0.8974 (pm20) cc_final: 0.8617 (tp30) REVERT: C 603 PHE cc_start: 0.5842 (m-80) cc_final: 0.5196 (m-80) REVERT: C 616 LEU cc_start: 0.8537 (mt) cc_final: 0.8295 (mt) REVERT: C 637 MET cc_start: 0.8253 (mmt) cc_final: 0.7963 (ppp) REVERT: C 646 LYS cc_start: 0.9332 (mmpt) cc_final: 0.8839 (tttm) REVERT: D 99 TYR cc_start: 0.9092 (t80) cc_final: 0.8369 (t80) REVERT: E 79 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8043 (mmtm) REVERT: E 88 TYR cc_start: 0.8409 (m-10) cc_final: 0.7782 (m-10) REVERT: E 98 TYR cc_start: 0.8914 (m-80) cc_final: 0.8634 (m-80) REVERT: F 61 GLU cc_start: 0.9050 (tp30) cc_final: 0.8532 (tp30) REVERT: F 90 ASP cc_start: 0.8735 (t0) cc_final: 0.7996 (t70) REVERT: G 29 THR cc_start: 0.7833 (p) cc_final: 0.7623 (p) REVERT: G 40 LYS cc_start: 0.9326 (mttt) cc_final: 0.9023 (mmtp) REVERT: G 64 ASN cc_start: 0.9095 (m-40) cc_final: 0.8710 (t0) REVERT: G 81 ASN cc_start: 0.8826 (t0) cc_final: 0.8507 (t0) REVERT: G 102 GLU cc_start: 0.7565 (tp30) cc_final: 0.7282 (tp30) REVERT: H 80 THR cc_start: 0.7157 (t) cc_final: 0.6681 (t) REVERT: H 107 THR cc_start: 0.9490 (m) cc_final: 0.9054 (p) REVERT: H 120 MET cc_start: 0.8066 (mtt) cc_final: 0.7551 (mmm) REVERT: H 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8608 (m-30) REVERT: H 124 ILE cc_start: 0.9037 (tt) cc_final: 0.8692 (tt) REVERT: I 37 LEU cc_start: 0.9395 (mt) cc_final: 0.9051 (mt) REVERT: I 43 VAL cc_start: 0.9448 (t) cc_final: 0.9101 (p) REVERT: I 52 GLU cc_start: 0.7848 (pm20) cc_final: 0.7642 (pm20) REVERT: I 65 VAL cc_start: 0.9097 (t) cc_final: 0.8751 (p) REVERT: J 36 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8708 (mttp) REVERT: J 39 TYR cc_start: 0.8526 (m-80) cc_final: 0.8274 (m-80) REVERT: J 56 GLU cc_start: 0.8502 (tt0) cc_final: 0.8234 (tt0) REVERT: J 64 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8368 (tp30) REVERT: J 68 ASN cc_start: 0.8084 (m-40) cc_final: 0.7697 (m-40) REVERT: J 94 ASN cc_start: 0.8630 (t0) cc_final: 0.8096 (m-40) REVERT: J 95 LYS cc_start: 0.9123 (tttt) cc_final: 0.8703 (ttpt) REVERT: J 99 ARG cc_start: 0.7958 (mpt180) cc_final: 0.7556 (mmt180) REVERT: K 49 THR cc_start: 0.7796 (m) cc_final: 0.7316 (p) REVERT: K 90 GLU cc_start: 0.9444 (mp0) cc_final: 0.9015 (mp0) REVERT: K 103 LEU cc_start: 0.8443 (mm) cc_final: 0.8179 (mm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1374 time to fit residues: 53.7137 Evaluate side-chains 207 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS F 38 ASN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.068394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054115 restraints weight = 90345.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055481 restraints weight = 50676.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.056397 restraints weight = 34290.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057040 restraints weight = 26450.