Starting phenix.real_space_refine on Fri Aug 7 22:44:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3u_47496/08_2026/9e3u_47496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3u_47496/08_2026/9e3u_47496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3u_47496/08_2026/9e3u_47496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3u_47496/08_2026/9e3u_47496.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3u_47496/08_2026/9e3u_47496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3u_47496/08_2026/9e3u_47496.cif" } resolution = 4.9 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= 0.010 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 9 6.06 5 P 330 5.49 5 S 116 5.16 5 C 13969 2.51 5 N 4349 2.21 5 O 4998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23771 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "L" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3398 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3367 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "V" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2793 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 3 Chain: "Z" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1478 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 4 Chain: "U" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "Y" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12794 SG CYS V 415 31.463 66.816 138.563 1.00999.99 S ATOM 12814 SG CYS V 418 35.095 67.616 137.169 1.00999.99 S ATOM 12944 SG CYS V 435 35.069 66.892 140.707 1.00999.99 S ATOM 12966 SG CYS V 438 33.731 69.825 139.744 1.00999.99 S ATOM 13148 SG CYS V 458 25.135 78.579 139.823 1.00999.99 S ATOM 13168 SG CYS V 461 27.662 76.788 137.037 1.00999.99 S ATOM 13310 SG CYS V 480 25.554 79.264 135.929 1.00999.99 S ATOM 13332 SG CYS V 483 24.528 76.014 136.544 1.00999.99 S ATOM 13237 SG CYS V 470 15.434 84.658 145.974 1.00999.99 S ATOM 13270 SG CYS V 475 17.652 82.489 148.614 1.00967.66 S ATOM 13485 SG CYS V 504 16.190 80.918 145.883 1.00984.89 S ATOM 13511 SG CYS V 507 14.129 81.711 148.569 1.00981.96 S ATOM 17069 SG CYS U 494 64.232 110.167 156.068 1.00795.71 S ATOM 17089 SG CYS U 497 60.555 110.120 154.255 1.00862.15 S ATOM 17211 SG CYS U 514 61.098 107.970 157.479 1.00852.40 S ATOM 17234 SG CYS U 517 62.294 107.141 154.749 1.00888.10 S ATOM 17402 SG CYS U 537 68.963 105.971 145.777 1.00964.65 S ATOM 17423 SG CYS U 540 65.335 107.141 147.220 1.00939.52 S ATOM 17560 SG CYS U 559 66.978 108.496 144.003 1.00853.47 S ATOM 17582 SG CYS U 562 67.664 109.848 146.790 1.00782.87 S ATOM 17486 SG CYS U 549 80.325 102.528 141.482 1.00920.09 S ATOM 17520 SG CYS U 554 80.010 100.301 144.299 1.00854.55 S ATOM 17733 SG CYS U 583 79.387 104.089 144.653 1.00866.46 S ATOM 17759 SG CYS U 586 82.701 102.384 145.094 1.00862.36 S ATOM 20473 SG CYS Y 494 76.077 25.554 106.318 1.00619.87 S ATOM 20493 SG CYS Y 497 74.050 27.796 103.241 1.00659.34 S ATOM 20615 SG CYS Y 514 77.714 28.224 103.957 1.00617.10 S ATOM 20638 SG CYS Y 517 75.416 29.522 105.503 1.00620.56 S ATOM 20806 SG CYS Y 537 68.419 30.353 114.241 1.00730.33 S ATOM 20827 SG CYS Y 540 68.458 30.668 110.382 1.00713.74 S ATOM 20964 SG CYS Y 559 65.192 29.810 112.182 1.00725.86 S ATOM 20986 SG CYS Y 562 67.728 27.374 111.511 1.00701.19 S ATOM 20890 SG CYS Y 549 66.897 30.914 127.154 1.00703.29 S ATOM 20924 SG CYS Y 554 70.109 32.264 127.104 1.00612.90 S ATOM 21137 SG CYS Y 583 69.333 28.412 125.957 1.00682.05 S ATOM 21163 SG CYS Y 586 70.245 28.835 129.055 1.00649.03 S Time building chain proxies: 4.84, per 1000 atoms: 0.20 Number of scatterers: 23771 At special positions: 0 Unit cell: (133.4, 150.88, 205.16, 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 9 29.99 S 116 16.00 P 330 15.00 O 4998 8.00 N 4349 7.00 C 13969 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: 1.51 Conformation dependent library (CDL) restraints added in 880.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U1001 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 517 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 494 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 514 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 497 " pdb=" ZN U1002 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 537 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 562 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 540 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 559 " pdb=" ZN U1003 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 554 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 583 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 549 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 586 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 435 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 418 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 415 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 438 " pdb=" ZN V1002 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 458 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 483 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 461 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 480 " pdb=" ZN V1003 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 504 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 475 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 470 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 507 " pdb=" ZN Y1001 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 494 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 497 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 514 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 517 " pdb=" ZN Y1002 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 562 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 537 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 540 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 559 " pdb=" ZN Y1003 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 583 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 549 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 554 