Starting phenix.real_space_refine on Sat Jul 4 19:51:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.cif" model { file = "/net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8grm_34207/07_2026/8grm_34207.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10341 atoms to isotropic. 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 4 6.06 5 P 289 5.49 5 S 38 5.16 5 C 8805 2.51 5 N 2856 2.21 5 O 3423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15415 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 753 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 92} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} 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: "P" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1169 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 130} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6391 SG CYS M 39 41.225 89.870 60.488 1.00 36.05 S ATOM 6413 SG CYS M 42 37.771 87.794 58.649 1.00 38.01 S ATOM 6350 SG CYS M 34 45.303 77.408 52.391 1.00 28.86 S ATOM 6508 SG CYS M 53 42.351 79.379 51.567 1.00 36.39 S ATOM 6529 SG CYS M 56 44.443 77.373 48.319 1.00 36.87 S ATOM 7206 SG CYS N 51 67.205 82.068 57.667 1.00 35.68 S ATOM 7227 SG CYS N 54 70.266 83.831 55.992 1.00 38.12 S ATOM 7375 SG CYS N 72 66.888 82.641 53.908 1.00 30.84 S ATOM 7394 SG CYS N 75 69.602 79.730 55.415 1.00 30.00 S ATOM 7329 SG CYS N 67 56.883 74.476 65.266 1.00 24.81 S ATOM 7483 SG CYS N 87 60.911 75.821 64.242 1.00 27.17 S ATOM 7503 SG CYS N 90 58.841 77.321 67.718 1.00 32.49 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY O 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.25 residue: pdb=" N GLY O 76 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY O 76 " occ=0.25 Time building chain proxies: 3.16, per 1000 atoms: 0.20 Number of scatterers: 15415 At special positions: 0 Unit cell: (117.066, 117.066, 123.51, 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 4 29.99 S 38 16.00 P 289 15.00 O 3423 8.00 N 2856 7.00 C 8805 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: 1.18 Conformation dependent library (CDL) restraints added in 486.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 42 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " Number of angles added : 12 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 52.6% alpha, 5.7% beta 128 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.737A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.566A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.757A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.702A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.489A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.534A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.637A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.658A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.511A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.718A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.584A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.511A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 4.048A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 74 removed outlier: 3.770A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.667A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.489A pdb=" N GLU G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.534A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.539A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.762A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 removed outlier: 3.788A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.807A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 47 removed outlier: 4.626A pdb=" N ARG M 45 " --> pdb=" O THR M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 83 removed outlier: 3.782A pdb=" N GLN M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 81 " --> pdb=" O ASP M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 99 removed outlier: 3.636A pdb=" N MET M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 45 through 50 removed outlier: 3.787A pdb=" N LEU N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET N 50 " --> pdb=" O HIS N 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 50' Processing helix chain 'N' and resid 73 through 82 removed outlier: 3.555A pdb=" N ILE N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 