Starting phenix.real_space_refine (version: dev) on Fri Feb 24 05:53:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/02_2023/6ziq_11228_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/02_2023/6ziq_11228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/02_2023/6ziq_11228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/02_2023/6ziq_11228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/02_2023/6ziq_11228_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/02_2023/6ziq_11228_trim_updated.pdb" } resolution = 4.33 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 ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "8 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 203": "OE1" <-> "OE2" Residue "a PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 35": "OE1" <-> "OE2" Residue "d GLU 46": "OE1" <-> "OE2" Residue "d TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d ASP 96": "OD1" <-> "OD2" Residue "d GLU 102": "OE1" <-> "OE2" Residue "d PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 81": "OE1" <-> "OE2" Residue "f ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 58": "OE1" <-> "OE2" Residue "O PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 7": "OE1" <-> "OE2" Residue "b ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 106": "OD1" <-> "OD2" Residue "b ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 171": "OE1" <-> "OE2" Residue "h GLU 17": "OE1" <-> "OE2" Residue "h PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ASP 65": "OD1" <-> "OD2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S ASP 155": "OD1" <-> "OD2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 188": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 79": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 22255 Number of models: 1 Model: "" Number of chains: 15 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "d" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2549 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 143} Chain: "e" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 687 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "M" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 975 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 688 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3456 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "S" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2048 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1333 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 10.76, per 1000 atoms: 0.48 Number of scatterers: 22255 At special positions: 0 Unit cell: (103.752, 125.76, 246.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1948 8.00 N 1803 7.00 C 7133 6.00 H 11316 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 3 sheets defined 68.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain '8' and resid 2 through 4 No H-bonds generated for 'chain '8' and resid 2 through 4' Processing helix chain '8' and resid 6 through 20 removed outlier: 4.332A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU 8 18 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 29 Processing helix chain 'a' and resid 6 through 9 Processing helix chain 'a' and resid 19 through 30 removed outlier: 3.921A pdb=" N PHE a 26 " --> pdb=" O ILE a 23 " (cutoff:3.500A) Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 58 removed outlier: 4.163A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 87 removed outlier: 4.196A pdb=" N TRP a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR a 69 " --> pdb=" O GLY a 65 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 98 through 119 Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 122 through 126 Processing helix chain 'a' and resid 135 through 183 Proline residue: a 139 - end of helix removed outlier: 5.029A pdb=" N ILE a 143 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR a 146 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE a 151 " --> pdb=" O SER a 148 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN a 152 " --> pdb=" O LEU a 149 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 3.525A pdb=" N THR a 161 " --> pdb=" O VAL a 158 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN a 163 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR a 165 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU a 181 " --> pdb=" O THR a 178 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 224 removed outlier: 3.826A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 removed outlier: 3.737A pdb=" N GLU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 43 removed outlier: 4.199A pdb=" N ALA d 25 " --> pdb=" O ASN d 22 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL d 26 " --> pdb=" O GLN d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 65 through 75 Processing helix chain 'd' and resid 88 through 101 removed outlier: 3.919A pdb=" N ALA d 101 " --> pdb=" O LYS d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 120 