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 586 " Number of angles added : 54 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 21 sheets defined 50.2% alpha, 7.2% beta 163 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.629A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.727A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.030A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.610A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.633A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.624A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.641A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.328A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.557A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.538A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.616A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.815A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.565A pdb=" N ILE E 74 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.721A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.632A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.887A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.627A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.510A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.695A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.551A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.621A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.508A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.579A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 741 through 746 removed outlier: 3.733A pdb=" N LYS L 745 " --> pdb=" O GLY L 741 " (cutoff:3.500A) Processing helix chain 'V' and resid 396 through 407 removed outlier: 3.928A pdb=" N ALA V 405 " --> pdb=" O ALA V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 445 Processing helix chain 'V' and resid 481 through 487 Processing helix chain 'V' and resid 491 through 499 removed outlier: 4.027A pdb=" N LEU V 498 " --> pdb=" O ALA V 494 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 532 Processing helix chain 'V' and resid 565 through 575 Processing helix chain 'V' and resid 589 through 598 removed outlier: 3.782A pdb=" N VAL V 593 " --> pdb=" O GLU V 589 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL V 596 " --> pdb=" O ALA V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 613 through 620 removed outlier: 3.811A pdb=" N GLU V 617 " --> pdb=" O LYS V 613 " (cutoff:3.500A) Processing helix chain 'V' and resid 650 through 663 removed outlier: 3.525A pdb=" N GLU V 654 " --> pdb=" O ARG V 650 " (cutoff:3.500A) Processing helix chain 'V' and resid 683 through 695 Processing helix chain 'V' and resid 751 through 760 removed outlier: 4.424A pdb=" N VAL V 755 " --> pdb=" O TRP V 751 " (cutoff:3.500A) Processing helix chain 'V' and resid 760 through 766 removed outlier: 3.889A pdb=" N LYS V 764 " --> pdb=" O PHE V 760 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP V 765 " --> pdb=" O ALA V 761 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR V 766 " --> pdb=" O PRO V 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 760 through 766' Processing helix chain 'Z' and resid 565 through 574 Processing helix chain 'Z' and resid 587 through 598 removed outlier: 3.703A pdb=" N ILE Z 591 " --> pdb=" O CYS Z 587 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS Z 598 " --> pdb=" O GLY Z 594 " (cutoff:3.500A) Processing helix chain 'Z' and resid 612 through 620 Processing helix chain 'Z' and resid 645 through 663 Processing helix chain 'Z' and resid 683 through 695 Processing helix chain 'Z' and resid 741 through 746 removed outlier: 3.990A pdb=" N LYS Z 745 " --> pdb=" O GLY Z 741 " (cutoff:3.500A) Processing helix chain 'Z' and resid 753 through 760 removed outlier: 3.502A pdb=" N LEU Z 759 " --> pdb=" O VAL Z 755 " (cutoff:3.500A) Processing helix chain 'Z' and resid 760 through 767 Processing helix chain 'U' and resid 477 through 485 Processing helix chain 'U' and resid 489 through 493 removed outlier: 3.521A pdb=" N ILE U 493 " --> pdb=" O ILE U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 514 through 525 Processing helix chain 'U' and resid 560 through 567 Processing helix chain 'U' and resid 570 through 578 Processing helix chain 'U' and resid 600 through 611 removed outlier: 3.628A pdb=" N PHE U 609 " --> pdb=" O LEU U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 631 removed outlier: 3.571A pdb=" N ARG U 631 " --> pdb=" O ALA U 628 " (cutoff:3.500A) Processing helix chain 'U' and resid 644 through 654 removed outlier: 3.545A pdb=" N LEU U 648 " --> pdb=" O ALA U 644 " (cutoff:3.500A) Processing helix chain 'U' and resid 666 through 677 Processing helix chain 'U' and resid 691 through 698 Processing helix chain 'U' and resid 729 through 742 Processing helix chain 'U' and resid 762 through 774 Processing helix chain 'U' and resid 814 through 819 removed outlier: 3.662A pdb=" N CYS U 818 " --> pdb=" O GLU U 814 " (cutoff:3.500A) Processing helix chain 'U' and resid 860 through 868 Processing helix chain 'U' and resid 881 through 892 Processing helix chain 'U' and resid 894 through 903 Processing helix chain 'U' and resid 904 through 908 removed outlier: 3.514A pdb=" N GLU U 907 " --> pdb=" O PRO U 904 " (cutoff:3.500A) Processing helix chain 'Y' and resid 477 through 484 Processing helix chain 'Y' and resid 489 through 493 removed outlier: 3.610A pdb=" N ILE Y 493 " --> pdb=" O ILE Y 490 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 525 Processing helix chain 'Y' and resid 560 through 566 Processing helix chain 'Y' and resid 571 through 578 Processing helix chain 'Y' and resid 600 through 611 removed outlier: 3.725A pdb=" N GLN Y 606 " --> pdb=" O PRO Y 602 " (cutoff:3.500A) Processing helix chain 'Y' and resid 644 through 654 removed outlier: 3.691A pdb=" N LEU Y 648 " --> pdb=" O ALA Y 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 666 through 677 Processing helix chain 'Y' and resid 691 through 698 Processing helix chain 'Y' and resid 729 through 742 removed outlier: 3.870A pdb=" N GLU Y 