removed outlier: 4.536A pdb=" N LEU N 109 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE N 110 " --> pdb=" O PHE N 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.610A pdb=" N ILE O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.736A pdb=" N HIS P 7 " --> pdb=" O LEU P 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS P 8 " --> pdb=" O LYS P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.961A pdb=" N LEU P 104 " --> pdb=" O SER P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 128 removed outlier: 4.033A pdb=" N TYR P 127 " --> pdb=" O ILE P 123 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 123 through 128' Processing helix chain 'P' and resid 133 through 141 removed outlier: 4.058A pdb=" N ARG P 139 " --> pdb=" O ASN P 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.885A 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 96 through 98 removed outlier: 6.400A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.135A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.196A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 7 through 8 Processing sheet with id=AB3, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AB4, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'O' and resid 13 through 16 removed outlier: 3.584A pdb=" N LEU O 15 " --> pdb=" O ILE O 3 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 41 through 42 removed outlier: 3.603A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 44 through 45 Processing sheet with id=AB8, first strand: chain 'P' and resid 21 through 25 removed outlier: 3.501A pdb=" N SER P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3139 1.33 - 1.45: 4865 1.45 - 1.57: 7649 1.57 - 1.69: 576 1.69 - 1.81: 57 Bond restraints: 16286 Sorted by residual: bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.334 1.376 -0.043 8.40e-03 1.42e+04 2.58e+01 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.03e+01 bond pdb=" C1' DC I -71 " pdb=" N1 DC I -71 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.68e+01 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.367 0.146 3.90e-02 6.57e+02 1.40e+01 ... (remaining 16281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 22485 2.42 - 4.85: 659 4.85 - 7.27: 77 7.27 - 9.69: 12 9.69 - 12.12: 7 Bond angle restraints: 23240 Sorted by residual: angle pdb=" C LYS C 15 " pdb=" N THR C 16 " pdb=" CA THR C 16 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 angle pdb=" C LYS G 15 " pdb=" N THR G 16 " pdb=" CA THR G 16 " ideal model delta sigma weight residual 121.54 133.09 -11.55 1.91e+00 2.74e-01 3.66e+01 angle pdb=" CB ARG M 70 " pdb=" CG ARG M 70 " pdb=" CD ARG M 70 " ideal model delta sigma weight residual 111.30 122.60 -11.30 2.30e+00 1.89e-01 2.41e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 35 " pdb=" C4 DT J 35 " pdb=" O4 DT J 35 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 23235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 7860 35.42 - 70.83: 1255 70.83 - 106.25: 1 106.25 - 141.67: 0 141.67 - 177.09: 2 Dihedral angle restraints: 9118 sinusoidal: 5639 harmonic: 3479 Sorted by residual: dihedral pdb=" CA GLY P 48 " pdb=" C GLY P 48 " pdb=" N VAL P 49 " pdb=" CA VAL P 49 " ideal model delta harmonic sigma weight residual 180.00 -134.44 -45.56 0 5.00e+00 4.00e-02 8.30e+01 dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N ARG B 40 " pdb=" CA ARG B 40 " ideal model delta harmonic sigma weight residual 180.00 149.13 30.87 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA ILE H 69 " pdb=" C ILE H 69 " pdb=" N PHE H 70 " pdb=" CA PHE H 70 " ideal model delta harmonic sigma weight residual 180.00 149.72 30.28 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 9115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2536 0.123 - 0.246: 101 0.246 - 0.368: 6 0.368 - 0.491: 0 0.491 - 0.614: 1 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE E 62 " pdb=" CA ILE E 62 " pdb=" CG1 ILE E 62 " pdb=" CG2 ILE E 62 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB THR C 16 " pdb=" CA THR C 16 " pdb=" OG1 THR C 16 " pdb=" CG2 THR C 16 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2641 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " -0.002 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR F 98 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY P 48 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C