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.057408 restraints weight = 22291.478| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.225 16904 Z= 0.150 Angle : 0.662 26.545 24155 Z= 0.360 Chirality : 0.041 0.208 2706 Planarity : 0.004 0.051 1989 Dihedral : 29.584 89.605 4740 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1155 helix: 1.44 (0.20), residues: 693 sheet: -0.64 (1.67), residues: 10 loop : -1.31 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 92 TYR 0.014 0.001 TYR J 39 PHE 0.012 0.001 PHE G 67 TRP 0.018 0.002 TRP C 617 HIS 0.011 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (16876) covalent geometry : angle 0.61921 / 0.36 (24119) hydrogen bonds : bond 0.04436 / 2.85 ( 900) hydrogen bonds : angle 3.51282 / 2.40 ( 2290) metal coordination : bond 0.04291 / 2.15 ( 28) metal coordination : angle 6.06879 / 3.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.3083 (ptm) cc_final: 0.2443 (tmm) REVERT: A 473 GLU cc_start: 0.9510 (pt0) cc_final: 0.9258 (mm-30) REVERT: A 537 ASN cc_start: 0.8586 (t0) cc_final: 0.8084 (t0) REVERT: A 687 LEU cc_start: 0.8956 (tp) cc_final: 0.8380 (tp) REVERT: A 696 THR cc_start: 0.7862 (m) cc_final: 0.7609 (p) REVERT: C 590 GLU cc_start: 0.8980 (pm20) cc_final: 0.8594 (tp30) REVERT: C 603 PHE cc_start: 0.5603 (m-80) cc_final: 0.5059 (m-80) REVERT: C 614 MET cc_start: 0.6085 (mtm) cc_final: 0.5571 (mtp) REVERT: C 637 MET cc_start: 0.8356 (mmt) cc_final: 0.8091 (ppp) REVERT: C 646 LYS cc_start: 0.9317 (mmpt) cc_final: 0.8821 (tttm) REVERT: D 90 MET cc_start: 0.8519 (mmp) cc_final: 0.8206 (mmm) REVERT: D 97 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7816 (mt-10) REVERT: D 99 TYR cc_start: 0.9054 (t80) cc_final: 0.8272 (t80) REVERT: E 79 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8139 (mmtm) REVERT: E 88 TYR cc_start: 0.8377 (m-10) cc_final: 0.7750 (m-10) REVERT: F 57 TYR cc_start: 0.9064 (t80) cc_final: 0.8433 (t80) REVERT: F 61 GLU cc_start: 0.9057 (tp30) cc_final: 0.8533 (tp30) REVERT: F 90 ASP cc_start: 0.8792 (t0) cc_final: 0.8359 (t70) REVERT: G 40 LYS cc_start: 0.9315 (mttt) cc_final: 0.8999 (mmtp) REVERT: G 64 ASN cc_start: 0.9091 (m-40) cc_final: 0.8747 (t0) REVERT: G 83 ARG cc_start: 0.8231 (mtt-85) cc_final: 0.7864 (mmm-85) REVERT: G 99 LEU cc_start: 0.8386 (mt) cc_final: 0.8126 (mp) REVERT: G 102 GLU cc_start: 0.7786 (tp30) cc_final: 0.7454 (tp30) REVERT: H 80 THR cc_start: 0.7172 (t) cc_final: 0.6735 (t) REVERT: H 107 THR cc_start: 0.9472 (m) cc_final: 0.8998 (p) REVERT: H 120 MET cc_start: 0.8064 (mtt) cc_final: 0.7491 (mmm) REVERT: H 123 ASP cc_start: 0.8845 (m-30) cc_final: 0.8611 (m-30) REVERT: H 124 ILE cc_start: 0.9038 (tt) cc_final: 0.8693 (tt) REVERT: I 43 VAL cc_start: 0.9446 (t) cc_final: 0.9045 (p) REVERT: I 64 ASN cc_start: 0.8487 (m-40) cc_final: 0.8056 (m-40) REVERT: I 68 ASP cc_start: 0.8563 (m-30) cc_final: 0.8245 (m-30) REVERT: J 39 TYR cc_start: 0.8565 (m-80) cc_final: 0.8278 (m-80) REVERT: J 56 GLU cc_start: 0.8490 (tt0) cc_final: 0.8252 (tt0) REVERT: J 64 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8414 (tm-30) REVERT: J 68 ASN cc_start: 0.8137 (m-40) cc_final: 0.7762 (m-40) REVERT: J 94 ASN cc_start: 0.8583 (t0) cc_final: 0.8108 (m-40) REVERT: J 95 LYS cc_start: 0.9168 (tttt) cc_final: 0.8754 (tmmt) REVERT: J 99 ARG cc_start: 0.8001 (mpt180) cc_final: 0.7603 (mmt180) REVERT: K 49 THR cc_start: 0.7794 (m) cc_final: 0.7258 (p) REVERT: K 70 ILE cc_start: 0.9658 (mm) cc_final: 0.9458 (mm) REVERT: K 90 GLU cc_start: 0.9526 (mp0) cc_final: 0.9055 (mp0) REVERT: K 103 LEU cc_start: 0.8425 (mm) cc_final: 0.8025 (mm) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1464 time to fit residues: 55.8779 Evaluate side-chains 204 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 71 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 111 optimal weight: 0.0040 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS D 68 GLN E 93 GLN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053579 restraints weight = 91859.