733 " --> pdb=" O ARG Y 729 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Y' and resid 814 through 819 removed outlier: 3.752A pdb=" N CYS Y 818 " --> pdb=" O GLU Y 814 " (cutoff:3.500A) Processing helix chain 'Y' and resid 860 through 869 Processing helix chain 'Y' and resid 881 through 892 Processing helix chain 'Y' and resid 894 through 903 Processing helix chain 'Y' and resid 904 through 908 removed outlier: 3.778A pdb=" N GLU Y 907 " --> pdb=" O PRO Y 904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.177A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.266A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.821A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.662A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'V' and resid 467 through 469 removed outlier: 3.672A pdb=" N PHE V 479 " --> pdb=" O LEU V 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 512 through 513 Processing sheet with id=AB1, first strand: chain 'V' and resid 578 through 584 removed outlier: 5.627A pdb=" N ILE V 555 " --> pdb=" O VAL V 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS V 580 " --> pdb=" O ILE V 555 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER V 584 " --> pdb=" O SER V 559 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL V 625 " --> pdb=" O MET V 675 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU V 677 " --> pdb=" O VAL V 625 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY V 627 " --> pdb=" O GLU V 677 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL V 679 " --> pdb=" O GLY V 627 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG V 713 " --> pdb=" O ILE V 701 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE V 701 " --> pdb=" O ARG V 713 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 603 through 605 removed outlier: 8.965A pdb=" N LYS Z 603 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR Z 581 " --> pdb=" O LYS Z 603 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL Z 605 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 605 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE Z 555 " --> pdb=" O VAL Z 578 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS Z 580 " --> pdb=" O ILE Z 555 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Z 557 " --> pdb=" O LYS Z 580 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL Z 582 " --> pdb=" O VAL Z 557 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL Z 625 " --> pdb=" O MET Z 675 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N GLU Z 677 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY Z 627 " --> pdb=" O GLU Z 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 504 through 505 Processing sheet with id=AB4, first strand: chain 'U' and resid 546 through 548 Processing sheet with id=AB5, first strand: chain 'U' and resid 591 through 592 Processing sheet with id=AB6, first strand: chain 'U' and resid 682 through 684 removed outlier: 9.008A pdb=" N MET U 682 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR U 660 " --> pdb=" O MET U 682 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL U 684 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA U 662 " --> pdb=" O VAL U 684 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE U 634 " --> pdb=" O VAL U 657 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG U 659 " --> pdb=" O ILE U 634 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY U 707 " --> pdb=" O LEU U 639 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL U 704 " --> pdb=" O LEU U 754 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N GLU U 756 " --> pdb=" O VAL U 704 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLY U 706 " --> pdb=" O GLU U 756 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N VAL U 758 " --> pdb=" O GLY U 706 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 823 through 825 removed outlier: 4.335A pdb=" N VAL U 850 " --> pdb=" O ASP U 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 504 through 505 Processing sheet with id=AB9, first strand: chain 'Y' and resid 546 through 548 Processing sheet with id=AC1, first strand: chain 'Y' and resid 591 through 592 Processing sheet with id=AC2, first strand: chain 'Y' and resid 682 through 684 removed outlier: 7.747A pdb=" N ILE Y 634 " --> pdb=" O ASP Y 658 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR Y 660 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL Y 636 " --> pdb=" O TYR Y 660 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA Y 662 " --> pdb=" O VAL Y 636 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER Y 638 " --> pdb=" O ALA Y 662 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY Y 707 " --> pdb=" O LEU Y 639 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL Y 704 " --> pdb=" O LEU Y 754 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLU Y 756 " --> pdb=" O VAL Y 704 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY Y 706 " --> pdb=" O GLU Y 756 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N VAL Y 758 " --> pdb=" O GLY Y 706 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 824 through 825 removed outlier: 3.958A pdb=" N VAL Y 850 " --> pdb=" O ASP Y 857 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 424 hydrogen bonds 848 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 6.01 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3928 1.33 - 1.45: 7902 1.45 - 1.57: 12285 1.57 - 1.69: 658 1.69 - 1.82: 162 Bond restraints: 24935 Sorted by residual: bond pdb=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta sigma weight residual 1.453 1.487 -0.033 8.30e-03 1.45e+04 1.63e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.60e+01 bond pdb=" N ASP U 579 " pdb=" CA ASP U 579 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.51e+01 bond pdb=" N VAL U 785 " pdb=" CA VAL U 785 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.38e+01 bond pdb=" N ILE U 493 " pdb=" CA ILE U 493 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 ... (remaining 24930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 25938 1.51 - 3.02: 7530 3.02 - 