Starting phenix.real_space_refine on Sun Feb 18 06:01:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/02_2024/6ftx_4318_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/02_2024/6ftx_4318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/02_2024/6ftx_4318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/02_2024/6ftx_4318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/02_2024/6ftx_4318_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/02_2024/6ftx_4318_neut_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 320 5.49 5 S 41 5.16 5 Be 1 3.05 5 C 12267 2.51 5 N 3844 2.21 5 O 4573 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "N GLU 24": "OE1" <-> "OE2" Residue "W ARG 807": "NH1" <-> "NH2" Residue "W PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 1202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21049 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" 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: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 686 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3238 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "J" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3298 Classifications: {'DNA': 160} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 159} Chain: "N" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "W" Number of atoms: 7220 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 880, 7204 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'peptide': 878, 'undetermined': 2} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 848, None: 2} Not linked: pdbres="ASN W1268 " pdbres="BEF W1301 " Not linked: pdbres="BEF W1301 " pdbres="ADP W1302 " Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 880, 7204 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'peptide': 878, 'undetermined': 2} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 848, None: 2} Not linked: pdbres="ASN W1268 " pdbres="BEF W1301 " Not linked: pdbres="BEF W1301 " pdbres="ADP W1302 " Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7326 Time building chain proxies: 14.52, per 1000 atoms: 0.69 Number of scatterers: 21049 At special positions: 0 Unit cell: (152.6, 147, 173.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 41 16.00 P 320 15.00 F 3 9.00 O 4573 8.00 N 3844 7.00 C 12267 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS W 207 " - pdb=" SG CYS W 246 " distance=2.82 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.65 Conformation dependent library (CDL) restraints added in 3.9 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 10 sheets defined 47.3% alpha, 4.4% beta 84 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 10.03 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.580A pdb=" N GLN A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.541A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.627A pdb=" N ALA B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.781A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 63 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 70 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 18 through 21 No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 27 through 36 removed outlier: 4.092A pdb=" N HIS C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.961A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.561A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 55 through 78 removed outlier: 3.602A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.587A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.752A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.535A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.721A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.730A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.789A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.877A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 47 through 72 removed outlier: 4.232A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.544A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 removed outlier: 4.680A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.643A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.661A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 98 removed outlier: 3.524A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.736A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 30 removed outlier: 3.546A pdb=" N LYS N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'O' and resid 23 through 34 Processing helix chain 'O' and resid 57 through 59 No H-bonds generated for 'chain 'O' and resid 57 through 59' Processing helix chain 'W' and resid 204 through 210 Processing helix chain 'W' and resid 240 through 256 removed outlier: 3.506A pdb=" N ASN W 244 " --> pdb=" O LYS W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 284 removed outlier: 4.161A pdb=" N ARG W 274 " --> pdb=" O MET W 270 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU W 283 " --> pdb=" O ASP W 279 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE W 284 " --> pdb=" O GLU W 280 " (cutoff:3.500A) Processing