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054955 restraints weight = 51723.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055876 restraints weight = 35134.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056464 restraints weight = 27162.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056891 restraints weight = 23022.521| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.245 16904 Z= 0.162 Angle : 0.699 35.283 24155 Z= 0.370 Chirality : 0.041 0.199 2706 Planarity : 0.004 0.054 1989 Dihedral : 29.609 89.945 4740 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1155 helix: 1.44 (0.20), residues: 693 sheet: -0.57 (1.65), residues: 10 loop : -1.29 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 81 TYR 0.030 0.001 TYR E 98 PHE 0.015 0.001 PHE A 295 TRP 0.020 0.003 TRP C 591 HIS 0.009 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (16876) covalent geometry : angle 0.63764 / 0.36 (24119) hydrogen bonds : bond 0.04458 / 2.87 ( 900) hydrogen bonds : angle 3.53964 / 2.41 ( 2290) metal coordination : bond 0.04658 / 2.34 ( 28) metal coordination : angle 7.42745 / 4.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.2988 (ptm) cc_final: 0.2358 (tmm) REVERT: A 473 GLU cc_start: 0.9492 (pt0) cc_final: 0.9227 (mm-30) REVERT: A 537 ASN cc_start: 0.8563 (t0) cc_final: 0.8055 (t0) REVERT: A 687 LEU cc_start: 0.8977 (tp) cc_final: 0.8414 (tp) REVERT: C 590 GLU cc_start: 0.9011 (pm20) cc_final: 0.8657 (mm-30) REVERT: C 603 PHE cc_start: 0.5664 (m-80) cc_final: 0.5194 (m-80) REVERT: C 614 MET cc_start: 0.5923 (mtm) cc_final: 0.5657 (mtp) REVERT: C 616 LEU cc_start: 0.8487 (mt) cc_final: 0.8284 (mt) REVERT: C 637 MET cc_start: 0.8361 (mmt) cc_final: 0.8124 (ppp) REVERT: C 646 LYS cc_start: 0.9309 (mmpt) cc_final: 0.8800 (tttm) REVERT: C 683 GLU cc_start: 0.7324 (mp0) cc_final: 0.7026 (pm20) REVERT: D 99 TYR cc_start: 0.9128 (t80) cc_final: 0.8344 (t80) REVERT: E 79 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8107 (mmtm) REVERT: E 88 TYR cc_start: 0.8448 (m-10) cc_final: 0.7754 (m-10) REVERT: F 57 TYR cc_start: 0.9025 (t80) cc_final: 0.8422 (t80) REVERT: F 61 GLU cc_start: 0.9031 (tp30) cc_final: 0.8546 (tp30) REVERT: G 40 LYS cc_start: 0.9310 (mttt) cc_final: 0.8997 (mmtp) REVERT: G 64 ASN cc_start: 0.9039 (m-40) cc_final: 0.8756 (t0) REVERT: G 83 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7829 (mtt-85) REVERT: G 99 LEU cc_start: 0.8442 (mt) cc_final: 0.8085 (mp) REVERT: G 105 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8865 (mtmm) REVERT: H 80 THR cc_start: 0.6972 (t) cc_final: 0.6337 (t) REVERT: H 107 THR cc_start: 0.9479 (m) cc_final: 0.9010 (p) REVERT: H 123 ASP cc_start: 0.8696 (m-30) cc_final: 0.8410 (m-30) REVERT: H 124 ILE cc_start: 0.9079 (tt) cc_final: 0.8711 (tt) REVERT: I 43 VAL cc_start: 0.9450 (t) cc_final: 0.9090 (p) REVERT: I 64 ASN cc_start: 0.8525 (m-40) cc_final: 0.8057 (m-40) REVERT: I 68 ASP cc_start: 0.8574 (m-30) cc_final: 0.8251 (m-30) REVERT: J 39 TYR cc_start: 0.8597 (m-80) cc_final: 0.8298 (m-80) REVERT: J 56 GLU cc_start: 0.8484 (tt0) cc_final: 0.8264 (tt0) REVERT: J 64 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8504 (tm-30) REVERT: J 68 ASN cc_start: 0.8217 (m-40) cc_final: 0.7833 (m-40) REVERT: J 94 ASN cc_start: 0.8654 (t0) cc_final: 0.8114 (m-40) REVERT: J 95 LYS cc_start: 0.9204 (tttt) cc_final: 0.8748 (tmmt) REVERT: J 99 ARG cc_start: 0.8044 (mpt180) cc_final: 0.7636 (mmt180) REVERT: K 49 THR cc_start: 0.7718 (m) cc_final: 0.7234 (p) REVERT: K 90 GLU cc_start: 0.9467 (mp0) cc_final: 0.9118 (mp0) REVERT: K 103 LEU cc_start: 0.8475 (mm) cc_final: 0.8066 (mm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1420 time to fit residues: 52.1916 Evaluate side-chains 200 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053923 restraints weight = 91252.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055289 restraints weight = 51213.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056193 restraints weight = 34733.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056819 restraints weight = 26836.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057171 restraints weight = 22672.261| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.257 16904 Z= 0.151 Angle : 0.680 31.967 24155 Z= 0.365 Chirality : 0.041 0.186 2706 Planarity : 0.004 0.054 1989 Dihedral : 29.608 89.626 4740 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1155 helix: 1.44 (0.20), residues: 693 sheet: -1.61 (1.59), residues: 12 loop : -1.18 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 35 TYR 0.027 0.001 TYR E 98 PHE 0.028 0.001 PHE H 104 TRP 0.017 0.002 TRP C 617 HIS 0.010 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (16876) covalent geometry : angle 0.63189 / 0.36 (24119) hydrogen bonds : bond 0.04313 / 2.78 ( 900) hydrogen bonds : angle 3.55186 / 2.47 ( 2290) metal coordination : bond 0.04912 / 2.48 ( 28) metal coordination : angle 6.55824 / 4.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.2359 (ptm) cc_final: 0.1757 (tmm) REVERT: A 473 GLU cc_start: 0.9488 (pt0) cc_final: 0.9219 (mm-30) REVERT: A 537 ASN cc_start: 0.8544 (t0) cc_final: 0.8031 (t0) REVERT: A 687 LEU cc_start: 0.9008 (tp) cc_final: 0.8442 (tp) REVERT: C 590 GLU cc_start: 0.8981 (pm20) cc_final: 0.8663 (mm-30) REVERT: C 603 PHE cc_start: 0.5387 (m-80) cc_final: 0.5129 (m-80) REVERT: C 614 MET cc_start: 0.6057 (mtm) cc_final: 0.5481 (mtp) REVERT: C 616 LEU cc_start: 0.8476 (mt) cc_final: 0.8267 (mt) REVERT: C 646 LYS cc_start: 0.9283 (mmpt) cc_final: 0.8779 (tttm) REVERT: D 90 MET cc_start: 0.8358 (mmp) cc_final: 0.8036 (mmp) REVERT: D 94 GLU cc_start: 0.8556 (pm20) cc_final: 0.8343 (pm20) REVERT: D 99 TYR cc_start: 0.9045 (t80) cc_final: 0.8316 (t80) REVERT: E 79 LYS cc_start: 0.8570 (mtpp) cc_final: 0.8097 (mmtm) REVERT: E 88 TYR cc_start: 0.8335 (m-10) cc_final: 0.7821 (m-10) REVERT: F 56 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8569 (mm-30) REVERT: F 57 TYR cc_start: 0.8845 (t80) cc_final: 0.8382 (t80) REVERT: F 61 GLU cc_start: 0.8997 (tp30) cc_final: 0.8500 (tp30) REVERT: F 97 LEU cc_start: 0.9256 (mp) cc_final: 0.9046 (mp) REVERT: G 40 LYS cc_start: 0.9306 (mttt) cc_final: 