Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 16:02:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/10_2023/7ch7_30370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/10_2023/7ch7_30370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/10_2023/7ch7_30370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/10_2023/7ch7_30370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/10_2023/7ch7_30370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/10_2023/7ch7_30370.pdb" } resolution = 3.9 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= 0.002 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5914 2.51 5 N 1572 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ASP 260": "OD1" <-> "OD2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 9198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Time building chain proxies: 5.38, per 1000 atoms: 0.58 Number of scatterers: 9198 At special positions: 0 Unit cell: (99, 111, 110, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1654 8.00 N 1572 7.00 C 5914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 4.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 57.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.787A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 4.387A pdb=" N LEU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.552A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 4.154A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 4.169A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.560A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 138 through 175 removed outlier: 4.742A pdb=" N SER A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix removed outlier: 3.541A pdb=" N ILE A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 224 removed outlier: 3.715A pdb=" N LEU A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 3.917A pdb=" N SER A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 removed outlier: 3.787A pdb=" N LEU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 52 removed outlier: 4.388A pdb=" N LEU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 79 removed outlier: 3.551A pdb=" N ILE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.152A pdb=" N LEU B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.170A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 removed outlier: 4.561A pdb=" N LEU B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 138 through 175 removed outlier: 4.742A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix removed outlier: 3.541A pdb=" N ILE B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 195 through 224 removed outlier: 3.714A pdb=" N LEU B 199 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 3.916A pdb=" N SER B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 101 through 114 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 117 through 133 removed outlier: 3.710A pdb=" N GLU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 146 through 160 removed outlier: 3.726A pdb=" N ARG C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.725A pdb=" N SER C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 237 through 246 removed outlier: 3.683A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 101 through 114 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 117 through 133 removed outlier: 3.709A pdb=" N GLU D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.726A pdb=" N ARG D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.725A pdb=" N SER D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.682A pdb=" N PHE D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 removed outlier: 3.696A pdb=" N GLU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 51 through 66 Processing helix chain 'E' and resid 78 through 88 Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.697A pdb=" N GLU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 51 through 66 Processing helix chain 'F' and resid 78 through 88 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 32 removed outlier: 4.512A pdb=" N LEU C 29 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG C 12 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL C 31 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP C 10 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 91 removed outlier: 5.894A pdb=" N PHE C 168 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 37 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER C 202 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE C 39 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA C 219 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.511A pdb=" N LEU D 29 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG D 12 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL D 31 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP D 10 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 90 through 91 removed outlier: 5.894A pdb=" N PHE D 168 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 37 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER D 202 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE D 39 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA D 219 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 9 removed outlier: 3.893A pdb=" N LEU E 16 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE E 42 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 9 removed outlier: 3.893A pdb=" N LEU F 16 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE F 42 " --> pdb=" O GLN F 75 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1374 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: 2.37 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2996 1.34 - 1.46: 1730 1.46 - 1.57: 4536 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 9370 Sorted by residual: bond pdb=" CA GLU C 162 " pdb=" C GLU C 162 " ideal model delta sigma weight residual 1.531 1.517 0.014 7.40e-03 1.83e+04 3.68e+00 bond pdb=" CA GLU D 162 " pdb=" C GLU D 162 " ideal model delta sigma weight residual 1.531 1.518 0.013 7.40e-03 1.83e+04 3.06e+00 bond pdb=" CA GLU D 170 " pdb=" C GLU D 170 " ideal model delta sigma weight residual 1.531 1.520 