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 Processing helix chain 'e' and resid 8 through 41 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 16 through 25 Proline residue: f 20 - end of helix removed outlier: 3.927A pdb=" N LEU f 24 " --> pdb=" O PRO f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 48 removed outlier: 4.331A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 74 removed outlier: 3.752A pdb=" N MET f 61 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL f 62 " --> pdb=" O GLY f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 78 No H-bonds generated for 'chain 'f' and resid 76 through 78' Processing helix chain 'g' and resid 22 through 36 removed outlier: 4.569A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 61 Proline residue: g 46 - end of helix Processing helix chain 'g' and resid 64 through 66 No H-bonds generated for 'chain 'g' and resid 64 through 66' Processing helix chain 'g' and resid 69 through 93 removed outlier: 3.659A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 9 Processing helix chain 'j' and resid 14 through 18 Processing helix chain 'j' and resid 22 through 46 Processing helix chain 'k' and resid 13 through 17 Processing helix chain 'k' and resid 23 through 44 Processing helix chain 'M' and resid 9 through 38 removed outlier: 5.133A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'N' and resid 2 through 38 removed outlier: 4.956A pdb=" N VAL N 16 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY N 17 " --> pdb=" O ALA N 13 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA N 19 " --> pdb=" O THR N 15 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY N 20 " --> pdb=" O VAL N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 45 through 71 removed outlier: 3.608A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 29 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 47 Processing helix chain 'b' and resid 55 through 186 removed outlier: 4.326A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS b 120 " --> pdb=" O ALA b 116 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU b 124 " --> pdb=" O LYS b 120 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE b 125 " --> pdb=" O ARG b 121 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 9 through 26 removed outlier: 4.832A pdb=" N GLY h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 50 removed outlier: 4.124A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 44 removed outlier: 4.034A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 112 Processing helix chain 'S' and resid 128 through 141 Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'C' and resid 7 through 17 Processing sheet with id= A, first strand: chain 'S' and resid 115 through 117 removed outlier: 7.087A pdb=" N VAL S 147 " --> pdb=" O VAL S 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'S' and resid 118 through 122 Processing sheet with id= C, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.732A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 19.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11308 1.03 - 1.23: 34 1.23 - 1.42: 4455 1.42 - 1.62: 6575 1.62 - 1.81: 102 Bond restraints: 22474 Sorted by residual: bond pdb=" CA THR d 142 " pdb=" C THR d 142 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.41e-02 5.03e+03 5.42e+00 bond pdb=" CB MET j 31 " pdb=" CG MET j 31 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.08e+00 bond pdb=" CG MET j 31 " pdb=" SD MET j 31 " ideal model delta sigma weight residual 1.803 1.761 0.042 2.50e-02 1.60e+03 2.76e+00 bond pdb=" CB PRO a 107 " pdb=" CG PRO a 107 " ideal model delta sigma weight residual 1.492 1.417 0.075 5.00e-02 4.00e+02 2.25e+00 bond pdb=" CB LEU N 65 " pdb=" CG LEU N 65 " ideal model delta sigma weight residual 1.530 1.502 0.028 2.00e-02 2.50e+03 1.92e+00 ... (remaining 22469 not shown) Histogram of bond angle deviations from ideal: 83.76 - 93.82: 9 93.82 - 103.88: 171 103.88 - 113.95: 27749 113.95 - 124.01: 11356 124.01 - 134.07: 1523 Bond angle restraints: 40808 Sorted by residual: angle pdb=" CB LEU O 65 " pdb=" CG LEU O 65 " pdb=" HG LEU O 65 " ideal model delta sigma weight residual 109.00 83.81 25.19 3.00e+00 1.11e-01 7.05e+01 angle pdb=" CB LEU O 52 " pdb=" CG LEU O 52 " pdb=" HG LEU O 52 " ideal model delta sigma weight residual 109.00 84.69 24.31 3.00e+00 1.11e-01 6.56e+01 angle pdb=" CD2 LEU O 65 " pdb=" CG LEU O 65 " pdb=" HG LEU O 65 " ideal model delta sigma weight residual 108.00 83.76 24.24 3.00e+00 1.11e-01 6.53e+01 angle pdb=" CD1 LEU O 65 " pdb=" CG LEU O 65 " pdb=" HG LEU O 65 " ideal model delta sigma weight residual 108.00 83.84 24.16 3.00e+00 1.11e-01 6.48e+01 angle pdb=" CB LEU O 70 " pdb=" CG LEU O 70 " pdb=" HG LEU O 70 " ideal model delta sigma weight residual 109.00 85.14 23.86 3.00e+00 1.11e-01 6.33e+01 ... (remaining 40803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8027 17.82 - 35.63: 768 35.63 - 53.45: 121 53.45 - 71.27: 36 71.27 - 89.09: 9 Dihedral angle restraints: 