helix chain 'W' and resid 332 through 343 removed outlier: 3.834A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 384 through 387 No H-bonds generated for 'chain 'W' and resid 384 through 387' Processing helix chain 'W' and resid 407 through 417 removed outlier: 3.514A pdb=" N THR W 411 " --> pdb=" O LYS W 407 " (cutoff:3.500A) Processing helix chain 'W' and resid 437 through 445 Processing helix chain 'W' and resid 461 through 470 removed outlier: 3.650A pdb=" N ARG W 467 " --> pdb=" O ARG W 463 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR W 469 " --> pdb=" O THR W 465 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 497 removed outlier: 3.814A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 499 through 504 Processing helix chain 'W' and resid 549 through 559 Processing helix chain 'W' and resid 579 through 593 removed outlier: 3.766A pdb=" N ARG W 588 " --> pdb=" O HIS W 584 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN W 591 " --> pdb=" O HIS W 587 " (cutoff:3.500A) Proline residue: W 592 - end of helix Processing helix chain 'W' and resid 620 through 630 removed outlier: 3.913A pdb=" N GLU W 624 " --> pdb=" O ASP W 620 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE W 629 " --> pdb=" O TYR W 625 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU W 630 " --> pdb=" O TYR W 626 " (cutoff:3.500A) Processing helix chain 'W' and resid 640 through 652 removed outlier: 4.161A pdb=" N GLY W 644 " --> pdb=" O GLY W 640 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HIS W 645 " --> pdb=" O ALA W 641 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE W 646 " --> pdb=" O LYS W 642 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU W 648 " --> pdb=" O GLY W 644 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU W 649 " --> pdb=" O HIS W 645 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE W 651 " --> pdb=" O SER W 647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET W 652 " --> pdb=" O LEU W 648 " (cutoff:3.500A) Processing helix chain 'W' and resid 669 through 672 No H-bonds generated for 'chain 'W' and resid 669 through 672' Processing helix chain 'W' and resid 684 through 692 Processing helix chain 'W' and resid 695 through 708 Processing helix chain 'W' and resid 721 through 731 removed outlier: 3.712A pdb=" N ASP W 725 " --> pdb=" O VAL W 721 " (cutoff:3.500A) Processing helix chain 'W' and resid 747 through 758 removed outlier: 3.679A pdb=" N SER W 753 " --> pdb=" O GLN W 749 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE W 754 " --> pdb=" O ARG W 750 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP W 755 " --> pdb=" O ARG W 751 " (cutoff:3.500A) Processing helix chain 'W' and resid 797 through 803 Processing helix chain 'W' and resid 826 through 837 Processing helix chain 'W' and resid 1011 through 1024 removed outlier: 3.835A pdb=" N LYS W1019 " --> pdb=" O ARG W1015 " (cutoff:3.500A) Processing helix chain 'W' and resid 1028 through 1036 removed outlier: 3.824A pdb=" N LEU W1031 " --> pdb=" O LYS W1028 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP W1032 " --> pdb=" O GLU W1029 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU W1034 " --> pdb=" O LEU W1031 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA W1036 " --> pdb=" O GLU W1033 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1090 removed outlier: 3.537A pdb=" N GLY W1049 " --> pdb=" O PHE W1045 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR W1051 " --> pdb=" O LYS W1047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET W1056 " --> pdb=" O TYR W1052 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP W1061 " --> pdb=" O GLU W1057 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS W1062 " --> pdb=" O ALA W1058 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL W1063 " --> pdb=" O ALA W1059 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS W1076 " --> pdb=" O GLU W1072 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA W1083 " --> pdb=" O LYS W1079 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS W1087 " --> pdb=" O ALA W1083 " (cutoff:3.500A) Processing helix chain 'W' and resid 1103 through 1111 Processing helix chain 'W' and resid 1129 through 1147 removed outlier: 3.512A pdb=" N LEU W1133 " --> pdb=" O ALA W1129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU W1137 " --> pdb=" O LEU W1133 " (cutoff:3.500A) Processing helix chain 'W' and resid 1154 through 1156 No H-bonds generated for 'chain 'W' and resid 1154 through 1156' Processing helix chain 'W' and resid 1176 through 1189 removed outlier: 3.541A pdb=" N ILE W1184 " --> pdb=" O GLU W1180 " (cutoff:3.500A) Processing helix chain 'W' and resid 1195 through 1199 Processing helix chain 'W' and resid 1249 through 1264 removed outlier: 3.761A pdb=" N ASP W1257 " --> pdb=" O GLY W1253 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR W1258 " --> pdb=" O ARG W1254 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG W1264 " --> pdb=" O LEU W1260 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.583A pdb=" N LEU N 15 " --> pdb=" O ILE N 