4.53: 1515 4.53 - 6.04: 110 6.04 - 7.55: 2 Bond angle restraints: 35095 Sorted by residual: angle pdb=" C SER V 752 " pdb=" N VAL V 753 " pdb=" CA VAL V 753 " ideal model delta sigma weight residual 120.33 125.15 -4.82 8.00e-01 1.56e+00 3.63e+01 angle pdb=" C SER Z 752 " pdb=" N VAL Z 753 " pdb=" CA VAL Z 753 " ideal model delta sigma weight residual 120.33 124.67 -4.34 8.00e-01 1.56e+00 2.95e+01 angle pdb=" O5' DA I 10 " pdb=" C5' DA I 10 " pdb=" C4' DA I 10 " ideal model delta sigma weight residual 109.40 113.20 -3.80 8.00e-01 1.56e+00 2.26e+01 angle pdb=" C VAL C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 119.98 125.16 -5.18 1.11e+00 8.12e-01 2.18e+01 angle pdb=" C THR U 645 " pdb=" N GLY U 646 " pdb=" CA GLY U 646 " ideal model delta sigma weight residual 119.98 125.00 -5.02 1.11e+00 8.12e-01 2.04e+01 ... (remaining 35090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 12616 35.99 - 71.99: 1394 71.99 - 107.98: 19 107.98 - 143.98: 0 143.98 - 179.97: 2 Dihedral angle restraints: 14031 sinusoidal: 7917 harmonic: 6114 Sorted by residual: dihedral pdb=" CA ASN V 422 " pdb=" C ASN V 422 " pdb=" N PRO V 423 " pdb=" CA PRO V 423 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLU U 523 " pdb=" C GLU U 523 " pdb=" N CYS U 524 " pdb=" CA CYS U 524 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C4' DG J 180 " pdb=" C3' DG J 180 " pdb=" O3' DG J 180 " pdb=" P DC J 181 " ideal model delta sinusoidal sigma weight residual -140.00 39.97 -179.97 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 14028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2185 0.066 - 0.131: 1420 0.131 - 0.197: 244 0.197 - 0.262: 3 0.262 - 0.327: 2 Chirality restraints: 3854 Sorted by residual: chirality pdb=" C3' DG J 180 " pdb=" C4' DG J 180 " pdb=" O3' DG J 180 " pdb=" C2' DG J 180 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C3' DG I 3 " pdb=" C4' DG I 3 " pdb=" O3' DG I 3 " pdb=" C2' DG I 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3851 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 182 " -0.021 2.00e-02 2.50e+03 1.21e-02 3.31e+00 pdb=" N1 DC J 182 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DC J 182 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC J 182 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC J 182 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 182 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 182 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J 182 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 182 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 37 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C GLY C 37 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY C 37 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN C 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 35 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ARG C 35 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG C 35 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS C 36 " -0.011 2.00e-02 2.50e+03 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 492 2.67 - 3.23: 18856 3.23 - 3.78: 40005 3.78 - 4.34: 51546 4.34 - 4.90: 77029 Nonbonded interactions: 187928 Sorted by model distance: nonbonded pdb=" NH2 ARG A 40 " pdb=" N3 DG J 265 " model vdw 2.110 3.200 nonbonded pdb=" OG SER U 663 " pdb=" O GLY U 685 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 304 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG A 42 " pdb=" OP1 DC I 154 " model vdw 2.363 3.120 nonbonded pdb=" OE2 GLU A 133 " pdb=" NH2 ARG B 95 " model vdw 2.384 3.120 ... (remaining 187923 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 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 111) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'U' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.810 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 25.390 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.046 24971 Z= 0.839 Angle : 1.499 28.005 35149 Z= 1.063 Chirality : 0.075 0.327 3854 Planarity : 0.002 0.021 3352 Dihedral : 21.442 179.973 10095 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -2.58 (0.15), residues: 2073 helix: -1.64 (0.13), residues: 987 sheet: -0.87 (0.43), residues: 115 loop : -1.80 (0.16), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 792 TYR 0.020 0.002 TYR A 99 PHE 0.020 0.002 PHE Z 652 TRP 0.014 0.002 TRP U 601 HIS 0.005 0.001 HIS V 758 Details of bonding type rmsd/Z covalent geometry : bond 0.01120 / 0.84 (24935) covalent geometry : angle 1.39511 / 1.06 (35095) hydrogen bonds : bond 0.17649 / 11.65 ( 1149) hydrogen bonds : angle 6.73203 / 4.75 ( 2957) metal coordination : bond 0.01263 / 0.80 ( 36) metal coordination : angle 14.05526 / 9.66 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.656 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: 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 105 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9136 (tm-30) REVERT: A 109 LEU cc_start: 0.9565 (mt) cc_final: 0.9201 (mm) REVERT: B 64 ASN cc_start: 0.9018 (m-40) cc_final: 0.8667 (t0) REVERT: C 33 LEU cc_start: 0.8665 (mt) cc_final: 0.8142 (mt) REVERT: C 108 LEU cc_start: 0.9401 (mt) cc_final: 0.9105 (pt) REVERT: D 41 VAL cc_start: 0.8967 (t) cc_final: 0.8715 (p) REVERT: D 51 ILE cc_start: 0.8859 (tt) cc_final: 0.5958 (tp) REVERT: D 68 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9041 (mm-30) REVERT: D 70 ILE cc_start: 0.9816 (mt) cc_final: 0.9544 (tp) REVERT: D 86 ILE cc_start: 0.9438 (mt) cc_final: 0.8977 (tp) REVERT: E 67 PHE cc_start: 0.8759 (t80) cc_final: 0.8278 (t80) REVERT: E 110 CYS cc_start: 0.9126 (m) cc_final: 0.8519 (t) REVERT: F 61 PHE cc_start: 0.9669 (t80) cc_final: 0.9438 (t80) REVERT: F 68 ASP cc_start: 0.9122 (m-30) cc_final: 0.8798 (m-30) REVERT: G 63 LEU cc_start: 0.9137 (mt) cc_final: 0.8919 (mt) REVERT: G 83 LEU cc_start: 0.9622 (mt) cc_final: 0.9415 (mp) REVERT: G 87 VAL cc_start: 0.9591 (t) cc_final: 0.9271 (p) REVERT: H 77 LEU cc_start: 0.9153 (mt) cc_final: 0.8825 (mt) REVERT: V 506 MET cc_start: 0.5189 (ttp) cc_final: 0.4874 (mmp) REVERT: U 761 MET cc_start: -0.2388 (ptm) cc_final: -0.2872 (ptt) REVERT: Y 801 MET cc_start: 0.0025 (ptm) cc_final: -0.0363 (ptt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1657 time to fit residues: 74.7270 Evaluate side-chains 163 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.1980 chunk 235 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN C 31 HIS C 68 ASN E 39 HIS V 657 HIS U 515 GLN U 789 HIS U 821 HIS U 873 HIS U 900 HIS Y 789 HIS Y 900 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.077096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.049975 restraints weight = 217445.