8961 sinusoidal: 4228 harmonic: 4733 Sorted by residual: dihedral pdb=" CA ILE d 18 " pdb=" C ILE d 18 " pdb=" N ILE d 19 " pdb=" CA ILE d 19 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA HIS 8 31 " pdb=" C HIS 8 31 " pdb=" N ASN 8 32 " pdb=" CA ASN 8 32 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA d 63 " pdb=" C ALA d 63 " pdb=" N GLY d 64 " pdb=" CA GLY d 64 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.357: 1742 0.357 - 0.714: 0 0.714 - 1.071: 0 1.071 - 1.427: 0 1.427 - 1.784: 3 Chirality restraints: 1745 Sorted by residual: chirality pdb=" CG LEU O 70 " pdb=" CB LEU O 70 " pdb=" CD1 LEU O 70 " pdb=" CD2 LEU O 70 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.96e+01 chirality pdb=" CG LEU O 52 " pdb=" CB LEU O 52 " pdb=" CD1 LEU O 52 " pdb=" CD2 LEU O 52 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.18e+01 chirality pdb=" CG LEU O 65 " pdb=" CB LEU O 65 " pdb=" CD1 LEU O 65 " pdb=" CD2 LEU O 65 " both_signs ideal model delta sigma weight residual False -2.59 -1.03 -1.56 2.00e-01 2.50e+01 6.05e+01 ... (remaining 1742 not shown) Planarity restraints: 3167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 109 " -0.026 2.00e-02 2.50e+03 1.69e-02 1.14e+01 pdb=" CG TRP a 109 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP a 109 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP a 109 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP a 109 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 109 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 109 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 109 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP a 109 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP a 109 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP a 109 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP a 109 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 63 " -0.032 2.00e-02 2.50e+03 1.47e-02 6.47e+00 pdb=" CG PHE O 63 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE O 63 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE O 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE O 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE O 63 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 63 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE O 63 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE O 63 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE O 63 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE O 63 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE O 63 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL d 78 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO d 79 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO d 79 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO d 79 " -0.027 5.00e-02 4.00e+02 ... (remaining 3164 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 588 2.08 - 2.71: 38360 2.71 - 3.34: 66840 3.34 - 3.97: 77962 3.97 - 4.60: 122377 Nonbonded interactions: 306127 Sorted by model distance: nonbonded pdb=" OE1 GLU S 33 " pdb=" H GLU S 33 " model vdw 1.445 1.850 nonbonded pdb=" O TYR d 56 " pdb=" H VAL d 60 " model vdw 1.455 1.850 nonbonded pdb=" OD1 ASN a 2 " pdb=" H GLU a 3 " model vdw 1.509 1.850 nonbonded pdb=" O M3L M 43 " pdb=" H LEU M 46 " model vdw 1.512 1.850 nonbonded pdb=" O VAL N 16 " pdb=" H ALA N 19 " model vdw 1.524 1.850 ... (remaining 306122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'N' and (resid 8 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name CG or name SD or name CE or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 7133 2.51 5 N 1803 2.21 5 O 1948 1.98 5 H 11316 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.340 Extract box with map and model: 29.770 Check model and map are aligned: 0.340 Process input model: 70.160 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.005 0.075 11158 Z= 0.303 Angle : 0.744 10.482 15079 Z= 0.408 Chirality : 0.081 1.784 1745 Planarity : 0.005 0.048 1860 Dihedral : 14.687 89.086 4138 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.22), residues: 1344 helix: -0.39 (0.16), residues: 922 sheet: -2.13 (0.85), residues: 41 loop : -2.13 (0.32), residues: 381 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3986 time to fit residues: 137.2214 Evaluate side-chains 178 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 101 ASN a 119 ASN a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 11158 Z= 0.220 Angle : 0.627 10.906 15079 Z= 0.329 Chirality : 0.081 1.770 1745 Planarity : 0.005 0.047 1860 Dihedral : 5.562 40.314 1494 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1344 helix: 0.04 (0.17), residues: 920 sheet: -1.75 (0.91), residues: 39 loop : -1.92 (0.32), residues: 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.3997 time to fit residues: 133.8159 Evaluate side-chains 172 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 11158 Z= 0.263 Angle : 0.631 11.049 15079 Z= 0.330 Chirality : 0.081 1.758 1745 Planarity : 0.005 0.045 1860 