0.012 7.40e-03 1.83e+04 2.43e+00 bond pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.02e-02 9.61e+03 2.27e+00 bond pdb=" CA GLU C 170 " pdb=" C GLU C 170 " ideal model delta sigma weight residual 1.531 1.520 0.011 7.40e-03 1.83e+04 2.24e+00 ... (remaining 9365 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.04: 258 106.04 - 113.02: 5394 113.02 - 120.01: 3230 120.01 - 126.99: 3731 126.99 - 133.98: 117 Bond angle restraints: 12730 Sorted by residual: angle pdb=" C PRO C 251 " pdb=" N VAL C 252 " pdb=" CA VAL C 252 " ideal model delta sigma weight residual 122.59 119.80 2.79 7.20e-01 1.93e+00 1.50e+01 angle pdb=" C PRO D 251 " pdb=" N VAL D 252 " pdb=" CA VAL D 252 " ideal model delta sigma weight residual 122.59 119.80 2.79 7.20e-01 1.93e+00 1.50e+01 angle pdb=" N ILE C 211 " pdb=" CA ILE C 211 " pdb=" C ILE C 211 " ideal model delta sigma weight residual 113.71 110.19 3.52 9.50e-01 1.11e+00 1.37e+01 angle pdb=" N GLY A 113 " pdb=" CA GLY A 113 " pdb=" C GLY A 113 " ideal model delta sigma weight residual 114.66 110.08 4.58 1.24e+00 6.50e-01 1.36e+01 angle pdb=" N ILE D 211 " pdb=" CA ILE D 211 " pdb=" C ILE D 211 " ideal model delta sigma weight residual 113.71 110.22 3.49 9.50e-01 1.11e+00 1.35e+01 ... (remaining 12725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4813 15.81 - 31.61: 534 31.61 - 47.42: 174 47.42 - 63.23: 79 63.23 - 79.04: 4 Dihedral angle restraints: 5604 sinusoidal: 2164 harmonic: 3440 Sorted by residual: dihedral pdb=" CA LEU F 95 " pdb=" C LEU F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU E 95 " pdb=" C LEU E 95 " pdb=" N PRO E 96 " pdb=" CA PRO E 96 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLU D 162 " pdb=" C GLU D 162 " pdb=" N PRO D 163 " pdb=" CA PRO D 163 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 717 0.030 - 0.060: 536 0.060 - 0.089: 179 0.089 - 0.119: 80 0.119 - 0.149: 16 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CA PRO D 163 " pdb=" N PRO D 163 " pdb=" C PRO D 163 " pdb=" CB PRO D 163 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO C 163 " pdb=" N PRO C 163 " pdb=" C PRO C 163 " pdb=" CB PRO C 163 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA PRO E 96 " pdb=" N PRO E 96 " pdb=" C PRO E 96 " pdb=" CB PRO E 96 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1525 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 95 " 0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO F 96 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 95 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO E 96 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 140 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C LEU B 140 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU B 140 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG B 141 " -0.008 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 301 2.66 - 3.22: 10345 3.22 - 3.78: 15437 3.78 - 4.34: 20279 4.34 - 4.90: 32211 Nonbonded interactions: 78573 Sorted by model distance: nonbonded pdb=" O TYR B 75 " pdb=" OG1 THR B 79 " model vdw 2.096 2.440 nonbonded pdb=" O TYR A 75 " pdb=" OG1 THR A 79 " model vdw 2.096 2.440 nonbonded pdb=" OG SER A 228 " pdb=" OG SER B 228 " model vdw 2.142 2.440 nonbonded pdb=" O VAL A 51 " pdb=" OG SER A 55 " model vdw 2.170 2.440 nonbonded pdb=" O TRP B 168 " pdb=" OG SER B 171 " model vdw 2.170 2.440 ... (remaining 78568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 2.130 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: 0.000 Extract box with map and model: 4.240 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.800 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.007 0.046 9370 Z= 0.491 Angle : 0.939 13.756 12730 Z= 0.514 Chirality : 0.047 0.149 1528 Planarity : 0.006 0.112 1604 Dihedral : 16.386 79.037 3392 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 18.11 % Allowed : 15.09 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.81 (0.20), residues: 1202 helix: -3.04 (0.15), residues: 646 sheet: -2.97 (0.57), residues: 66 loop : -3.26 (0.26), residues: 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 302 time to evaluate : 1.169 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 outliers start: 180 outliers final: 83 residues processed: 420 average time/residue: 0.2109 time to fit residues: 123.4899 Evaluate side-chains 308 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 225 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 0 residues processed: 83 average time/residue: 0.1050 time to fit residues: 16.2910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 220 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS F 60 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9370 Z= 0.293 Angle : 0.830 10.514 12730 Z= 0.394 Chirality : 0.047 0.257 1528 Planarity : 0.006 0.102 1604 Dihedral : 5.515 28.892 1294 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 6.34 % Allowed : 26.96 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.06 (0.22), residues: 1202 helix: -1.46 (0.19), residues: 636 sheet: -1.67 (0.60), residues: 62 loop : -2.78 (0.25), residues: 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 281 time to evaluate : 1.162 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 outliers start: 63 outliers final: 27 residues processed: 320 average time/residue: 0.1887 time to fit residues: 85.7122 Evaluate side-chains 252 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 225 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0831 time to fit residues: 5.