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.051109 restraints weight = 144488.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.051883 restraints weight = 107753.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.052386 restraints weight = 86765.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.052813 restraints weight = 74736.595| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24971 Z= 0.165 Angle : 0.656 12.399 35149 Z= 0.361 Chirality : 0.042 0.313 3854 Planarity : 0.004 0.044 3352 Dihedral : 27.005 176.645 5929 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -0.76 (0.17), residues: 2073 helix: 0.25 (0.15), residues: 993 sheet: -0.81 (0.39), residues: 138 loop : -1.23 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 128 TYR 0.016 0.001 TYR D 34 PHE 0.024 0.002 PHE E 84 TRP 0.009 0.001 TRP Y 860 HIS 0.005 0.001 HIS Z 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (24935) covalent geometry : angle 0.62697 / 0.36 (35095) hydrogen bonds : bond 0.05459 / 3.67 ( 1149) hydrogen bonds : angle 4.28388 / 3.07 ( 2957) metal coordination : bond 0.00853 / 0.62 ( 36) metal coordination : angle 4.99437 / 3.27 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.775 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: symmetry clash REVERT: B 26 ILE cc_start: 0.7843 (tp) cc_final: 0.7561 (tp) REVERT: B 81 VAL cc_start: 0.8566 (t) cc_final: 0.8275 (p) REVERT: C 39 TYR cc_start: 0.7530 (m-80) cc_final: 0.7279 (m-80) REVERT: D 56 MET cc_start: 0.9234 (mmp) cc_final: 0.8915 (mmm) REVERT: D 70 ILE cc_start: 0.9496 (mt) cc_final: 0.9264 (tp) REVERT: D 86 ILE cc_start: 0.9145 (mt) cc_final: 0.8701 (tp) REVERT: E 61 LEU cc_start: 0.4982 (mt) cc_final: 0.4614 (mt) REVERT: E 94 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9069 (mm-30) REVERT: E 110 CYS cc_start: 0.8547 (m) cc_final: 0.8067 (t) REVERT: G 58 LEU cc_start: 0.9510 (mt) cc_final: 0.9299 (mm) REVERT: G 87 VAL cc_start: 0.9202 (t) cc_final: 0.8981 (p) REVERT: H 70 ILE cc_start: 0.9226 (tp) cc_final: 0.8351 (tp) REVERT: H 98 LEU cc_start: 0.9458 (tt) cc_final: 0.8945 (tt) REVERT: U 864 MET cc_start: 0.8820 (mmp) cc_final: 0.8612 (mmt) REVERT: Y 801 MET cc_start: 0.2953 (ptm) cc_final: 0.2741 (ptt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1561 time to fit residues: 53.2321 Evaluate side-chains 149 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 185 optimal weight: 3.9990 chunk 199 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 20.0000 chunk 156 optimal weight: 50.0000 chunk 38 optimal weight: 10.0000 chunk 187 optimal weight: 50.0000 chunk 193 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 overall best weight: 11.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN E 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 31 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 92 GLN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 710 HIS ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 847 HIS Y 613 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.060347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033000 restraints weight = 236367.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033776 restraints weight = 150431.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.034308 restraints weight = 112062.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.034588 restraints weight = 92884.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.034704 restraints weight = 82596.385| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.155 24971 Z= 0.494 Angle : 1.237 17.012 35149 Z= 0.680 Chirality : 0.064 0.538 3854 Planarity : 0.011 0.153 3352 Dihedral : 28.764 174.499 5929 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 34.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 0.61 % Allowed : 3.86 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.54 (0.17), residues: 2073 helix: -0.95 (0.15), residues: 995 sheet: -0.62 (0.39), residues: 147 loop : -1.01 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG A 128 TYR 0.093 0.004 TYR F 72 PHE 0.039 0.003 PHE C 25 TRP 0.012 0.002 TRP Z 716 HIS 0.014 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00897 / 0.49 (24935) covalent geometry : angle 1.22431 / 0.68 (35095) hydrogen bonds : bond 0.23127 / 15.55 ( 1149) hydrogen bonds : angle 6.24076 / 4.57 ( 2957) metal coordination : bond 0.00931 / 0.70 ( 36) metal coordination : angle 4.61985 / 3.27 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.757 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: A 99 TYR cc_start: 0.9356 (t80) cc_final: 0.9093 (t80) REVERT: A 110 CYS cc_start: 0.9190 (m) cc_final: 0.8761 (t) REVERT: B 40 ARG cc_start: 0.9274 (ttm170) cc_final: 0.8917 (ttm110) REVERT: E 110 CYS cc_start: 0.9375 (m) cc_final: 0.8900 (t) REVERT: H 65 ASP cc_start: 0.9287 (t70) cc_final: 0.9085 (t0) REVERT: V 506 MET cc_start: 0.4359 (mmp) cc_final: 0.3457 (tmm) REVERT: V 700 MET cc_start: 0.7992 (mmp) cc_final: 0.7446 (mmp) REVERT: V 722 MET cc_start: 0.8124 (tpt) cc_final: 0.7904 (tpt) REVERT: Z 645 TYR cc_start: 0.8114 (p90) cc_final: 0.7754 (t80) REVERT: U 864 MET cc_start: 0.8847 (mmp) cc_final: 0.8635 (mmm) REVERT: Y 801 MET cc_start: 0.3430 (ptm) cc_final: 0.3083 (ptt) outliers start: 11 outliers final: 7 residues processed: 158 average time/residue: 0.1640 time to fit residues: 41.3607 Evaluate side-chains 109 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 213 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.061640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033161 restraints weight = 231937.