Dihedral : 5.552 46.954 1494 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1344 helix: 0.19 (0.17), residues: 922 sheet: -1.68 (0.92), residues: 39 loop : -1.85 (0.32), residues: 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.4174 time to fit residues: 131.6553 Evaluate side-chains 175 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 51 GLN a 119 ASN a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 11158 Z= 0.215 Angle : 0.617 12.483 15079 Z= 0.319 Chirality : 0.080 1.761 1745 Planarity : 0.005 0.041 1860 Dihedral : 5.443 52.218 1494 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1344 helix: 0.38 (0.17), residues: 929 sheet: -1.60 (0.92), residues: 39 loop : -1.59 (0.33), residues: 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3981 time to fit residues: 129.7808 Evaluate side-chains 171 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 11158 Z= 0.217 Angle : 0.599 10.561 15079 Z= 0.310 Chirality : 0.080 1.757 1745 Planarity : 0.004 0.048 1860 Dihedral : 5.368 53.606 1494 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1344 helix: 0.48 (0.17), residues: 929 sheet: -1.30 (0.94), residues: 37 loop : -1.50 (0.33), residues: 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.4242 time to fit residues: 136.7915 Evaluate side-chains 175 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.809 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11158 Z= 0.239 Angle : 0.616 10.731 15079 Z= 0.321 Chirality : 0.081 1.756 1745 Planarity : 0.004 0.044 1860 Dihedral : 5.346 52.711 1494 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.23), residues: 1344 helix: 0.48 (0.17), residues: 928 sheet: -1.74 (0.89), residues: 39 loop : -1.43 (0.33), residues: 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.4186 time to fit residues: 132.5479 Evaluate side-chains 176 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 125 optimal weight: 0.0020 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 36 ASN ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11158 Z= 0.186 Angle : 0.593 11.089 15079 Z= 0.304 Chirality : 0.080 1.758 1745 Planarity : 0.004 0.063 1860 Dihedral : 5.232 55.606 1494 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1344 helix: 0.69 (0.17), residues: 933 sheet: -1.35 (0.92), residues: 37 loop : -1.20 (0.34), residues: 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.4245 time to fit residues: 141.1227 Evaluate side-chains 182 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 119 ASN a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11158 Z= 0.187 Angle : 0.587 12.115 15079 Z= 0.300 Chirality : 0.080 1.744 1745 Planarity : 0.005 0.064 1860 Dihedral : 5.142 56.443 1494 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1344 helix: 0.75 (0.17), residues: 937 sheet: -1.36 (0.92), residues: 37 loop : -1.07 (0.35), residues: 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.4230 time to fit residues: 141.2104 Evaluate side-chains 183 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11158 Z= 0.174 Angle : 0.575 11.890 15079 Z= 0.290 Chirality : 0.080 1.745 1745 Planarity : 0.004 0.054 1860 Dihedral : 5.051 57.438 1494 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1344 helix: 0.89 (0.17), residues: 940 sheet: -1.30 (0.92), residues: 37 loop : -1.01 (0.35), residues: 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.4441 time to fit residues: 154.3910 Evaluate side-chains 181 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.976 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 129 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 163 ASN a 168 HIS ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11158 Z= 0.173 Angle : 0.573 11.218 15079 Z= 0.292 Chirality : 0.080 1.736 1745 Planarity : 0.004 0.051 1860 Dihedral : 5.008 58.837 1494 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1344 helix: 0.91 (0.17), residues: 940 sheet: -1.27 (0.92), residues: 37 loop : -1.00 (0.35), residues: 367 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.4347 time to fit residues: 153.9375 Evaluate side-chains 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 163 ASN a 168 HIS ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.077418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.067503 restraints weight = 158720.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069471 restraints weight = 75687.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070678 restraints weight = 46112.576| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11158 Z= 0.180 Angle : 0.577 11.759 15079 Z= 0.291 Chirality : 0.080 1.730 1745 Planarity : 0.004 0.045 1860 Dihedral : 4.964 58.874 1494 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1344 helix: 1.01 (0.17), residues: 934 sheet: -1.27 (0.92), residues: 37 loop : -0.92 (0.35), residues: 373 =============================================================================== Job complete usr+sys time: 4652.66 seconds wall clock time: 83 minutes 30.67 seconds (5010.67 seconds total)