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN D 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9370 Z= 0.248 Angle : 0.772 9.462 12730 Z= 0.366 Chirality : 0.048 0.356 1528 Planarity : 0.005 0.098 1604 Dihedral : 5.285 28.036 1294 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 5.13 % Allowed : 29.38 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.44 (0.23), residues: 1202 helix: -0.91 (0.19), residues: 650 sheet: -2.13 (0.53), residues: 80 loop : -2.46 (0.27), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 251 time to evaluate : 1.063 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 outliers start: 51 outliers final: 24 residues processed: 284 average time/residue: 0.1923 time to fit residues: 77.1780 Evaluate side-chains 250 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0881 time to fit residues: 5.2993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9370 Z= 0.323 Angle : 0.789 10.776 12730 Z= 0.375 Chirality : 0.048 0.352 1528 Planarity : 0.006 0.099 1604 Dihedral : 5.206 27.358 1294 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.83 % Allowed : 31.59 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.23), residues: 1202 helix: -0.75 (0.20), residues: 652 sheet: -2.59 (0.46), residues: 90 loop : -2.40 (0.28), residues: 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 1.123 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 outliers start: 48 outliers final: 25 residues processed: 262 average time/residue: 0.2103 time to fit residues: 76.8952 Evaluate side-chains 242 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.0935 time to fit residues: 5.9526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9370 Z= 0.205 Angle : 0.741 8.803 12730 Z= 0.350 Chirality : 0.046 0.331 1528 Planarity : 0.005 0.091 1604 Dihedral : 5.045 27.179 1294 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.62 % Allowed : 31.59 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.00 (0.23), residues: 1202 helix: -0.54 (0.19), residues: 664 sheet: -2.19 (0.48), residues: 90 loop : -2.24 (0.28), residues: 448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 249 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 271 average time/residue: 0.2002 time to fit residues: 75.5395 Evaluate side-chains 246 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0859 time to fit residues: 4.3361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9370 Z= 0.222 Angle : 0.751 7.827 12730 Z= 0.353 Chirality : 0.047 0.304 1528 Planarity : 0.005 0.090 1604 Dihedral : 4.941 26.083 1294 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.02 % Allowed : 33.50 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.76 (0.24), residues: 1202 helix: -0.41 (0.19), residues: 660 sheet: -1.83 (0.51), residues: 90 loop : -2.06 (0.29), residues: 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 260 average time/residue: 0.2041 time to fit residues: 74.1531 Evaluate side-chains 243 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1060 time to fit residues: 3.8891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9370 Z= 0.249 Angle : 0.761 8.592 12730 Z= 0.360 Chirality : 0.048 0.369 1528 Planarity : 0.005 0.089 1604 Dihedral : 4.966 25.658 1294 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.41 % Allowed : 35.61 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.24), residues: 1202 helix: -0.30 (0.20), residues: 660 sheet: -1.61 (0.52), residues: 90 loop : -2.08 (0.29), residues: 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 242 average time/residue: 0.2104 time to fit residues: 71.1505 Evaluate side-chains 237 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1528 time to fit residues: 4.0096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9370 Z= 0.238 Angle : 0.776 10.368 12730 Z= 0.363 Chirality : 0.047 0.325 1528 Planarity : 0.005 0.086 1604 Dihedral : 4.998 25.116 1294 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 1.61 % Allowed : 35.92 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.24), residues: 1202 helix: -0.20 (0.20), residues: 662 sheet: -1.56 (0.53), residues: 90 loop : -2.06 (0.29), residues: 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 246 average time/residue: 0.2075 time to fit residues: 71.0602 Evaluate side-chains 230 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0834 time to fit residues: 2.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9370 Z= 0.283 Angle : 0.800 9.830 12730 Z= 0.380 Chirality : 0.047 0.217 1528 Planarity : 0.005 0.083 1604 Dihedral : 5.138 24.594 1294 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.41 % Allowed : 36.92 % Favored : 61.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.47 (0.24), residues: 1202 helix: -0.14 (0.20), residues: 660 sheet: -1.62 (0.54), residues: 90 loop : -2.01 (0.29), residues: 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 230 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 235 average time/residue: 0.2107 time to fit residues: 69.7661 Evaluate side-chains 228 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0952 time to fit residues: 2.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9370 Z= 0.238 Angle : 0.817 10.683 12730 Z= 0.383 Chirality : 0.047 0.211 1528 Planarity : 0.005 0.079 1604 Dihedral : 5.147 24.666 1294 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.50 % Allowed : 37.53 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.41 (0.24), residues: 1202 helix: -0.03 (0.20), residues: 650 sheet: -1.73 (0.53), residues: 90 loop : -2.03 (0.29), residues: 462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 231 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 233 average time/residue: 0.2026 time to fit residues: 66.1804 Evaluate side-chains 227 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0929 time to fit residues: 2.0764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0000 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 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 = 0.3514 r_free = 0.3514 target = 0.088223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074638 restraints weight = 27048.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.076850 restraints weight = 14643.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.078384 restraints weight = 9656.160| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9370 Z= 0.245 Angle : 0.833 10.974 12730 Z= 0.387 Chirality : 0.047 0.272 1528 Planarity : 0.005 0.079 1604 Dihedral : 5.143 24.588 1294 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.70 % Allowed : 37.93 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.24), residues: 1202 helix: 0.12 (0.20), residues: 648 sheet: -1.68 (0.54), residues: 90 loop : -2.05 (0.28), residues: 464 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2128.12 seconds wall clock time: 39 minutes 22.56 seconds (2362.56 seconds total)