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.034055 restraints weight = 137823.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034636 restraints weight = 99465.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034954 restraints weight = 80327.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035207 restraints weight = 70866.474| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 24971 Z= 0.217 Angle : 0.757 10.038 35149 Z= 0.413 Chirality : 0.050 0.291 3854 Planarity : 0.005 0.058 3352 Dihedral : 29.457 175.169 5929 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.71 (0.17), residues: 2073 helix: -0.07 (0.16), residues: 1004 sheet: -0.45 (0.41), residues: 133 loop : -0.80 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 88 TYR 0.029 0.002 TYR C 50 PHE 0.014 0.001 PHE E 104 TRP 0.009 0.001 TRP U 795 HIS 0.015 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.22 (24935) covalent geometry : angle 0.74052 / 0.41 (35095) hydrogen bonds : bond 0.08996 / 5.95 ( 1149) hydrogen bonds : angle 4.84327 / 3.51 ( 2957) metal coordination : bond 0.01233 / 0.73 ( 36) metal coordination : angle 4.02622 / 2.93 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.687 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 110 CYS cc_start: 0.8984 (m) cc_final: 0.8526 (t) REVERT: D 51 ILE cc_start: 0.9283 (tt) cc_final: 0.8971 (tp) REVERT: D 65 ASP cc_start: 0.9434 (t70) cc_final: 0.9207 (t0) REVERT: E 110 CYS cc_start: 0.9180 (m) cc_final: 0.8519 (t) REVERT: V 506 MET cc_start: 0.4307 (mmp) cc_final: 0.3502 (tmm) REVERT: V 700 MET cc_start: 0.7970 (mmp) cc_final: 0.7630 (mmp) REVERT: Z 645 TYR cc_start: 0.8020 (p90) cc_final: 0.7811 (m-80) REVERT: Z 700 MET cc_start: 0.6253 (pmm) cc_final: 0.5441 (mmp) REVERT: U 779 MET cc_start: 0.5691 (mtt) cc_final: 0.5449 (mmt) REVERT: U 864 MET cc_start: 0.8739 (mmp) cc_final: 0.8525 (mmp) outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.1329 time to fit residues: 31.0754 Evaluate side-chains 106 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 108 optimal weight: 0.0060 chunk 161 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 chunk 46 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 chunk 186 optimal weight: 7.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 25 ASN V 610 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.062246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033154 restraints weight = 225089.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.034046 restraints weight = 131853.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.034627 restraints weight = 93470.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.035002 restraints weight = 75299.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.035177 restraints weight = 65632.739| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24971 Z= 0.162 Angle : 0.663 12.012 35149 Z= 0.366 Chirality : 0.044 0.244 3854 Planarity : 0.004 0.047 3352 Dihedral : 29.014 172.361 5929 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.17 % Allowed : 0.94 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -0.18 (0.18), residues: 2073 helix: 0.61 (0.16), residues: 1004 sheet: -0.45 (0.41), residues: 141 loop : -0.80 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.019 0.001 TYR H 37 PHE 0.012 0.001 PHE B 100 TRP 0.009 0.001 TRP U 601 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (24935) covalent geometry : angle 0.63898 / 0.36 (35095) hydrogen bonds : bond 0.07729 / 5.21 ( 1149) hydrogen bonds : angle 4.35215 / 3.16 ( 2957) metal coordination : bond 0.00632 / 0.42 ( 36) metal coordination : angle 4.54631 / 3.25 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.645 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 110 CYS cc_start: 0.8821 (m) cc_final: 0.8343 (t) REVERT: C 110 ASN cc_start: 0.8040 (m-40) cc_final: 0.7763 (m110) REVERT: E 110 CYS cc_start: 0.9161 (m) cc_final: 0.8442 (t) REVERT: H 73 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8523 (pt0) REVERT: H 98 LEU cc_start: 0.8860 (tt) cc_final: 0.8540 (tt) REVERT: V 506 MET cc_start: 0.4598 (mmp) cc_final: 0.3829 (tmm) REVERT: Z 645 TYR cc_start: 0.8006 (p90) cc_final: 0.7793 (m-80) REVERT: Z 700 MET cc_start: 0.6340 (pmm) cc_final: 0.5582 (mmp) REVERT: U 864 MET cc_start: 0.8721 (mmp) cc_final: 0.8502 (mmp) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.1372 time to fit residues: 33.8852 Evaluate side-chains 110 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 84 optimal weight: 50.0000 chunk 210 optimal weight: 50.0000 chunk 162 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 27 optimal weight: 0.0070 chunk 161 optimal weight: 9.9990 chunk 199 optimal weight: 30.0000 chunk 167 optimal weight: 9.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031440 restraints weight = 236412.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032218 restraints weight = 141279.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.032756 restraints weight = 102744.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.033024 restraints weight = 83393.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.033260 restraints weight = 73619.302| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 24971 Z= 0.240 Angle : 0.748 12.790 35149 Z= 0.408 Chirality : 0.046 0.286 3854 Planarity : 0.005 0.070 3352 Dihedral : 29.207 174.248 5929 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.11 % Allowed : 1.27 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.28 (0.18), residues: 2073 helix: 0.42 (0.16), residues: 1003 sheet: -0.39 (0.43), residues: 132 loop : -0.73 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 30 TYR 0.029 0.002 TYR C 50 PHE 0.016 0.001 PHE E 84 TRP 0.008 0.001 TRP U 601 HIS 0.016 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.24 (24935) covalent geometry : angle 0.73249 / 0.41 (35095) hydrogen bonds : bond 0.11404 / 7.66 ( 1149) hydrogen bonds : angle 4.73313 / 3.43 ( 2957) metal coordination : bond 0.01048 / 0.80 ( 36) metal coordination : angle 3.99057 / 2.82 