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL N 5 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE N 13 " --> pdb=" O VAL N 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'O' and resid 12 through 16 Processing sheet with id= D, first strand: chain 'W' and resid 184 through 187 removed outlier: 3.789A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE W 213 " --> pdb=" O GLU W 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'W' and resid 292 through 297 removed outlier: 4.005A pdb=" N ASP W 292 " --> pdb=" O LEU W 308 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'W' and resid 397 through 399 removed outlier: 3.952A pdb=" N LEU W 539 " --> pdb=" O GLY W 397 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'W' and resid 488 through 490 Processing sheet with id= H, first strand: chain 'W' and resid 815 through 818 removed outlier: 4.150A pdb=" N GLN W 739 " --> pdb=" O VAL W 766 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU W 768 " --> pdb=" O GLN W 739 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'W' and resid 179 through 182 removed outlier: 7.269A pdb=" N LYS W 216 " --> pdb=" O ASP W 180 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'W' and resid 287 through 290 removed outlier: 6.867A pdb=" N LYS W 310 " --> pdb=" O GLU W 288 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 10.99 Time building geometry restraints manager: 11.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.26: 2383 1.26 - 1.43: 7265 1.43 - 1.59: 11902 1.59 - 1.76: 452 1.76 - 1.92: 75 Bond restraints: 22077 Sorted by residual: bond pdb=" BE BEF W1301 " pdb=" F2 BEF W1301 " ideal model delta sigma weight residual 1.476 1.823 -0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" BE BEF W1301 " pdb=" F3 BEF W1301 " ideal model delta sigma weight residual 1.476 1.783 -0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" BE BEF W1301 " pdb=" F1 BEF W1301 " ideal model delta sigma weight residual 1.476 1.744 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C ILE C 102 " pdb=" O ILE C 102 " ideal model delta sigma weight residual 1.236 1.356 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" C THR D 87 " pdb=" O THR D 87 " ideal model delta sigma weight residual 1.234 1.097 0.137 1.16e-02 7.43e+03 1.39e+02 ... (remaining 22072 not shown) Histogram of bond angle deviations from ideal: 88.29 - 98.01: 22 98.01 - 107.74: 4041 107.74 - 117.46: 13775 117.46 - 127.19: 12457 127.19 - 136.91: 873 Bond angle restraints: 31168 Sorted by residual: angle pdb=" CA ALA G 47 " pdb=" C ALA G 47 " pdb=" N PRO G 48 " ideal model delta sigma weight residual 120.52 109.66 10.86 8.30e-01 1.45e+00 1.71e+02 angle pdb=" N TYR C 39 " pdb=" CA TYR C 39 " pdb=" C TYR C 39 " ideal model delta sigma weight residual 110.97 121.99 -11.02 1.09e+00 8.42e-01 1.02e+02 angle pdb=" CB GLU O 64 " pdb=" CG GLU O 64 " pdb=" CD GLU O 64 " ideal model delta sigma weight residual 112.60 128.89 -16.29 1.70e+00 3.46e-01 9.18e+01 angle pdb=" NE ARG B 40 " pdb=" CZ ARG B 40 " pdb=" NH1 ARG B 40 " ideal model delta sigma weight residual 121.50 112.46 9.04 1.00e+00 1.00e+00 8.18e+01 angle pdb=" CA ARG G 17 " pdb=" C ARG G 17 " pdb=" O ARG G 17 " ideal model delta sigma weight residual 120.82 111.56 9.26 1.05e+00 9.07e-01 7.78e+01 ... (remaining 31163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10784 35.12 - 70.24: 1671 70.24 - 105.36: 67 105.36 - 140.49: 4 140.49 - 175.61: 1 Dihedral angle restraints: 12527 sinusoidal: 7266 harmonic: 5261 Sorted by residual: dihedral pdb=" CD ARG D 30 " pdb=" NE ARG D 30 " pdb=" CZ ARG D 30 " pdb=" NH1 ARG D 30 " ideal model delta sinusoidal sigma weight residual 0.00 87.52 -87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CD ARG G 77 " pdb=" NE ARG G 77 " pdb=" CZ ARG G 77 " pdb=" NH1 ARG G 77 " ideal model delta sinusoidal sigma weight residual 0.00 87.05 -87.05 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" C ASN D 81 " pdb=" N ASN D 81 " pdb=" CA ASN D 81 " pdb=" CB ASN D 81 " ideal model delta harmonic sigma weight residual -122.60 -144.97 22.37 0 2.50e+00 1.60e-01 8.01e+01 ... (remaining 12524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2942 0.157 - 0.314: 505 0.314 - 0.471: 50 0.471 - 0.628: 9 0.628 - 0.784: 2 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CA ASN D 81 " pdb=" N ASN D 81 " pdb=" C ASN D 81 " pdb=" CB ASN D 81 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3' DG I -52 " pdb=" C4' DG I -52 " pdb=" O3' DG I -52 " pdb=" C2' DG I -52 " both_signs ideal model delta sigma weight residual False -2.66 -1.96 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA LEU O 71 " pdb=" N LEU O 71 " pdb=" C LEU O 71 " pdb=" CB LEU O 71 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 8.92e+00 ... (remaining 3505 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 30 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG D 30 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 30 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 30 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 30 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 77 