GLY P 48 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY P 48 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL P 49 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 13 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C LYS C 13 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS C 13 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA C 14 " -0.014 2.00e-02 2.50e+03 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3654 2.81 - 3.33: 11961 3.33 - 3.86: 27397 3.86 - 4.38: 35337 4.38 - 4.90: 50424 Nonbonded interactions: 128773 Sorted by model distance: nonbonded pdb=" OG SER P 22 " pdb=" OG1 THR P 36 " model vdw 2.289 3.040 nonbonded pdb=" O ILE N 53 " pdb=" NH1 ARG P 5 " model vdw 2.317 3.120 nonbonded pdb=" NH1 ARG D 31 " pdb=" OP1 DG J 51 " model vdw 2.333 3.120 nonbonded pdb=" OH TYR M 80 " pdb=" OE1 GLU M 90 " model vdw 2.338 3.040 nonbonded pdb=" NH2 ARG G 29 " pdb=" OP1 DC I 49 " model vdw 2.349 3.120 ... (remaining 128768 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = chain 'H' } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.190 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.013 0.817 16300 Z= 0.712 Angle : 1.036 15.625 23252 Z= 0.719 Chirality : 0.063 0.614 2644 Planarity : 0.006 0.057 1942 Dihedral : 23.197 177.086 6866 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.29 % Allowed : 1.27 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -5.38 (0.17), residues: 1171 helix: -4.45 (0.09), residues: 631 sheet: -1.78 (0.72), residues: 53 loop : -2.25 (0.23), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG P 5 TYR 0.048 0.004 TYR F 98 PHE 0.041 0.005 PHE F 61 TRP 0.027 0.003 TRP P 33 HIS 0.011 0.003 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.66 (16286) covalent geometry : angle 1.01842 / 0.72 (23240) hydrogen bonds : bond 0.29765 / 19.89 ( 725) hydrogen bonds : angle 10.28662 / 7.30 ( 1833) metal coordination : bond 0.31899 / 22.63 ( 14) metal coordination : angle 8.48797 / 4.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 367 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 106 ASP cc_start: 0.8163 (m-30) cc_final: 0.7757 (m-30) REVERT: D 63 ASN cc_start: 0.7781 (m-40) cc_final: 0.7540 (m110) REVERT: E 58 THR cc_start: 0.8968 (p) cc_final: 0.8754 (p) REVERT: N 22 TYR cc_start: 0.7669 (t80) cc_final: 0.7377 (t80) outliers start: 3 outliers final: 0 residues processed: 369 average time/residue: 0.2131 time to fit residues: 100.7408 Evaluate side-chains 266 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 82 HIS C 112 GLN D 47 GLN D 82 HIS E 108 ASN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS G 94 ASN M 76 GLN O 25 ASN O 31 GLN P 79 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098286 restraints weight = 22365.966| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.82 r_work: 0.2991 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16300 Z= 0.218 Angle : 0.820 7.921 23252 Z= 0.447 Chirality : 0.054 0.340 2644 Planarity : 0.006 0.058 1942 Dihedral : 28.894 176.076 4475 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.33 % Allowed : 10.76 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.30 (0.20), residues: 1171 helix: -2.31 (0.16), residues: 648 sheet: -0.99 (0.66), residues: 68 loop : -1.95 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 45 TYR 0.019 0.002 TYR E 99 PHE 0.029 0.003 PHE P 50 TRP 0.007 0.001 TRP P 33 HIS 0.013 0.002 HIS P 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (16286) covalent geometry : angle 0.81820 / 0.45 (23240) hydrogen bonds : bond 0.06501 / 4.33 ( 725) hydrogen bonds : angle 4.03254 / 2.84 ( 1833) metal coordination : bond 0.01802 / 1.31 ( 14) metal coordination : angle 2.21558 / 1.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 288 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8200 (mt-10) REVERT: D 108 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8523 (mttp) REVERT: E 58 THR cc_start: 0.9324 (p) cc_final: 0.9102 (p) REVERT: E 129 ARG cc_start: 0.8905 (ttm170) cc_final: 0.8544 (tpt90) REVERT: M 11 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: M 43 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8534 (tp) REVERT: M 64 ARG cc_start: 0.9433 (OUTLIER) cc_final: 0.9211 (mtp180) REVERT: M 70 ARG cc_start: 0.8652 (mtt-85) cc_final: 0.8408 (mtm-85) REVERT: O 1 MET cc_start: 0.6622 (pmm) cc_final: 0.6312 (pmm) REVERT: P 55 HIS cc_start: 0.7554 (m90) cc_final: 0.7268 (m-70) REVERT: P 105 SER cc_start: 0.9069 (t) cc_final: 0.8588 (p) outliers start: 34 outliers final: 21 residues processed: 303 average time/residue: 0.1627 time to fit residues: 66.7330 Evaluate side-chains 285 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 11 GLU Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 64 ARG Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 107 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN B 27 GLN D 47 GLN D 63 ASN D 82 HIS F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 84 ASN M 15 HIS P 32 HIS P 79 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096439 restraints weight = 22330.991| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.82 r_work: 0.2965 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16300 Z= 0.173 Angle : 0.683 7.653 23252 Z= 0.384 Chirality : 0.049 0.282 2644 Planarity : 0.005 0.042 1942 Dihedral : 29.196 172.843 4475 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.23 % Allowed : 11.55 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.09 (0.22), residues: 1171 helix: -1.08 (0.19), residues: 657 sheet: -0.95 (0.72), residues: 58 loop : -1.74 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 53 TYR 0.030 0.002 TYR C 57 PHE 0.031 0.002 PHE P 50 TRP 0.009 0.001 TRP P 33 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (16286) covalent geometry : angle 0.68162 / 0.38 (23240) hydrogen bonds : bond 0.05500 / 3.63 ( 725) hydrogen bonds : angle 3.51059 / 2.46 ( 1833) metal coordination : bond 0.02277 / 1.75 ( 14) metal coordination : angle 1.96884 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 17 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8256 (mtm180) REVERT: D 63 ASN cc_start: 0.9008 (m-40) cc_final: 0.8733 (m110) REVERT: E 58 THR cc_start: 0.9474 (p) cc_final: 0.9217 (p) REVERT: E 129 ARG cc_start: 0.8926 (ttm170) cc_final: 0.8556 (tpt90) REVERT: G 95 LYS cc_start: 0.9144 (mtpp) cc_final: 0.8897 (mtpp) REVERT: M 11 GLU cc_start: 0.7999 (mp0) cc_final: 0.7581 (pm20) REVERT: M 64 ARG cc_start: 0.9426 (OUTLIER) cc_final: 0.9216 (mtp180) REVERT: M 92 LYS cc_start: 0.8677 (ttmm) cc_final: 0.8419 (ttmt) REVERT: N 103 ASP cc_start: 0.7782 (t0) cc_final: 0.7461 (t0) REVERT: P 59 ASP cc_start: 0.8794 (p0) cc_final: 0.8591 (p0) REVERT: P 105 SER cc_start: 0.9038 (t) cc_final: 0.8513 (p) outliers start: 33 outliers final: 19 residues processed: 301 average time/residue: 0.1529 time to fit residues: 62.2220 Evaluate side-chains 296 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 9 ILE Chi-restraints excluded: chain M residue 64 ARG Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN B 75 HIS D 47 GLN D 82 HIS D 84 ASN E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096597 restraints weight = 22169.276| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.81 r_work: 0.2965 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16300 Z= 0.147 Angle : 0.643 9.209 23252 Z= 0.363 Chirality : 0.047 0.282 2644 Planarity : 0.004 0.043 1942 Dihedral : 29.164 171.321 4475 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.62 % Allowed : 12.72 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.34 (0.24), residues: 1171 helix: -0.38 (0.20), residues: 658 sheet: -0.86 (0.71), residues: 58 loop : -1.53 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 53 TYR 0.027 0.002 TYR N 22 PHE 0.032 0.002 PHE P 50 TRP 0.009 0.001 TRP P 33 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (16286) covalent geometry : angle 0.64122 / 0.36 (23240) hydrogen bonds : bond 0.04709 / 3.13 ( 725) hydrogen bonds : angle 3.26127 / 2.28 ( 1833) metal coordination : bond 0.01816 / 1.41 ( 14) metal coordination : angle 2.01572 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9128 (mttm) cc_final: 0.8865 (mtpt) REVERT: C 64 GLU cc_start: 0.8214 (tt0) cc_final: 0.7999 (tt0) REVERT: D 36 SER cc_start: 0.9384 (p) cc_final: 0.9167 (p) REVERT: D 63 ASN cc_start: 0.8921 (m-40) cc_final: 0.8672 (m110) REVERT: E 58 THR cc_start: 0.9506 (p) cc_final: 0.9262 (p) REVERT: E 129 ARG cc_start: 0.8909 (ttm170) cc_final: 0.8573 (tpt90) REVERT: F 44 LYS cc_start: 0.9041 (mtpt) cc_final: 0.8718 (mtpt) REVERT: G 61 GLU cc_start: 0.9062 (tp30) cc_final: 0.8708 (tp30) REVERT: G 84 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8870 (mm-40) REVERT: H 105 