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.775 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: A 99 TYR cc_start: 0.9141 (t80) cc_final: 0.8721 (t80) REVERT: D 51 ILE cc_start: 0.9342 (tt) cc_final: 0.8976 (tp) REVERT: E 110 CYS cc_start: 0.9342 (m) cc_final: 0.8707 (t) REVERT: F 68 ASP cc_start: 0.9290 (m-30) cc_final: 0.8969 (p0) REVERT: H 98 LEU cc_start: 0.8894 (tt) cc_final: 0.8694 (tt) REVERT: V 506 MET cc_start: 0.4720 (mmp) cc_final: 0.4000 (tmm) REVERT: Z 645 TYR cc_start: 0.7990 (p90) cc_final: 0.7759 (p90) REVERT: Z 700 MET cc_start: 0.6149 (pmm) cc_final: 0.5336 (mmp) REVERT: U 864 MET cc_start: 0.8755 (mmp) cc_final: 0.8533 (mmp) REVERT: Y 761 MET cc_start: 0.4126 (mpp) cc_final: 0.3784 (mpp) REVERT: Y 852 MET cc_start: 0.5647 (mtp) cc_final: 0.5282 (mmt) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.1432 time to fit residues: 28.2705 Evaluate side-chains 91 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030517 restraints weight = 248881.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031329 restraints weight = 143868.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.031855 restraints weight = 103501.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.032136 restraints weight = 83750.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.032378 restraints weight = 73842.477| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24971 Z= 0.213 Angle : 0.695 10.103 35149 Z= 0.386 Chirality : 0.045 0.283 3854 Planarity : 0.004 0.044 3352 Dihedral : 29.453 174.491 5929 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.18), residues: 2073 helix: 0.57 (0.16), residues: 1003 sheet: -0.42 (0.43), residues: 132 loop : -0.73 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG V 551 TYR 0.022 0.001 TYR C 50 PHE 0.013 0.001 PHE E 104 TRP 0.009 0.001 TRP U 601 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.21 (24935) covalent geometry : angle 0.67594 / 0.38 (35095) hydrogen bonds : bond 0.09128 / 6.12 ( 1149) hydrogen bonds : angle 4.59791 / 3.34 ( 2957) metal coordination : bond 0.00624 / 0.46 ( 36) metal coordination : angle 4.17504 / 3.00 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.764 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: A 99 TYR cc_start: 0.9087 (t80) cc_final: 0.8847 (t80) REVERT: C 111 ILE cc_start: 0.6326 (mm) cc_final: 0.6093 (mm) REVERT: D 51 ILE cc_start: 0.9319 (tt) cc_final: 0.9020 (tt) REVERT: E 110 CYS cc_start: 0.9263 (m) cc_final: 0.8572 (t) REVERT: E 124 ILE cc_start: 0.8963 (pt) cc_final: 0.8696 (pt) REVERT: F 53 GLU cc_start: 0.8755 (mp0) cc_final: 0.8552 (mp0) REVERT: V 506 MET cc_start: 0.4760 (mmp) cc_final: 0.4127 (tmm) REVERT: Z 645 TYR cc_start: 0.7950 (p90) cc_final: 0.7735 (p90) REVERT: Z 700 MET cc_start: 0.6033 (pmm) cc_final: 0.5291 (mmp) REVERT: U 801 MET cc_start: 0.3401 (tmm) cc_final: 0.1862 (ptt) REVERT: U 864 MET cc_start: 0.8697 (mmp) cc_final: 0.8481 (mmp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1516 time to fit residues: 29.9267 Evaluate side-chains 86 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 168 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 chunk 120 optimal weight: 50.0000 chunk 234 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 180 optimal weight: 0.1980 chunk 201 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.061215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.031586 restraints weight = 247244.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.032460 restraints weight = 137882.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.033015 restraints weight = 96161.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.033334 restraints weight = 76823.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.033586 restraints weight = 66983.605| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.7886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24971 Z= 0.130 Angle : 0.643 9.951 35149 Z= 0.352 Chirality : 0.044 0.265 3854 Planarity : 0.004 0.046 3352 Dihedral : 29.229 174.899 5929 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.30 (0.18), residues: 2073 helix: 1.14 (0.16), residues: 1001 sheet: -0.43 (0.42), residues: 140 loop : -0.69 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.014 0.001 TYR C 50 PHE 0.044 0.001 PHE A 104 TRP 0.010 0.001 TRP U 601 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (24935) covalent geometry : angle 0.62599 / 0.35 (35095) hydrogen bonds : bond 0.05712 / 3.82 ( 1149) hydrogen bonds : angle 4.12419 / 2.99 ( 2957) metal coordination : bond 0.00536 / 0.35 ( 36) metal coordination : angle 3.85036 / 2.77 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.844 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: A 99 TYR cc_start: 0.9022 (t80) cc_final: 0.8819 (t80) REVERT: D 51 ILE cc_start: 0.9332 (tt) cc_final: 0.9048 (tt) REVERT: D 73 GLU cc_start: 0.8859 (mp0) cc_final: 0.8623 (mp0) REVERT: D 98 LEU cc_start: 0.6310 (mm) cc_final: 0.5446 (mm) REVERT: E 107 THR cc_start: 0.8677 (m) cc_final: 0.8417 (m) REVERT: E 110 CYS cc_start: 0.9091 (m) cc_final: 0.8625 (p) REVERT: E 124 ILE cc_start: 0.8825 (pt) cc_final: 0.8532 (pt) REVERT: F 53 GLU cc_start: 0.8612 (mp0) cc_final: 0.8369 (mp0) REVERT: H 73 GLU cc_start: 0.8110 (pt0) cc_final: 0.7335 (pt0) REVERT: V 506 MET cc_start: 0.4752 (mmp) cc_final: 0.4121 (tmm) REVERT: Z 645 TYR cc_start: 0.7926 (p90) cc_final: 0.7713 (p90) REVERT: Z 700 MET cc_start: 0.6218 (pmm) cc_final: 0.5511 (mmp) REVERT: U 864 MET cc_start: 0.8667 (mmp) cc_final: 0.8450 (mmp) REVERT: Y 761 MET cc_start: 0.4273 (mpp) cc_final: 0.3773 (mpp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1441 time to fit residues: 31.1276 Evaluate side-chains 101 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 50.0000 chunk 222 optimal weight: 6.9990 chunk 177 optimal weight: 30.0000 chunk 120 optimal weight: 50.0000 chunk 147 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN D 64 ASN Y 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.057790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029794 restraints weight = 249355.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.030595 restraints weight = 144030.