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG G 77 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 77 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 77 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 77 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " -0.149 2.00e-02 2.50e+03 6.23e-02 1.16e+02 pdb=" N9 DG J -19 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " 0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " 0.034 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.027 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " -0.050 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.046 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " 0.049 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " -0.024 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " 0.073 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " 0.070 2.00e-02 2.50e+03 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 159 2.37 - 3.00: 11702 3.00 - 3.63: 33752 3.63 - 4.27: 51080 4.27 - 4.90: 74096 Nonbonded interactions: 170789 Sorted by model distance: nonbonded pdb=" NH1 ARG E 63 " pdb=" C5' DA I 17 " model vdw 1.732 3.520 nonbonded pdb=" OE2 GLU A 59 " pdb=" O LEU A 60 " model vdw 1.840 3.040 nonbonded pdb=" O2 DC I 22 " pdb=" N1 DG J -21 " model vdw 1.851 2.496 nonbonded pdb=" O2 DT I 62 " pdb=" N1 DA J -62 " model vdw 1.868 2.496 nonbonded pdb=" NE ARG C 17 " pdb=" OP1 DT I -43 " model vdw 1.868 2.520 ... (remaining 170784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and ((resid 20 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 102)) selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.19 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 71.100 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.020 0.347 22077 Z= 1.253 Angle : 2.387 21.835 31168 Z= 1.545 Chirality : 0.121 0.784 3508 Planarity : 0.039 0.492 2863 Dihedral : 26.058 175.606 9122 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 68.74 Ramachandran Plot: Outliers : 1.63 % Allowed : 8.11 % Favored : 90.26 % Rotamer: Outliers : 3.23 % Allowed : 10.85 % Favored : 85.92 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.16), residues: 1778 helix: -1.38 (0.14), residues: 885 sheet: -0.70 (0.49), residues: 96 loop : -2.77 (0.18), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.016 TRP W 447 HIS 0.036 0.008 HIS G 31 PHE 0.098 0.016 PHE A 67 TYR 0.143 0.020 TYR H 34 ARG 0.080 0.006 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 389 time to evaluate : 2.069 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: 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 41 TYR cc_start: 0.8554 (m-80) cc_final: 0.8288 (m-80) REVERT: A 107 THR cc_start: 0.7686 (m) cc_final: 0.7039 (p) REVERT: C 36 LYS cc_start: 0.9568 (mmtm) cc_final: 0.9283 (mtmt) REVERT: C 38 ASN cc_start: 0.9311 (m-40) cc_final: 0.9025 (m-40) REVERT: C 71 ARG cc_start: 0.7346 (mmt-90) cc_final: 0.6965 (mmt-90) REVERT: D 48 ASP cc_start: 0.9288 (m-30) cc_final: 0.9029 (m-30) REVERT: D 86 ILE cc_start: 0.7982 (mp) cc_final: 0.7730 (mt) REVERT: E 120 MET cc_start: 0.2022 (mmm) cc_final: 0.1515 (mmt) REVERT: G 15 LYS cc_start: 0.6591 (tttt) cc_final: 0.6097 (mmtp) REVERT: G 92 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: H 51 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7230 (pt) REVERT: H 56 MET cc_start: 0.8524 (ttm) cc_final: 0.8042 (tmm) REVERT: W 305 LEU cc_start: 0.7616 (tp) cc_final: 0.7403 (tp) REVERT: W 322 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6190 (mm-30) REVERT: W 376 LEU cc_start: 0.7258 (mt) cc_final: 0.6374 (mp) REVERT: W 379 PHE cc_start: 0.8831 (t80) cc_final: 0.8180 (t80) REVERT: W 463 ARG cc_start: 0.9171 (ttp-170) cc_final: 0.8514 (ttm-80) REVERT: W 467 ARG cc_start: 0.9677 (mtt180) cc_final: 0.9435 (mtm180) REVERT: W 495 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.6957 (mp) REVERT: W 594 ILE cc_start: 0.8875 (mm) cc_final: 0.8579 (mm) REVERT: W 637 LEU cc_start: 0.8843 (tt) cc_final: 0.8560 (mt) REVERT: W 670 GLU cc_start: 0.9330 (mp0) cc_final: 0.9047 (tp30) REVERT: W 741 LEU cc_start: 0.9370 (tt) cc_final: 0.9143 (tt) REVERT: W 817 TYR cc_start: 0.9381 (m-80) cc_final: 0.8961 (m-80) REVERT: W 832 ARG cc_start: 0.9312 (mtp180) cc_final: 0.8980 (ptm-80) REVERT: W 1053 ASP cc_start: 0.9121 (t70) cc_final: 0.8908 (m-30) REVERT: W 1255 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.6807 (tpm170) REVERT: W 1259 LEU cc_start: 0.8589 (mt) cc_final: 0.7316 (mt) outliers start: 50 outliers final: 13 residues processed: 428 average time/residue: 0.3930 time to fit residues: 243.0723 Evaluate side-chains 265 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 247 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.4980 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 188 optimal weight: 40.