Starting phenix.real_space_refine on Mon Mar 18 21:35:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/03_2024/6ziq_11228_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/03_2024/6ziq_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_11228/03_2024/6ziq_11228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/03_2024/6ziq_11228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/03_2024/6ziq_11228_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ziq_11228/03_2024/6ziq_11228_trim_updated.pdb" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. 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-5265/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: 9.83, per 1000 atoms: 0.44 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: 18.23 Conformation dependent library (CDL) restraints added in 2.3 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: 3.45 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: 7.90 Time building geometry restraints manager: 18.65 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: 9303 17.82 - 35.63: 861 35.63 - 53.45: 238 53.45 - 71.27: 80 71.27 - 89.09: 9 Dihedral angle restraints: 10491 sinusoidal: 5758 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 10488 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 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: 9.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 27.470 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 70.130 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 % Allowed : 0.34 % Favored : 99.66 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP a 109 HIS 0.003 0.001 HIS a 168 PHE 0.036 0.002 PHE O 63 TYR 0.022 0.002 TYR S 23 ARG 0.027 0.001 ARG a 159 *********************** 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 : 1.903 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: a 100 MET cc_start: 0.7905 (ttm) cc_final: 0.7683 (ttm) REVERT: j 31 MET cc_start: 0.7879 (mmt) cc_final: 0.7114 (mmp) REVERT: N 51 ILE cc_start: 0.8038 (mp) cc_final: 0.7394 (tp) REVERT: b 142 GLU cc_start: 0.8128 (pp20) cc_final: 0.7898 (pp20) REVERT: b 173 MET cc_start: 0.8544 (ttp) cc_final: 0.7862 (tpp) REVERT: S 126 LEU cc_start: 0.8194 (mm) cc_final: 0.7989 (mm) REVERT: S 159 MET cc_start: 0.5535 (tpt) cc_final: 0.5239 (tpt) REVERT: C 11 ILE cc_start: 0.8658 (tp) cc_final: 0.8410 (tp) REVERT: C 42 HIS cc_start: 0.7030 (t70) cc_final: 0.6790 (t-90) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3997 time to fit residues: 138.0459 Evaluate side-chains 180 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.006 ------------------------------------------------------------------------------- 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: 0.9980 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7399 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11158 Z= 0.200 Angle : 0.617 10.888 15079 Z= 0.323 Chirality : 0.081 1.768 1745 Planarity : 0.005 0.053 1860 Dihedral : 5.494 41.731 1494 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % 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: -0.78 (0.23), residues: 1344 helix: 0.13 (0.17), residues: 923 sheet: -1.66 (0.91), residues: 39 loop : -1.80 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP a 109 HIS 0.004 0.001 HIS a 172 PHE 0.041 0.001 PHE O 63 TYR 0.014 0.001 TYR N 49 ARG 0.006 0.000 ARG b 154 *********************** 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 220 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.643 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: f 81 GLU cc_start: 0.7605 (tt0) cc_final: 0.6979 (tm-30) REVERT: j 31 MET cc_start: 0.7868 (mmt) cc_final: 0.7325 (mmp) REVERT: N 51 ILE cc_start: 0.8097 (mp) cc_final: 0.7529 (tp) REVERT: b 173 MET cc_start: 0.8566 (ttp) cc_final: 0.8197 (tpp) REVERT: S 126 LEU cc_start: 0.8142 (mm) cc_final: 0.7903 (mm) REVERT: C 42 HIS cc_start: 0.6931 (t70) cc_final: 0.6663 (t-90) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.3871 time to fit residues: 133.7596 Evaluate side-chains 177 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.7394 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11158 Z= 0.233 Angle : 0.615 11.101 15079 Z= 0.319 Chirality : 0.081 1.754 1745 Planarity : 0.005 0.041 1860 Dihedral : 5.425 47.348 1494 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.08 % Allowed : 2.63 % Favored : 97.29 % 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: -0.51 (0.23), residues: 1344 helix: 0.31 (0.17), residues: 928 sheet: -1.54 (0.92), residues: 39 loop : -1.66 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 PHE 0.038 0.001 PHE O 63 TYR 0.015 0.001 TYR f 66 ARG 0.005 0.000 ARG h 19 *********************** 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 214 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.734 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: e 24 TYR cc_start: 0.9030 (t80) cc_final: 0.8809 (t80) REVERT: N 51 ILE cc_start: 0.8108 (mp) cc_final: 0.7531 (tp) REVERT: S 126 LEU cc_start: 0.8164 (mm) cc_final: 0.7928 (mm) REVERT: S 159 MET cc_start: 0.5523 (tpt) cc_final: 0.5259 (tpt) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.4022 time to fit residues: 130.7173 Evaluate side-chains 179 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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: 4.9990 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11158 Z= 0.283 Angle : 0.643 13.371 15079 Z= 0.338 Chirality : 0.080 1.759 1745 Planarity : 0.005 0.040 1860 Dihedral : 5.461 50.940 1494 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -0.56 (0.23), residues: 1344 helix: 0.28 (0.17), residues: 929 sheet: -1.62 (0.91), residues: 39 loop : -1.67 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 109 HIS 0.005 0.001 HIS b 145 PHE 0.041 0.002 PHE O 63 TYR 0.015 0.001 TYR d 85 ARG 0.008 0.000 ARG h 19 *********************** 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 217 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 24 TYR cc_start: 0.9047 (t80) cc_final: 0.8769 (t80) REVERT: f 81 GLU cc_start: 0.6800 (mp0) cc_final: 0.6435 (tm-30) REVERT: N 51 ILE cc_start: 0.8117 (mp) cc_final: 0.7533 (tp) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.3930 time to fit residues: 129.3930 Evaluate side-chains 176 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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: 0.7980 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 112 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** O 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11158 Z= 0.208 Angle : 0.599 10.728 15079 Z= 0.311 Chirality : 0.080 1.764 1745 Planarity : 0.004 0.040 1860 Dihedral : 5.345 54.061 1494 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -0.21 (0.23), residues: 1344 helix: 0.50 (0.17), residues: 930 sheet: -1.52 (0.90), residues: 39 loop : -1.45 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 PHE 0.040 0.001 PHE O 63 TYR 0.016 0.001 TYR f 66 ARG 0.007 0.000 ARG h 19 *********************** 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 223 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.914 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: N 51 ILE cc_start: 0.8123 (mp) cc_final: 0.7525 (tp) REVERT: b 165 MET cc_start: 0.8400 (mtt) cc_final: 0.8199 (mtt) REVERT: S 15 GLU cc_start: 0.6877 (pp20) cc_final: 0.6627 (pp20) REVERT: S 159 MET cc_start: 0.5449 (tpt) cc_final: 0.5038 (tpt) REVERT: C 11 ILE cc_start: 0.8476 (tp) cc_final: 0.8095 (tp) REVERT: C 14 GLU cc_start: 0.8915 (mp0) cc_final: 0.8636 (mp0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.4260 time to fit residues: 144.6200 Evaluate side-chains 176 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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: 4.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** 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: 0.7436 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11158 Z= 0.349 Angle : 0.676 10.589 15079 Z= 0.359 Chirality : 0.082 1.765 1745 Planarity : 0.005 0.039 1860 Dihedral : 5.570 50.536 1494 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.65 (0.23), residues: 1344 helix: 0.22 (0.17), residues: 922 sheet: -1.80 (0.89), residues: 39 loop : -1.71 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 109 HIS 0.005 0.001 HIS b 145 PHE 0.021 0.002 PHE a 204 TYR 0.018 0.002 TYR d 85 ARG 0.006 0.001 ARG h 19 *********************** 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 206 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.799 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: N 51 ILE cc_start: 0.8114 (mp) cc_final: 0.7862 (mm) REVERT: b 165 MET cc_start: 0.8440 (mtt) cc_final: 0.8220 (mtt) REVERT: h 10 LEU cc_start: 0.8738 (pp) cc_final: 0.8519 (pp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.4454 time to fit residues: 139.2805 Evaluate side-chains 169 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 125 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7373 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11158 Z= 0.189 Angle : 0.606 12.463 15079 Z= 0.307 Chirality : 0.080 1.779 1745 Planarity : 0.004 0.048 1860 Dihedral : 5.329 56.708 1494 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.08 % Allowed : 1.10 % Favored : 98.81 % 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: -0.08 (0.24), residues: 1344 helix: 0.56 (0.17), residues: 930 sheet: -1.53 (0.92), residues: 39 loop : -1.27 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 109 HIS 0.004 0.001 HIS a 168 PHE 0.039 0.001 PHE O 63 TYR 0.018 0.001 TYR f 66 ARG 0.007 0.000 ARG h 19 *********************** 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: 1 poor density : 221 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 18 LEU cc_start: 0.8821 (tt) cc_final: 0.8620 (tt) REVERT: N 51 ILE cc_start: 0.8074 (mp) cc_final: 0.7453 (tp) REVERT: b 165 MET cc_start: 0.8426 (mtt) cc_final: 0.8219 (mtt) REVERT: S 15 GLU cc_start: 0.6841 (pp20) cc_final: 0.6627 (pp20) REVERT: S 159 MET cc_start: 0.5349 (tpt) cc_final: 0.4997 (tpt) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.4415 time to fit residues: 147.9836 Evaluate side-chains 182 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 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: 