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.031083 restraints weight = 102803.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.031400 restraints weight = 83478.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.031540 restraints weight = 73066.382| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.8554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 24971 Z= 0.260 Angle : 0.751 9.690 35149 Z= 0.416 Chirality : 0.047 0.300 3854 Planarity : 0.005 0.089 3352 Dihedral : 29.405 174.410 5929 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.12 (0.18), residues: 2073 helix: 0.57 (0.16), residues: 1003 sheet: -0.41 (0.43), residues: 139 loop : -0.65 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 30 TYR 0.051 0.002 TYR E 54 PHE 0.028 0.001 PHE A 104 TRP 0.008 0.001 TRP U 601 HIS 0.013 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.26 (24935) covalent geometry : angle 0.73504 / 0.42 (35095) hydrogen bonds : bond 0.12745 / 8.58 ( 1149) hydrogen bonds : angle 4.78635 / 3.48 ( 2957) metal coordination : bond 0.00576 / 0.40 ( 36) metal coordination : angle 3.96407 / 2.81 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.789 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: A 99 TYR cc_start: 0.9141 (t80) cc_final: 0.8810 (t80) REVERT: A 110 CYS cc_start: 0.9002 (m) cc_final: 0.8574 (p) REVERT: D 51 ILE cc_start: 0.9306 (tt) cc_final: 0.9099 (tt) REVERT: E 107 THR cc_start: 0.9022 (m) cc_final: 0.8795 (m) REVERT: E 110 CYS cc_start: 0.9442 (m) cc_final: 0.9039 (p) REVERT: E 120 MET cc_start: 0.6215 (tmm) cc_final: 0.5921 (tmm) REVERT: F 68 ASP cc_start: 0.9366 (m-30) cc_final: 0.9103 (p0) REVERT: V 506 MET cc_start: 0.4673 (mmp) cc_final: 0.4019 (tmm) REVERT: Z 645 TYR cc_start: 0.7984 (p90) cc_final: 0.7772 (p90) REVERT: Z 700 MET cc_start: 0.6002 (pmm) cc_final: 0.5228 (mmp) REVERT: U 801 MET cc_start: 0.3227 (tmm) cc_final: 0.1450 (ptt) REVERT: U 864 MET cc_start: 0.8625 (mmp) cc_final: 0.8398 (mmp) REVERT: Y 852 MET cc_start: 0.6155 (mtp) cc_final: 0.5945 (mmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1501 time to fit residues: 25.1045 Evaluate side-chains 76 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 41 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 50.0000 chunk 169 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 136 optimal weight: 50.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030657 restraints weight = 241425.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.031505 restraints weight = 135805.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032021 restraints weight = 94817.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032304 restraints weight = 76307.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.032520 restraints weight = 67222.703| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.8583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24971 Z= 0.149 Angle : 0.660 9.391 35149 Z= 0.365 Chirality : 0.045 0.267 3854 Planarity : 0.004 0.045 3352 Dihedral : 29.442 175.757 5929 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2073 helix: 0.97 (0.16), residues: 1004 sheet: -0.40 (0.44), residues: 131 loop : -0.60 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 77 TYR 0.023 0.001 TYR E 54 PHE 0.031 0.001 PHE A 104 TRP 0.010 0.001 TRP U 601 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (24935) covalent geometry : angle 0.64288 / 0.36 (35095) hydrogen bonds : bond 0.06832 / 4.58 ( 1149) hydrogen bonds : angle 4.35441 / 3.16 ( 2957) metal coordination : bond 0.00489 / 0.34 ( 36) metal coordination : angle 3.86030 / 2.74 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.788 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: D 51 ILE cc_start: 0.9332 (tt) cc_final: 0.9108 (tt) REVERT: E 107 THR cc_start: 0.8936 (m) cc_final: 0.8700 (m) REVERT: E 110 CYS cc_start: 0.9374 (m) cc_final: 0.8978 (p) REVERT: E 120 MET cc_start: 0.6041 (tmm) cc_final: 0.5799 (tmm) REVERT: F 43 VAL cc_start: 0.5393 (t) cc_final: 0.5174 (t) REVERT: V 506 MET cc_start: 0.4662 (mmp) cc_final: 0.4010 (tmm) REVERT: Z 645 TYR cc_start: 0.7958 (p90) cc_final: 0.7748 (p90) REVERT: Z 700 MET cc_start: 0.6071 (pmm) cc_final: 0.5344 (mmp) REVERT: U 801 MET cc_start: 0.3564 (tmm) cc_final: 0.2031 (ptt) REVERT: U 864 MET cc_start: 0.8595 (mmp) cc_final: 0.8369 (mmp) REVERT: Y 761 MET cc_start: 0.4208 (mpp) cc_final: 0.3228 (mpp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1422 time to fit residues: 26.4311 Evaluate side-chains 87 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 206 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 219 optimal weight: 0.7980 chunk 226 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.058130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.029839 restraints weight = 246839.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.030676 restraints weight = 138754.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031097 restraints weight = 98373.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031428 restraints weight = 80593.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.031674 restraints weight = 70930.002| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24971 Z= 0.198 Angle : 0.693 11.339 35149 Z= 0.382 Chirality : 0.045 0.272 3854 Planarity : 0.004 0.053 3352 Dihedral : 29.413 174.844 5929 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.11 (0.18), residues: 2073 helix: 0.82 (0.16), residues: 1003 sheet: -0.34 (0.45), residues: 121 loop : -0.60 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 556 TYR 0.029 0.002 TYR E 54 PHE 0.027 0.001 PHE A 104 TRP 0.009 0.001 TRP U 601 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.20 (24935) covalent geometry : angle 0.67404 / 0.38 (35095) hydrogen bonds : bond 0.09649 / 6.50 ( 1149) hydrogen bonds : angle 4.53796 / 3.29 ( 2957) metal coordination : bond 0.00626 / 0.47 ( 36) metal coordination : angle 4.16477 / 3.17 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5678.64 seconds wall clock time: 98 minutes 4.65 seconds (5884.65 seconds total)