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN N 2 GLN N 25 ASN N 40 GLN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 474 ASN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 579 GLN W 645 HIS ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 739 GLN W 756 HIS W 813 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22077 Z= 0.274 Angle : 0.797 9.356 31168 Z= 0.441 Chirality : 0.045 0.192 3508 Planarity : 0.006 0.084 2863 Dihedral : 29.324 172.130 5475 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.49 % Favored : 96.00 % Rotamer: Outliers : 0.32 % Allowed : 3.10 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 1778 helix: 0.07 (0.16), residues: 896 sheet: -0.91 (0.48), residues: 107 loop : -2.14 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP W 391 HIS 0.007 0.002 HIS W 806 PHE 0.026 0.002 PHE W 789 TYR 0.024 0.003 TYR H 37 ARG 0.010 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 331 time to evaluate : 1.848 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: 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 41 TYR cc_start: 0.8326 (m-80) cc_final: 0.7970 (m-10) REVERT: A 110 CYS cc_start: 0.8850 (m) cc_final: 0.8489 (t) REVERT: C 36 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9293 (mttt) REVERT: D 86 ILE cc_start: 0.8311 (mp) cc_final: 0.7941 (mt) REVERT: E 50 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9016 (mm-30) REVERT: E 55 GLN cc_start: 0.9530 (mt0) cc_final: 0.8716 (mt0) REVERT: E 120 MET cc_start: 0.1624 (mmm) cc_final: 0.1053 (mmt) REVERT: G 15 LYS cc_start: 0.7054 (ttpt) cc_final: 0.6633 (tppt) REVERT: G 100 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8416 (m) REVERT: H 56 MET cc_start: 0.8730 (ttm) cc_final: 0.8502 (tpp) REVERT: W 429 ILE cc_start: 0.9031 (tp) cc_final: 0.8715 (tp) REVERT: W 437 MET cc_start: 0.8006 (ptm) cc_final: 0.7771 (ppp) REVERT: W 463 ARG cc_start: 0.9041 (ttp-170) cc_final: 0.8744 (tpp-160) REVERT: W 525 LEU cc_start: 0.9176 (pp) cc_final: 0.8870 (mt) REVERT: W 560 MET cc_start: 0.9655 (mtp) cc_final: 0.9233 (ttm) REVERT: W 670 GLU cc_start: 0.9304 (mp0) cc_final: 0.8965 (tp30) REVERT: W 681 MET cc_start: 0.9449 (tpt) cc_final: 0.9186 (tpt) REVERT: W 794 ASN cc_start: 0.9223 (t0) cc_final: 0.8685 (p0) outliers start: 5 outliers final: 1 residues processed: 333 average time/residue: 0.3881 time to fit residues: 187.9771 Evaluate side-chains 237 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 128 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 40.0000 chunk 168 optimal weight: 9.9990 chunk 187 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 357 GLN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 557 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22077 Z= 0.217 Angle : 0.691 9.452 31168 Z= 0.379 Chirality : 0.040 0.187 3508 Planarity : 0.005 0.042 2863 Dihedral : 28.731 170.891 5475 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.77 % Favored : 95.83 % Rotamer: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.19), residues: 1778 helix: 0.17 (0.16), residues: 915 sheet: -0.82 (0.48), residues: 109 loop : -1.78 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP W1194 HIS 0.007 0.001 HIS W1251 PHE 0.032 0.002 PHE G 25 TYR 0.024 0.002 TYR H 37 ARG 0.010 0.001 ARG W 597 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 2.052 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 41 TYR cc_start: 0.8336 (m-80) cc_final: 0.7908 (m-10) REVERT: A 77 ASP cc_start: 0.9453 (m-30) cc_final: 0.9244 (m-30) REVERT: C 34 LEU cc_start: 0.8163 (mt) cc_final: 0.7947 (mt) REVERT: D 86 ILE cc_start: 0.8455 (mp) cc_final: 0.8208 (mt) REVERT: E 55 GLN cc_start: 0.9464 (mt0) cc_final: 0.8862 (mp10) REVERT: E 110 CYS cc_start: 0.8319 (t) cc_final: 0.7287 (t) REVERT: E 123 ASP cc_start: 0.8770 (m-30) cc_final: 0.7428 (t70) REVERT: G 15 LYS cc_start: 0.6979 (ttpt) cc_final: 0.6569 (tppt) REVERT: H 56 MET cc_start: 0.8669 (ttm) cc_final: 0.8005 (tmm) REVERT: W 230 TYR cc_start: 0.8791 (m-80) cc_final: 0.8468 (m-80) REVERT: W 271 ASP cc_start: 0.8715 (m-30) cc_final: 0.8085 (p0) REVERT: W 272 MET cc_start: 0.0888 (tpp) cc_final: 0.0471 (ttt) REVERT: W 282 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8665 (pp20) REVERT: W 437 MET cc_start: 0.7842 (ptm) cc_final: 0.7552 (ppp) REVERT: W 463 ARG cc_start: 0.9080 (ttp-170) cc_final: 0.8772 (ttm170) REVERT: W 560 MET cc_start: 0.9689 (mtp) cc_final: 0.9252 (ttm) REVERT: W 595 LEU cc_start: 0.8949 (tt) cc_final: 0.8674 (mt) REVERT: W 670 GLU cc_start: 0.9247 (mp0) cc_final: 0.8911 (tp30) REVERT: W 794 ASN cc_start: 0.9381 (t0) cc_final: 0.8910 (p0) REVERT: W 1055 MET cc_start: 0.1810 (ptm) cc_final: 0.1571 (ptp) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.3877 time to fit residues: 175.3478 Evaluate side-chains 225 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 98 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 68 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN W 660 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22077 Z= 0.216 Angle : 0.653 7.882 31168 Z= 0.360 Chirality : 0.038 0.181 3508 Planarity : 0.004 0.058 2863 Dihedral : 28.299 173.730 5475 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 3.83 % Favored : 95.83 % Rotamer: Outliers : 0.06 % Allowed : 2.07 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 1778 helix: 0.25 (0.16), residues: 907 sheet: -0.53 (0.47), residues: 113 loop : -1.64 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W1194 HIS 0.007 0.001 HIS W 222 PHE 0.020 0.002 PHE W1121 TYR 0.026 0.002 TYR E 54 ARG 0.008 0.001 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 1.885 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: A 41 TYR cc_start: 0.8395 (m-80) cc_final: 0.7963 (m-10) REVERT: C 71 ARG cc_start: 0.7217 (mmt-90) cc_final: 0.6989 (mpt180) REVERT: D 42 LEU cc_start: 0.9106 (tp) cc_final: 0.8905 (tp) REVERT: D 86 ILE cc_start: 0.8353 (mp) cc_final: 0.8091 (mt) REVERT: E 50 GLU cc_start: 0.9278 (mp0) cc_final: 0.9055 (mp0) REVERT: E 55 GLN cc_start: 0.9396 (mt0) cc_final: 0.8629 (mt0) REVERT: E 110 CYS cc_start: 0.8312 (t) cc_final: 0.7821 (t) REVERT: E 123 ASP cc_start: 0.8808 (m-30) cc_final: 0.8515 (m-30) REVERT: G 15 LYS cc_start: 0.6887 (ttpt) cc_final: 0.6438 (tppt) REVERT: O 1 MET cc_start: 0.3252 (ptt) cc_final: 0.2993 (ptt) REVERT: W 230 TYR cc_start: 0.8767 (m-80) cc_final: 0.8346 (m-80) REVERT: W 282 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8515 (pp20) REVERT: W 386 TRP cc_start: 0.8415 (m100) cc_final: 0.8202 (m100) REVERT: W 463 ARG cc_start: 0.9113 (ttp-170) cc_final: 0.8880 (ttm170) REVERT: W 518 LEU cc_start: 0.8665 (pp) cc_final: 0.8265 (mt) REVERT: W 555 LEU cc_start: 0.8932 (mp) cc_final: 0.8660 (mp) REVERT: W 560 MET cc_start: 0.9702 (mtp) cc_final: 0.9295 (mmm) REVERT: W 614 LEU cc_start: 0.9407 (tp) cc_final: 0.9170 (tt) REVERT: W 670 GLU cc_start: 0.9216 (mp0) cc_final: 0.8901 (tp30) REVERT: W 681 MET cc_start: 0.9260 (tpt) cc_final: 0.9053 (tpt) REVERT: W 794 ASN cc_start: 0.9446 (t0) cc_final: 0.9132 (p0) REVERT: W 1255 ARG cc_start: 0.8764 (mmm160) cc_final: 0.8192 (mtp180) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.3925 time to fit residues: 169.5024 Evaluate side-chains 224 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN ** W 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W1161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 22077 Z= 0.325 Angle : 0.731 11.078 31168 Z= 0.406 Chirality : 0.041 0.236 3508 Planarity : 0.006 0.067 2863 Dihedral : 28.295 172.183 5475 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.50 % Favored : 95.21 % Rotamer: Outliers : 0.13 % Allowed : 2.97 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1778 helix: -0.07 (0.16), residues: 906 sheet: -0.52 (0.43), residues: 134 loop : -1.56 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP W 447 HIS 0.011 0.002 HIS W 806 PHE 0.027 0.003 PHE W1121 TYR 0.023 0.002 TYR D 118 ARG 0.009 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 1.909 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: A 41 TYR cc_start: 0.8667 (m-80) cc_final: 0.8065 (m-80) REVERT: B 36 ARG cc_start: 0.8827 (mtp180) cc_final: 0.8420 (mmp80) REVERT: C 112 GLN cc_start: 0.9361 (pm20) cc_final: 0.9158 (pm20) REVERT: D 86 ILE cc_start: 0.8569 (mp) cc_final: 0.8359 (mt) REVERT: E 110 CYS cc_start: 0.8129 (t) cc_final: 0.7638 (t) REVERT: E 120 MET cc_start: 0.2652 (mmt) cc_final: 0.2208 (mtt) REVERT: E 123 ASP cc_start: 0.8881 (m-30) cc_final: 0.8517 (m-30) REVERT: G 15 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6491 (tppt) REVERT: W 230 TYR cc_start: 0.8796 (m-80) cc_final: 0.8272 (m-80) REVERT: W 315 ASN cc_start: 0.8911 (t0) cc_final: 0.8428 (p0) REVERT: W 463 ARG cc_start: 0.9096 (ttp-170) cc_final: 0.8833 (ttm170) REVERT: W 518 LEU cc_start: 0.8843 (pp) cc_final: 0.8314 (mt) REVERT: W 555 LEU cc_start: 0.9023 (mp) cc_final: 0.8731 (mp) REVERT: W 560 MET cc_start: 0.9708 (mtp) cc_final: 0.9356 (mmm) REVERT: W 670 GLU cc_start: 0.9200 (mp0) cc_final: 0.8856 (tp30) REVERT: W 794 ASN cc_start: 0.9450 (t0) cc_final: 0.9064 (p0) outliers start: 2 outliers final: 0 residues processed: 276 average time/residue: 0.3645 time to fit residues: 149.1052 Evaluate side-chains 200 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 201 optimal weight: 0.4980 chunk 167 optimal weight: 0.4980 chunk 93 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 10.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 46 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN W 557 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 22077 Z= 0.183 Angle : 0.640 8.739 31168 Z= 0.351 Chirality : 0.038 0.221 3508 Planarity : 0.004 0.051 2863 Dihedral : 28.338 177.057 5475 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 0.13 % Allowed : 1.68 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1778 helix: 0.24 (0.17), residues: 905 sheet: -0.17 (0.46), residues: 122 loop : -1.44 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 386 HIS 0.006 0.001 HIS W 222 PHE 0.021 0.002 PHE W 767 TYR 0.020 0.002 TYR A 99 ARG 0.011 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 280 time to evaluate : 1.905 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: A 41 TYR cc_start: 0.8441 (m-80) cc_final: 0.7778 (m-80) REVERT: C 36 LYS cc_start: 0.9669 (mmtm) cc_final: 0.9373 (mttt) REVERT: C 104 GLN cc_start: 0.8816 (mt0) cc_final: 0.8467 (mp10) REVERT: C 112 GLN cc_start: 0.9281 (pm20) cc_final: 0.8983 (tm-30) REVERT: C 116 LEU cc_start: 0.8118 (pp) cc_final: 