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: M 11 GLU cc_start: 0.8085 (mp0) cc_final: 0.7656 (pm20) REVERT: M 45 ARG cc_start: 0.9279 (tpp80) cc_final: 0.8996 (ttm-80) REVERT: M 92 LYS cc_start: 0.8723 (ttmm) cc_final: 0.8441 (ttmt) REVERT: N 74 ASP cc_start: 0.8910 (m-30) cc_final: 0.8682 (p0) REVERT: P 30 MET cc_start: 0.8081 (mmm) cc_final: 0.7847 (mmm) REVERT: P 105 SER cc_start: 0.8986 (t) cc_final: 0.8415 (p) REVERT: P 147 MET cc_start: 0.6358 (tpt) cc_final: 0.6122 (tpt) outliers start: 37 outliers final: 21 residues processed: 295 average time/residue: 0.1649 time to fit residues: 65.4780 Evaluate side-chains 287 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 95 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 27 GLN D 47 GLN D 82 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.094421 restraints weight = 22252.207| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.82 r_work: 0.2928 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16300 Z= 0.161 Angle : 0.630 7.813 23252 Z= 0.356 Chirality : 0.047 0.294 2644 Planarity : 0.004 0.041 1942 Dihedral : 29.222 169.176 4475 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.52 % Allowed : 12.82 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.87 (0.24), residues: 1171 helix: 0.10 (0.21), residues: 660 sheet: -0.63 (0.73), residues: 58 loop : -1.48 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.016 0.002 TYR C 57 PHE 0.032 0.002 PHE P 50 TRP 0.006 0.001 TRP P 141 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (16286) covalent geometry : angle 0.62824 / 0.36 (23240) hydrogen bonds : bond 0.04680 / 3.11 ( 725) hydrogen bonds : angle 3.17529 / 2.23 ( 1833) metal coordination : bond 0.01811 / 1.38 ( 14) metal coordination : angle 1.94123 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 270 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8837 (tt0) cc_final: 0.8380 (tt0) REVERT: B 25 ASN cc_start: 0.8317 (m-40) cc_final: 0.7908 (m110) REVERT: C 64 GLU cc_start: 0.8230 (tt0) cc_final: 0.8008 (tt0) REVERT: D 108 LYS cc_start: 0.8990 (mtpp) cc_final: 0.8454 (mttp) REVERT: E 58 THR cc_start: 0.9546 (p) cc_final: 0.9286 (p) REVERT: E 129 ARG cc_start: 0.8894 (ttm170) cc_final: 0.8588 (tpt90) REVERT: G 61 GLU cc_start: 0.9072 (tp30) cc_final: 0.8715 (tp30) REVERT: G 95 LYS cc_start: 0.9291 (mtpp) cc_final: 0.8696 (mtmm) REVERT: H 105 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: H 113 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7965 (mt-10) REVERT: M 11 GLU cc_start: 0.8009 (mp0) cc_final: 0.7637 (pm20) REVERT: M 45 ARG cc_start: 0.9236 (tpp80) cc_final: 0.9000 (ttm-80) REVERT: M 51 LYS cc_start: 0.8597 (mttt) cc_final: 0.8384 (mptt) REVERT: M 92 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8463 (ttmt) REVERT: N 16 THR cc_start: 0.8134 (t) cc_final: 0.7172 (p) REVERT: N 25 GLN cc_start: 0.8257 (pp30) cc_final: 0.8045 (pp30) REVERT: N 74 ASP cc_start: 0.8932 (m-30) cc_final: 0.8691 (p0) REVERT: P 30 MET cc_start: 0.8069 (mmm) cc_final: 0.7841 (mmm) REVERT: P 147 MET cc_start: 0.6378 (tpt) cc_final: 0.6151 (tpt) outliers start: 36 outliers final: 20 residues processed: 290 average time/residue: 0.1588 time to fit residues: 61.8440 Evaluate side-chains 284 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN D 63 ASN D 82 HIS E 76 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.092513 restraints weight = 22062.567| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.79 r_work: 0.2885 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16300 Z= 0.225 Angle : 0.682 9.388 23252 Z= 0.375 Chirality : 0.049 0.341 2644 Planarity : 0.005 0.047 1942 Dihedral : 29.429 168.401 4475 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.33 % Allowed : 14.29 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.24), residues: 1171 helix: 0.38 (0.21), residues: 659 sheet: -0.90 (0.67), residues: 68 loop : -1.37 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 53 TYR 0.021 0.002 TYR P 134 PHE 0.033 0.002 PHE P 50 TRP 0.008 0.001 TRP P 141 HIS 0.008 0.002 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 (16286) covalent geometry : angle 0.68079 / 0.38 (23240) hydrogen bonds : bond 0.04971 / 3.31 ( 725) hydrogen bonds : angle 3.21281 / 2.26 ( 1833) metal coordination : bond 0.01632 / 1.21 ( 14) metal coordination : angle 1.94308 / 1.21 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8494 (m-40) cc_final: 0.8252 (m110) REVERT: C 24 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7817 (mt0) REVERT: C 110 ASN cc_start: 0.8212 (m-40) cc_final: 0.7832 (p0) REVERT: D 108 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8541 (mttp) REVERT: E 58 THR cc_start: 0.9572 (p) cc_final: 0.9316 (p) REVERT: E 129 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8619 (tpt90) REVERT: F 44 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8763 (mtpt) REVERT: M 11 GLU cc_start: 0.8184 (mp0) cc_final: 0.7853 (pm20) REVERT: M 92 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8470 (ttmt) REVERT: N 25 GLN cc_start: 0.8463 (pp30) cc_final: 0.8259 (pp30) REVERT: P 127 TYR cc_start: 0.4952 (m-80) cc_final: 0.4513 (m-80) outliers start: 34 outliers final: 24 residues processed: 288 average time/residue: 0.1813 time to fit residues: 69.8927 Evaluate side-chains 292 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 267 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 84 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 63 ASN D 82 HIS E 76 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094822 restraints weight = 22012.998| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.79 r_work: 0.2933 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 16300 Z= 0.127 Angle : 0.614 7.618 23252 Z= 0.349 Chirality : 0.045 0.283 2644 Planarity : 0.004 0.036 1942 Dihedral : 29.231 169.611 4475 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.74 % Allowed : 14.58 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.20 (0.25), residues: 1171 helix: 0.79 (0.21), residues: 647 sheet: -0.96 (0.67), residues: 68 loop : -1.29 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 53 TYR 0.017 0.001 TYR P 134 PHE 0.048 0.002 PHE P 50 TRP 0.005 0.001 TRP N 17 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (16286) covalent geometry : angle 0.61249 / 0.35 (23240) hydrogen bonds : bond 0.04366 / 2.93 ( 725) hydrogen bonds : angle 3.07896 / 2.16 ( 1833) metal coordination : bond 0.01843 / 1.43 ( 14) metal coordination : angle 2.20396 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8799 (mm-40) REVERT: B 25 ASN cc_start: 0.8498 (m-40) cc_final: 0.8115 (m110) REVERT: B 59 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8561 (tptt) REVERT: C 110 ASN cc_start: 0.8163 (m-40) cc_final: 0.7782 (p0) REVERT: E 53 ARG cc_start: 0.8863 (ttm-80) cc_final: 0.8493 (ttm110) REVERT: E 58 THR cc_start: 0.9561 (p) cc_final: 0.9299 (p) REVERT: E 129 ARG cc_start: 0.8918 (ttm170) cc_final: 0.8633 (tpt90) REVERT: F 44 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8714 (mtpt) REVERT: G 61 GLU cc_start: 0.9225 (tp30) cc_final: 0.8991 (tp30) REVERT: G 95 LYS cc_start: 0.9294 (mtpp) cc_final: 0.8890 (mtmm) REVERT: H 113 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7796 (mt-10) REVERT: M 11 GLU cc_start: 0.8195 (mp0) cc_final: 0.7861 (pm20) REVERT: M 45 ARG cc_start: 0.9258 (tpp80) cc_final: 0.9032 (ttm-80) REVERT: M 92 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8406 (ttmm) REVERT: N 25 GLN cc_start: 0.8508 (pp30) cc_final: 0.8280 (pp30) REVERT: N 26 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.8360 (ttp80) REVERT: N 74 ASP cc_start: 0.8911 (m-30) cc_final: 0.8683 (p0) REVERT: P 30 MET cc_start: 0.8144 (mmt) cc_final: 0.7736 (mmm) REVERT: P 106 ILE cc_start: 0.9359 (mt) cc_final: 0.9134 (pt) REVERT: P 127 TYR cc_start: 0.4950 (m-80) cc_final: 0.4516 (m-80) REVERT: P 147 MET cc_start: 0.7111 (tpp) cc_final: 0.6457 (tpt) outliers start: 28 outliers final: 17 residues processed: 284 average time/residue: 0.1623 time to fit residues: 62.0955 Evaluate side-chains 282 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 0.9980 chunk 17 optimal weight: 0.0000 chunk 139 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095940 restraints weight = 22193.271| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.77 r_work: 0.2945 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16300 Z= 0.131 Angle : 0.601 9.375 23252 Z= 0.344 Chirality : 0.045 0.297 2644 Planarity : 0.004 0.050 1942 Dihedral : 29.078 171.058 4475 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.35 % Allowed : 15.36 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.02 (0.25), residues: 1171 helix: 0.97 (0.21), residues: 648 sheet: -0.91 (0.67), residues: 68 loop : -1.20 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 