0.8952 (mmtp) REVERT: G 64 ASN cc_start: 0.9063 (m-40) cc_final: 0.8740 (t0) REVERT: G 99 LEU cc_start: 0.8397 (mt) cc_final: 0.8063 (mp) REVERT: H 80 THR cc_start: 0.6983 (t) cc_final: 0.6337 (t) REVERT: H 90 MET cc_start: 0.8808 (mmp) cc_final: 0.8550 (ptp) REVERT: H 107 THR cc_start: 0.9460 (m) cc_final: 0.9096 (p) REVERT: H 123 ASP cc_start: 0.8635 (m-30) cc_final: 0.8355 (m-30) REVERT: H 124 ILE cc_start: 0.9053 (tt) cc_final: 0.8694 (tt) REVERT: I 43 VAL cc_start: 0.9437 (t) cc_final: 0.9037 (p) REVERT: I 64 ASN cc_start: 0.8463 (m-40) cc_final: 0.8078 (m-40) REVERT: I 68 ASP cc_start: 0.8439 (m-30) cc_final: 0.8198 (m-30) REVERT: J 39 TYR cc_start: 0.8605 (m-80) cc_final: 0.8301 (m-80) REVERT: J 56 GLU cc_start: 0.8444 (tt0) cc_final: 0.8217 (tt0) REVERT: J 64 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8574 (tm-30) REVERT: J 68 ASN cc_start: 0.8267 (m-40) cc_final: 0.7877 (m-40) REVERT: J 90 ASP cc_start: 0.8688 (t70) cc_final: 0.8375 (t70) REVERT: J 94 ASN cc_start: 0.8619 (t0) cc_final: 0.8163 (m-40) REVERT: J 95 LYS cc_start: 0.9194 (tttt) cc_final: 0.8749 (tmmt) REVERT: J 99 ARG cc_start: 0.7972 (mpt180) cc_final: 0.7589 (mmt180) REVERT: K 49 THR cc_start: 0.7740 (m) cc_final: 0.7213 (p) REVERT: K 70 ILE cc_start: 0.9671 (mm) cc_final: 0.9465 (mm) REVERT: K 90 GLU cc_start: 0.9543 (mp0) cc_final: 0.9054 (mp0) REVERT: K 103 LEU cc_start: 0.8415 (mm) cc_final: 0.8174 (mm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1423 time to fit residues: 52.2896 Evaluate side-chains 203 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.066406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.052276 restraints weight = 92293.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053567 restraints weight = 53509.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054435 restraints weight = 37028.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055001 restraints weight = 28957.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055384 restraints weight = 24645.582| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 16904 Z= 0.199 Angle : 0.737 36.040 24155 Z= 0.389 Chirality : 0.042 0.188 2706 Planarity : 0.005 0.054 1989 Dihedral : 29.688 89.143 4740 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1155 helix: 1.29 (0.20), residues: 698 sheet: -0.38 (1.06), residues: 28 loop : -1.31 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 92 TYR 0.026 0.002 TYR E 98 PHE 0.026 0.002 PHE A 295 TRP 0.019 0.003 TRP C 591 HIS 0.009 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.20 (16876) covalent geometry : angle 0.68158 / 0.38 (24119) hydrogen bonds : bond 0.05059 / 3.26 ( 900) hydrogen bonds : angle 3.73998 / 2.58 ( 2290) metal coordination : bond 0.04477 / 2.26 ( 28) metal coordination : angle 7.31798 / 4.46 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.2591 (ptm) cc_final: 0.1838 (tmm) REVERT: A 473 GLU cc_start: 0.9504 (pt0) cc_final: 0.9230 (mm-30) REVERT: A 537 ASN cc_start: 0.8825 (t0) cc_final: 0.8372 (t0) REVERT: A 687 LEU cc_start: 0.8876 (tp) cc_final: 0.8343 (tp) REVERT: C 590 GLU cc_start: 0.8958 (pm20) cc_final: 0.8550 (mm-30) REVERT: C 603 PHE cc_start: 0.5584 (m-80) cc_final: 0.5209 (m-80) REVERT: C 614 MET cc_start: 0.6713 (mtm) cc_final: 0.6102 (mtp) REVERT: C 634 HIS cc_start: 0.8610 (m90) cc_final: 0.8341 (m90) REVERT: C 646 LYS cc_start: 0.9308 (mmpt) cc_final: 0.8750 (ttmt) REVERT: D 93 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8866 (tm-30) REVERT: D 99 TYR cc_start: 0.9122 (t80) cc_final: 0.8423 (t80) REVERT: E 79 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8108 (mmtm) REVERT: E 88 TYR cc_start: 0.8438 (m-10) cc_final: 0.7656 (m-10) REVERT: E 98 TYR cc_start: 0.8936 (m-80) cc_final: 0.8226 (m-80) REVERT: F 61 GLU cc_start: 0.9049 (tp30) cc_final: 0.8520 (tp30) REVERT: F 97 LEU cc_start: 0.9339 (mp) cc_final: 0.9128 (mp) REVERT: G 40 LYS cc_start: 0.9326 (mttt) cc_final: 0.8972 (mmtp) REVERT: G 64 ASN cc_start: 0.9142 (m-40) cc_final: 0.8774 (t0) REVERT: G 99 LEU cc_start: 0.8367 (mt) cc_final: 0.8127 (mp) REVERT: H 107 THR cc_start: 0.9445 (m) cc_final: 0.9041 (t) REVERT: H 123 ASP cc_start: 0.8766 (m-30) cc_final: 0.8535 (m-30) REVERT: H 124 ILE cc_start: 0.9156 (tt) cc_final: 0.8744 (tt) REVERT: I 43 VAL cc_start: 0.9359 (t) cc_final: 0.8982 (p) REVERT: J 56 GLU cc_start: 0.8483 (tt0) cc_final: 0.8268 (tt0) REVERT: J 64 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8656 (tm-30) REVERT: J 68 ASN cc_start: 0.8395 (m-40) cc_final: 0.7946 (m-40) REVERT: J 94 ASN cc_start: 0.8700 (t0) cc_final: 0.8189 (m-40) REVERT: J 95 LYS cc_start: 0.9236 (tttt) cc_final: 0.8796 (ttpt) REVERT: J 99 ARG cc_start: 0.8099 (mpt180) cc_final: 0.7631 (mmt180) REVERT: K 49 THR cc_start: 0.7660 (m) cc_final: 0.7185 (p) REVERT: K 61 SER cc_start: 0.9614 (m) cc_final: 0.9336 (m) REVERT: K 65 ASP cc_start: 0.8717 (t70) cc_final: 0.8499 (t0) REVERT: K 90 GLU cc_start: 0.9441 (mp0) cc_final: 0.9005 (mp0) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1363 time to fit residues: 49.9929 Evaluate side-chains 202 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS E 93 GLN H 68 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.066882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053067 restraints weight = 91424.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054251 restraints weight = 55231.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055050 restraints weight = 39164.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055520 restraints weight = 31124.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.055886 restraints weight = 27040.636| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 16904 Z= 0.161 Angle : 0.698 32.987 24155 Z= 0.373 Chirality : 0.041 0.186 2706 Planarity : 0.004 0.053 1989 Dihedral : 29.676 89.672 4740 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1155 helix: 1.38 (0.20), residues: 698 sheet: -1.72 (1.53), residues: 12 loop : -1.22 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 35 TYR 0.026 0.001 TYR E 98 PHE 0.016 0.001 PHE A 295 TRP 0.028 0.003 TRP C 617 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (16876) covalent geometry : angle 0.64822 / 0.37 (24119) hydrogen bonds : bond 0.04446 / 2.87 ( 900) hydrogen bonds : angle 3.60910 / 2.50 ( 2290) metal coordination : bond 0.04443 / 2.23 ( 28) metal coordination : angle 6.71352 / 4.18 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2875.32 seconds wall clock time: 50 minutes 21.01 seconds (3021.01 seconds total)