0.7769 (pt) REVERT: D 42 LEU cc_start: 0.9053 (tp) cc_final: 0.8842 (tp) REVERT: D 86 ILE cc_start: 0.8858 (mp) cc_final: 0.8612 (mt) REVERT: E 55 GLN cc_start: 0.9322 (mt0) cc_final: 0.9017 (mt0) REVERT: E 123 ASP cc_start: 0.8915 (m-30) cc_final: 0.8653 (m-30) REVERT: G 15 LYS cc_start: 0.7006 (ttpt) cc_final: 0.6577 (tppt) REVERT: G 36 LYS cc_start: 0.8844 (pptt) cc_final: 0.8641 (pptt) REVERT: W 315 ASN cc_start: 0.8807 (t0) cc_final: 0.8315 (p0) REVERT: W 463 ARG cc_start: 0.9126 (ttp-170) cc_final: 0.8883 (ttm170) REVERT: W 510 MET cc_start: 0.9292 (tpt) cc_final: 0.8970 (tmm) REVERT: W 518 LEU cc_start: 0.8526 (pp) cc_final: 0.8003 (mt) REVERT: W 555 LEU cc_start: 0.8872 (mp) cc_final: 0.8631 (mp) REVERT: W 560 MET cc_start: 0.9709 (mtp) cc_final: 0.9293 (mmm) REVERT: W 614 LEU cc_start: 0.9399 (tt) cc_final: 0.8835 (mm) REVERT: W 670 GLU cc_start: 0.9180 (mp0) cc_final: 0.8865 (tp30) REVERT: W 681 MET cc_start: 0.9289 (tpt) cc_final: 0.9083 (tpt) REVERT: W 1255 ARG cc_start: 0.8711 (mmm160) cc_final: 0.8110 (mtp180) outliers start: 2 outliers final: 1 residues processed: 281 average time/residue: 0.3503 time to fit residues: 148.8709 Evaluate side-chains 218 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 169 optimal weight: 0.2980 chunk 112 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 334 GLN ** W 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 587 HIS W 660 ASN W 779 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 22077 Z= 0.283 Angle : 0.697 10.194 31168 Z= 0.387 Chirality : 0.040 0.220 3508 Planarity : 0.005 0.052 2863 Dihedral : 28.321 174.656 5475 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.79 % Favored : 94.99 % Rotamer: Outliers : 0.13 % Allowed : 1.42 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1778 helix: 0.04 (0.16), residues: 904 sheet: -0.07 (0.45), residues: 127 loop : -1.50 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP W 447 HIS 0.009 0.001 HIS W 806 PHE 0.024 0.002 PHE A 104 TYR 0.028 0.002 TYR E 99 ARG 0.009 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.900 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: B 36 ARG cc_start: 0.9054 (mtp180) cc_final: 0.8463 (mmp80) REVERT: C 36 LYS cc_start: 0.9619 (mmtm) cc_final: 0.9313 (mttt) REVERT: C 104 GLN cc_start: 0.8756 (mt0) cc_final: 0.8360 (mp10) REVERT: C 112 GLN cc_start: 0.9283 (pm20) cc_final: 0.8993 (tm-30) REVERT: C 116 LEU cc_start: 0.8233 (pp) cc_final: 0.8031 (pt) REVERT: D 86 ILE cc_start: 0.8638 (mp) cc_final: 0.8437 (mt) REVERT: D 98 LEU cc_start: 0.7335 (tp) cc_final: 0.7085 (tp) REVERT: G 15 LYS cc_start: 0.7146 (ttpt) cc_final: 0.6694 (tppt) REVERT: W 315 ASN cc_start: 0.8803 (t0) cc_final: 0.8235 (p0) REVERT: W 396 ASN cc_start: 0.9327 (m-40) cc_final: 0.9035 (m-40) REVERT: W 463 ARG cc_start: 0.9093 (ttp-170) cc_final: 0.8829 (ttm170) REVERT: W 518 LEU cc_start: 0.8836 (pp) cc_final: 0.8134 (mt) REVERT: W 555 LEU cc_start: 0.9036 (mp) cc_final: 0.8775 (mp) REVERT: W 560 MET cc_start: 0.9711 (mtp) cc_final: 0.9310 (mmm) REVERT: W 1255 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8123 (mmm160) outliers start: 2 outliers final: 0 residues processed: 255 average time/residue: 0.3432 time to fit residues: 132.3640 Evaluate side-chains 204 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 557 ASN ** W 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.7182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22077 Z= 0.219 Angle : 0.657 9.516 31168 Z= 0.362 Chirality : 0.038 0.240 3508 Planarity : 0.004 0.051 2863 Dihedral : 28.440 176.943 5475 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.94 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.19), residues: 1778 helix: 0.13 (0.17), residues: 926 sheet: 0.02 (0.45), residues: 125 loop : -1.48 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP W 386 HIS 0.006 0.001 HIS F 75 PHE 0.022 0.002 PHE G 25 TYR 0.023 0.002 TYR A 41 ARG 0.006 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.830 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: B 36 ARG cc_start: 0.8982 (mtp180) cc_final: 0.8350 (mmp80) REVERT: C 36 LYS cc_start: 0.9616 (mmtm) cc_final: 0.9330 (mttt) REVERT: C 104 GLN cc_start: 0.8735 (mt0) cc_final: 0.8347 (mp10) REVERT: C 112 GLN cc_start: 0.9225 (pm20) cc_final: 0.8944 (tm-30) REVERT: C 116 LEU cc_start: 0.8344 (pp) cc_final: 0.8111 (pt) REVERT: D 98 LEU cc_start: 0.7415 (tp) cc_final: 0.7146 (tp) REVERT: G 15 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6696 (tppt) REVERT: O 1 MET cc_start: 0.3240 (ptt) cc_final: 0.2856 (ptt) REVERT: W 315 ASN cc_start: 0.8785 (t0) cc_final: 0.8213 (p0) REVERT: W 334 GLN cc_start: 0.9678 (mp10) cc_final: 0.9476 (mt0) REVERT: W 463 ARG cc_start: 0.9090 (ttp-170) cc_final: 0.8829 (ttm170) REVERT: W 510 MET cc_start: 0.9263 (tpt) cc_final: 0.8986 (mmm) REVERT: W 518 LEU cc_start: 0.8481 (pp) cc_final: 0.7718 (mt) REVERT: W 555 LEU cc_start: 0.9007 (mp) cc_final: 0.8744 (mp) REVERT: W 560 MET cc_start: 0.9770 (mtp) cc_final: 0.9425 (mmm) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3349 time to fit residues: 130.9095 Evaluate side-chains 