0.7398 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11158 Z= 0.241 Angle : 0.617 11.829 15079 Z= 0.318 Chirality : 0.080 1.764 1745 Planarity : 0.004 0.043 1860 Dihedral : 5.303 56.150 1494 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.08 % Allowed : 1.10 % Favored : 98.81 % 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: -0.14 (0.23), residues: 1344 helix: 0.58 (0.17), residues: 919 sheet: -1.64 (0.90), residues: 39 loop : -1.41 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 109 HIS 0.005 0.001 HIS b 145 PHE 0.040 0.002 PHE O 63 TYR 0.014 0.001 TYR d 85 ARG 0.008 0.000 ARG h 19 *********************** 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 216 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 51 ILE cc_start: 0.8064 (mp) cc_final: 0.7446 (tp) REVERT: b 165 MET cc_start: 0.8445 (mtt) cc_final: 0.8224 (mtt) REVERT: S 15 GLU cc_start: 0.6860 (pp20) cc_final: 0.6624 (pp20) REVERT: S 159 MET cc_start: 0.5399 (tpt) cc_final: 0.5022 (tpt) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.4291 time to fit residues: 141.2568 Evaluate side-chains 181 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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: 3.9990 chunk 116 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7372 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11158 Z= 0.195 Angle : 0.607 12.412 15079 Z= 0.311 Chirality : 0.080 1.767 1745 Planarity : 0.005 0.068 1860 Dihedral : 5.241 58.476 1494 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.13 (0.24), residues: 1344 helix: 0.69 (0.17), residues: 929 sheet: -1.30 (0.94), residues: 37 loop : -1.09 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 PHE 0.039 0.001 PHE O 63 TYR 0.011 0.001 TYR N 49 ARG 0.007 0.000 ARG h 19 *********************** 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 224 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 51 ILE cc_start: 0.8039 (mp) cc_final: 0.7411 (tp) REVERT: S 15 GLU cc_start: 0.6831 (pp20) cc_final: 0.6616 (pp20) REVERT: S 126 LEU cc_start: 0.8088 (mm) cc_final: 0.7848 (mm) REVERT: S 159 MET cc_start: 0.5486 (tpt) cc_final: 0.5104 (tpt) REVERT: C 11 ILE cc_start: 0.8347 (tp) cc_final: 0.8143 (tp) REVERT: C 13 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8163 (tm-30) REVERT: C 14 GLU cc_start: 0.9005 (mp0) cc_final: 0.8675 (mp0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.4353 time to fit residues: 147.5227 Evaluate side-chains 186 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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: 0.2980 chunk 85 optimal weight: 0.0070 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- 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: 0.7352 moved from start: 0.2436 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= 0.171 Angle : 0.584 11.690 15079 Z= 0.297 Chirality : 0.080 1.754 1745 Planarity : 0.004 0.057 1860 Dihedral : 5.071 58.690 1494 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % 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: 0.33 (0.24), residues: 1344 helix: 0.83 (0.17), residues: 930 sheet: -1.18 (0.94), residues: 37 loop : -1.01 (0.35), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 PHE 0.034 0.001 PHE O 63 TYR 0.021 0.001 TYR N 49 ARG 0.005 0.000 ARG h 19 ********************** 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 233 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 18 LEU cc_start: 0.8829 (tt) cc_final: 0.8600 (tt) REVERT: M 66 MET cc_start: 0.8298 (tpt) cc_final: 0.7799 (mmp) REVERT: N 51 ILE cc_start: 0.7994 (mp) cc_final: 0.7389 (tp) REVERT: b 109 ASP cc_start: 0.8050 (m-30) cc_final: 0.7635 (t0) REVERT: S 126 LEU cc_start: 0.8093 (mm) cc_final: 0.7846 (mm) REVERT: S 159 MET cc_start: 0.5482 (tpt) cc_final: 0.5093 (tpt) REVERT: C 11 ILE cc_start: 0.8259 (tp) cc_final: 0.8038 (tp) REVERT: C 13 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 14 GLU cc_start: 0.8954 (mp0) cc_final: 0.8628 (mp0) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.4378 time to fit residues: 152.5453 Evaluate side-chains 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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: 0.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.077229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066811 restraints weight = 156870.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.068867 restraints weight = 72120.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.070121 restraints weight = 43305.831| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11158 Z= 0.175 Angle : 0.582 12.172 15079 Z= 0.295 Chirality : 0.080 1.754 1745 Planarity : 0.004 0.051 1860 Dihedral : 4.999 58.510 1494 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.47 (0.24), residues: 1344 helix: 0.90 (0.17), residues: 936 sheet: -1.14 (0.95), residues: 37 loop : -0.88 (0.36), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 PHE 0.040 0.001 PHE M 69 TYR 0.015 0.001 TYR N 49 ARG 0.006 0.000 ARG h 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.56 seconds wall clock time: 86 minutes 51.98 seconds (5211.98 seconds total)