129 TYR 0.019 0.001 TYR N 22 PHE 0.041 0.002 PHE P 50 TRP 0.003 0.001 TRP N 17 HIS 0.008 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (16286) covalent geometry : angle 0.59952 / 0.34 (23240) hydrogen bonds : bond 0.04247 / 2.85 ( 725) hydrogen bonds : angle 3.01503 / 2.12 ( 1833) metal coordination : bond 0.01900 / 1.48 ( 14) metal coordination : angle 2.12515 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8811 (mm-40) REVERT: B 25 ASN cc_start: 0.8471 (m-40) cc_final: 0.8190 (m110) REVERT: B 59 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8744 (tttp) REVERT: C 24 GLN cc_start: 0.8218 (mt0) cc_final: 0.7929 (mt0) REVERT: C 110 ASN cc_start: 0.8136 (m-40) cc_final: 0.7793 (p0) REVERT: D 47 GLN cc_start: 0.9000 (mt0) cc_final: 0.8734 (mt0) REVERT: D 113 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8424 (mm-30) REVERT: E 53 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8427 (ttm110) REVERT: E 58 THR cc_start: 0.9570 (p) cc_final: 0.9304 (p) REVERT: E 129 ARG cc_start: 0.8893 (ttm170) cc_final: 0.8668 (tpt90) REVERT: F 25 ASN cc_start: 0.8691 (m110) cc_final: 0.8088 (m110) REVERT: G 61 GLU cc_start: 0.9179 (tp30) cc_final: 0.8917 (tp30) REVERT: H 113 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7920 (mt-10) REVERT: M 11 GLU cc_start: 0.8222 (mp0) cc_final: 0.7931 (pm20) REVERT: M 45 ARG cc_start: 0.9263 (tpp80) cc_final: 0.9052 (ttm-80) REVERT: M 92 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8427 (ttmm) REVERT: N 19 LEU cc_start: 0.8385 (mt) cc_final: 0.8118 (mt) REVERT: N 26 ARG cc_start: 0.8575 (ttt-90) cc_final: 0.8330 (ttp80) REVERT: P 106 ILE cc_start: 0.9344 (mt) cc_final: 0.9139 (pt) REVERT: P 127 TYR cc_start: 0.4868 (m-80) cc_final: 0.4459 (m-80) REVERT: P 147 MET cc_start: 0.7084 (tpp) cc_final: 0.6592 (tpt) outliers start: 24 outliers final: 19 residues processed: 278 average time/residue: 0.1697 time to fit residues: 63.0611 Evaluate side-chains 285 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 10.9990 chunk 11 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 79 optimal weight: 0.4980 chunk 123 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN M 76 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095994 restraints weight = 22039.794| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.80 r_work: 0.2957 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 16300 Z= 0.126 Angle : 0.592 9.629 23252 Z= 0.339 Chirality : 0.044 0.293 2644 Planarity : 0.004 0.044 1942 Dihedral : 29.014 173.095 4475 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.15 % Allowed : 15.66 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1171 helix: 1.10 (0.21), residues: 649 sheet: -0.75 (0.68), residues: 68 loop : -1.16 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 129 TYR 0.028 0.001 TYR N 22 PHE 0.036 0.002 PHE P 50 TRP 0.004 0.001 TRP N 17 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.13 (16286) covalent geometry : angle 0.58988 / 0.34 (23240) hydrogen bonds : bond 0.04158 / 2.80 ( 725) hydrogen bonds : angle 2.97033 / 2.08 ( 1833) metal coordination : bond 0.01939 / 1.52 ( 14) metal coordination : angle 2.12580 / 1.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8781 (mm-40) REVERT: B 25 ASN cc_start: 0.8545 (m-40) cc_final: 0.8317 (m110) REVERT: B 59 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8723 (tttp) REVERT: C 110 ASN cc_start: 0.8098 (m-40) cc_final: 0.7780 (p0) REVERT: D 113 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8421 (mm-30) REVERT: E 58 THR cc_start: 0.9548 (p) cc_final: 0.9283 (p) REVERT: E 129 ARG cc_start: 0.8927 (ttm170) cc_final: 0.8631 (tpt90) REVERT: F 25 ASN cc_start: 0.8685 (m110) cc_final: 0.8020 (m110) REVERT: G 61 GLU cc_start: 0.9220 (tp30) cc_final: 0.8975 (tp30) REVERT: H 113 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7836 (mt-10) REVERT: M 11 GLU cc_start: 0.8219 (mp0) cc_final: 0.7910 (pm20) REVERT: M 45 ARG cc_start: 0.9243 (tpp80) cc_final: 0.9027 (ttm-80) REVERT: M 92 LYS cc_start: 0.8659 (ttmm) cc_final: 0.8414 (ttmm) REVERT: N 19 LEU cc_start: 0.8256 (mt) cc_final: 0.7985 (mt) REVERT: N 26 ARG cc_start: 0.8573 (ttt-90) cc_final: 0.8334 (ttp80) REVERT: N 57 MET cc_start: 0.8908 (tpp) cc_final: 0.8436 (tpp) REVERT: P 55 HIS cc_start: 0.7561 (m-70) cc_final: 0.6862 (t70) REVERT: P 106 ILE cc_start: 0.9363 (mt) cc_final: 0.9132 (pt) REVERT: P 127 TYR cc_start: 0.4885 (m-80) cc_final: 0.4409 (m-80) REVERT: P 147 MET cc_start: 0.7194 (tpp) cc_final: 0.6729 (tpt) outliers start: 22 outliers final: 18 residues processed: 278 average time/residue: 0.1710 time to fit residues: 63.2100 Evaluate side-chains 286 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 266 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 106 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095900 restraints weight = 22098.111| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.80 r_work: 0.2958 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 16300 Z= 0.128 Angle : 0.589 9.556 23252 Z= 0.338 Chirality : 0.044 0.283 2644 Planarity : 0.004 0.043 1942 Dihedral : 28.983 175.774 4475 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.96 % Allowed : 15.66 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % 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 (0.25), residues: 1171 helix: 1.22 (0.22), residues: 647 sheet: -0.73 (0.67), residues: 68 loop : -1.12 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 129 TYR 0.014 0.001 TYR C 57 PHE 0.040 0.002 PHE P 50 TRP 0.003 0.001 TRP N 17 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (16286) covalent geometry : angle 0.58749 / 0.34 (23240) hydrogen bonds : bond 0.04153 / 2.80 ( 725) hydrogen bonds : angle 2.93291 / 2.06 ( 1833) metal coordination : bond 0.01928 / 1.52 ( 14) metal coordination : angle 2.12804 / 1.30 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8768 (mm-40) REVERT: B 25 ASN cc_start: 0.8588 (m-40) cc_final: 0.8350 (m110) REVERT: B 59 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8729 (tttp) REVERT: C 110 ASN cc_start: 0.8096 (m-40) cc_final: 0.7803 (p0) REVERT: D 47 GLN cc_start: 0.9061 (mt0) cc_final: 0.8707 (mt0) REVERT: E 129 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8630 (tpt90) REVERT: F 25 ASN cc_start: 0.8656 (m110) cc_final: 0.8099 (m110) REVERT: G 61 GLU cc_start: 0.9218 (tp30) cc_final: 0.8984 (tp30) REVERT: H 113 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7892 (mt-10) REVERT: M 11 GLU cc_start: 0.8281 (mp0) cc_final: 0.8022 (pm20) REVERT: M 45 ARG cc_start: 0.9241 (tpp80) cc_final: 0.9021 (ttm-80) REVERT: M 92 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8398 (ttmm) REVERT: N 19 LEU cc_start: 0.8224 (mt) cc_final: 0.7979 (mt) REVERT: N 22 TYR cc_start: 0.8270 (t80) cc_final: 0.8055 (t80) REVERT: N 26 ARG cc_start: 0.8592 (ttt-90) cc_final: 0.8311 (ttp80) REVERT: N 57 MET cc_start: 0.8910 (tpp) cc_final: 0.8426 (tpp) REVERT: P 32 HIS cc_start: 0.7870 (m-70) cc_final: 0.7511 (m-70) REVERT: P 55 HIS cc_start: 0.7707 (m-70) cc_final: 0.6741 (t70) REVERT: P 106 ILE cc_start: 0.9361 (mt) cc_final: 0.9132 (pt) REVERT: P 127 TYR cc_start: 0.4897 (m-80) cc_final: 0.4409 (m-80) REVERT: P 147 MET cc_start: 0.7218 (tpp) cc_final: 0.6784 (tpt) outliers start: 20 outliers final: 16 residues processed: 276 average time/residue: 0.1746 time to fit residues: 64.1283 Evaluate side-chains 286 residues out of total 1031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 97 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.0020 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096107 restraints weight = 21972.851| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.79 r_work: 0.2966 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 16300 Z= 0.122 Angle : 0.582 8.634 23252 Z= 0.335 Chirality : 0.043 0.282 2644 Planarity : 0.004 0.040 1942 Dihedral : 28.960 177.247 4475 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.66 % Allowed : 16.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % 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: 0.39 (0.26), residues: 1171 helix: 1.30 (0.22), residues: 646 sheet: -0.67 (0.68), residues: 68 loop : -1.09 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 129 TYR 0.016 0.001 TYR M 46 PHE 0.040 0.002 PHE P 50 TRP 0.004 0.001 TRP P 33 HIS 0.007 0.001 HIS P 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.12 (16286) covalent geometry : angle 0.57991 / 0.33 (23240) hydrogen bonds : bond 0.04100 / 2.77 ( 725) hydrogen bonds : angle 2.91520 / 2.05 ( 1833) metal coordination : bond 0.02043 / 1.61 ( 14) metal coordination : angle 2.19914 / 1.36 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4854.34 seconds wall clock time: 83 minutes 10.22 seconds (4990.22 seconds total)