199 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 175 optimal weight: 0.0980 chunk 186 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 146 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 HIS ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN W 557 ASN W 779 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22077 Z= 0.253 Angle : 0.686 10.504 31168 Z= 0.381 Chirality : 0.039 0.217 3508 Planarity : 0.005 0.073 2863 Dihedral : 28.452 176.459 5475 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.84 % Favored : 94.93 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1778 helix: 0.03 (0.17), residues: 910 sheet: 0.03 (0.44), residues: 128 loop : -1.39 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W 386 HIS 0.007 0.001 HIS A 39 PHE 0.028 0.002 PHE G 25 TYR 0.021 0.002 TYR C 39 ARG 0.009 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.946 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: B 36 ARG cc_start: 0.9050 (mtp180) cc_final: 0.8392 (mmp80) REVERT: C 36 LYS cc_start: 0.9617 (mmtm) cc_final: 0.9319 (mtmt) REVERT: C 104 GLN cc_start: 0.8791 (mt0) cc_final: 0.8508 (mp10) REVERT: C 112 GLN cc_start: 0.9237 (pm20) cc_final: 0.8951 (tm-30) REVERT: C 116 LEU cc_start: 0.8280 (pp) cc_final: 0.8045 (pt) REVERT: D 98 LEU cc_start: 0.7474 (tp) cc_final: 0.7159 (tp) REVERT: G 15 LYS cc_start: 0.7296 (ttpt) cc_final: 0.6805 (mmtp) REVERT: N 1 MET cc_start: 0.7056 (mmm) cc_final: 0.6501 (mmm) REVERT: O 1 MET cc_start: 0.3373 (ptt) cc_final: 0.3148 (ptt) REVERT: W 315 ASN cc_start: 0.8804 (t0) cc_final: 0.8239 (p0) REVERT: W 463 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8748 (ttm170) REVERT: W 560 MET cc_start: 0.9680 (mtp) cc_final: 0.9415 (mmm) REVERT: W 614 LEU cc_start: 0.9531 (tp) cc_final: 0.9270 (tt) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.3596 time to fit residues: 136.9273 Evaluate side-chains 199 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 165 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 101 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 overall best weight: 3.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 424 GLN W 557 ASN ** W 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 779 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22077 Z= 0.298 Angle : 0.725 13.855 31168 Z= 0.402 Chirality : 0.041 0.221 3508 Planarity : 0.005 0.065 2863 Dihedral : 28.730 177.452 5475 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.67 % Favored : 95.10 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.19), residues: 1778 helix: -0.30 (0.16), residues: 913 sheet: -0.13 (0.43), residues: 145 loop : -1.39 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP W 386 HIS 0.013 0.002 HIS W 177 PHE 0.040 0.003 PHE G 25 TYR 0.023 0.002 TYR H 80 ARG 0.016 0.001 ARG W 537 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 2.005 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: B 36 ARG cc_start: 0.9039 (mtp180) cc_final: 0.8417 (mmp80) REVERT: C 36 LYS cc_start: 0.9558 (mmtm) cc_final: 0.9247 (mtmt) REVERT: C 104 GLN cc_start: 0.8854 (mt0) cc_final: 0.8566 (mp10) REVERT: G 15 LYS cc_start: 0.7389 (ttpt) cc_final: 0.6973 (mmtp) REVERT: H 56 MET cc_start: 0.8433 (tpp) cc_final: 0.8139 (tpp) REVERT: H 96 ARG cc_start: 0.9484 (mtm180) cc_final: 0.9017 (tpm170) REVERT: O 1 MET cc_start: 0.3563 (ptt) cc_final: 0.3335 (ptt) REVERT: W 315 ASN cc_start: 0.8849 (t0) cc_final: 0.8213 (p0) REVERT: W 463 ARG cc_start: 0.9011 (ttp-170) cc_final: 0.8744 (ttm170) REVERT: W 560 MET cc_start: 0.9698 (mtp) cc_final: 0.9421 (mmm) REVERT: W 652 MET cc_start: 0.8648 (tpp) cc_final: 0.8364 (tpt) outliers start: 1 outliers final: 0 residues processed: 231 average time/residue: 0.3579 time to fit residues: 125.1208 Evaluate side-chains 184 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 0.0020 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 165 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 145 optimal weight: 0.0770 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 557 ASN ** W 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 779 ASN ** W 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.092620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.057228 restraints weight = 215085.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.059604 restraints weight = 116518.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.060889 restraints weight = 80737.183| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.8197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22077 Z= 0.191 Angle : 0.660 11.687 31168 Z= 0.362 Chirality : 0.038 0.226 3508 Planarity : 0.004 0.057 2863 Dihedral : 28.582 178.241 5475 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1778 helix: 0.13 (0.17), residues: 911 sheet: 0.27 (0.44), residues: 134 loop : -1.29 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP W1194 HIS 0.012 0.001 HIS W 813 PHE 0.030 0.002 PHE H 62 TYR 0.020 0.002 TYR F 88 ARG 0.018 0.001 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4474.53 seconds wall clock time: 81 minutes 55.60 seconds (4915.60 seconds total)