Starting phenix.real_space_refine on Wed Feb 14 11:56:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/02_2024/7ch7_30370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/02_2024/7ch7_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_30370/02_2024/7ch7_30370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/02_2024/7ch7_30370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/02_2024/7ch7_30370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ch7_30370/02_2024/7ch7_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.13, per 1000 atoms: 0.56 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: 3.71 Conformation dependent library (CDL) restraints added in 1.9 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: 1.15 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: 2.53 Time building geometry restraints manager: 3.96 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: 0.690 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: 4.090 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.220 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.620 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.003 0.001 HIS C 203 PHE 0.016 0.002 PHE A 148 TYR 0.012 0.001 TYR B 49 ARG 0.005 0.001 ARG C 21 *********************** 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 : 1.081 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: A 26 MET cc_start: 0.8774 (ppp) cc_final: 0.8469 (ppp) REVERT: A 90 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9014 (tm) REVERT: A 106 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 134 MET cc_start: 0.8875 (tpt) cc_final: 0.8606 (tpt) REVERT: A 191 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8108 (p0) REVERT: A 197 MET cc_start: 0.7746 (tpt) cc_final: 0.7314 (tpp) REVERT: B 47 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7623 (mm-40) REVERT: B 90 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8948 (tm) REVERT: B 176 SER cc_start: 0.7851 (m) cc_final: 0.7525 (t) REVERT: B 197 MET cc_start: 0.8078 (tpt) cc_final: 0.7696 (tpp) REVERT: C 64 GLU cc_start: 0.5016 (mp0) cc_final: 0.4795 (mp0) REVERT: C 90 LEU cc_start: 0.8493 (tp) cc_final: 0.8007 (tt) REVERT: C 120 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8599 (tm) REVERT: C 130 GLU cc_start: 0.7540 (tp30) cc_final: 0.7273 (tp30) REVERT: C 207 GLU cc_start: 0.8465 (tp30) cc_final: 0.8230 (tp30) REVERT: D 130 GLU cc_start: 0.7718 (tp30) cc_final: 0.7293 (tp30) REVERT: D 187 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9179 (pt) REVERT: D 233 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8528 (tp-100) REVERT: D 256 TYR cc_start: 0.8482 (t80) cc_final: 0.8227 (t80) REVERT: E 44 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8839 (pt) REVERT: E 57 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9075 (tp) REVERT: E 66 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8591 (mmtm) REVERT: E 70 ASN cc_start: 0.6974 (t0) cc_final: 0.6232 (t0) REVERT: E 86 LYS cc_start: 0.8765 (tppp) cc_final: 0.8538 (tppt) REVERT: F 4 SER cc_start: 0.6724 (p) cc_final: 0.6164 (m) REVERT: F 44 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8753 (pt) REVERT: F 57 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9036 (tp) REVERT: F 70 ASN cc_start: 0.7320 (t0) cc_final: 0.6706 (t0) REVERT: F 80 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8537 (mmmm) REVERT: F 86 LYS cc_start: 0.8830 (tppp) cc_final: 0.8524 (tppt) outliers start: 180 outliers final: 83 residues processed: 420 average time/residue: 0.1950 time to fit residues: 114.2874 Evaluate side-chains 328 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 232 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 87 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 226 HIS E 60 HIS F 60 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9370 Z= 0.259 Angle : 0.807 10.023 12730 Z= 0.380 Chirality : 0.046 0.212 1528 Planarity : 0.006 0.101 1604 Dihedral : 12.376 62.011 1475 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 13.48 % Allowed : 24.25 % Favored : 62.27 % 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: -3.08 (0.22), residues: 1202 helix: -1.49 (0.19), residues: 644 sheet: -1.43 (0.61), residues: 62 loop : -2.81 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 7 HIS 0.004 0.001 HIS C 113 PHE 0.009 0.002 PHE C 172 TYR 0.011 0.002 TYR B 222 ARG 0.005 0.001 ARG B 97 *********************** 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 418 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 284 time to evaluate : 1.178 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: A 26 MET cc_start: 0.8729 (ppp) cc_final: 0.8482 (ppp) REVERT: A 89 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7478 (ppp) REVERT: A 90 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8791 (tm) REVERT: A 106 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7821 (mt) REVERT: A 191 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7815 (p0) REVERT: A 195 TRP cc_start: 0.7366 (p90) cc_final: 0.6725 (p90) REVERT: A 197 MET cc_start: 0.7473 (tpt) cc_final: 0.7064 (tpp) REVERT: A 198 ASP cc_start: 0.7644 (t0) cc_final: 0.7417 (m-30) REVERT: B 56 MET cc_start: 0.7682 (ttp) cc_final: 0.7116 (ptp) REVERT: B 58 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8421 (mp) REVERT: B 89 MET cc_start: 0.7799 (tmm) cc_final: 0.7574 (ppp) REVERT: B 90 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8693 (tm) REVERT: B 135 MET cc_start: 0.8074 (mtm) cc_final: 0.7523 (mtm) REVERT: B 161 ILE cc_start: 0.9270 (mt) cc_final: 0.8979 (tp) REVERT: B 176 SER cc_start: 0.7727 (m) cc_final: 0.7254 (t) REVERT: B 198 ASP cc_start: 0.7847 (t0) cc_final: 0.7434 (t0) REVERT: C 116 LEU cc_start: 0.9180 (tp) cc_final: 0.8918 (tp) REVERT: C 120 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8401 (tm) REVERT: C 130 GLU cc_start: 0.7683 (tp30) cc_final: 0.7268 (tp30) REVERT: C 207 GLU cc_start: 0.8154 (tp30) cc_final: 0.7751 (tp30) REVERT: D 87 MET cc_start: 0.7881 (mtm) cc_final: 0.7643 (mtp) REVERT: D 90 LEU cc_start: 0.8406 (tp) cc_final: 0.8134 (tt) REVERT: D 130 GLU cc_start: 0.7637 (tp30) cc_final: 0.7424 (tp30) REVERT: D 180 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7187 (ttt) REVERT: D 187 ILE cc_start: 0.9404 (pt) cc_final: 0.9153 (pt) REVERT: D 233 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8425 (tp-100) REVERT: D 235 ASN cc_start: 0.8347 (t0) cc_final: 0.8076 (t0) REVERT: D 256 TYR cc_start: 0.8299 (t80) cc_final: 0.8086 (t80) REVERT: E 44 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8690 (pp) REVERT: E 57 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9186 (tp) REVERT: E 79 ASP cc_start: 0.7910 (p0) cc_final: 0.7663 (p0) REVERT: E 80 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8522 (mmmm) REVERT: E 86 LYS cc_start: 0.8564 (tppp) cc_final: 0.8283 (tppt) REVERT: F 44 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8675 (pp) REVERT: F 79 ASP cc_start: 0.7939 (p0) cc_final: 0.7734 (p0) REVERT: F 80 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (mmmm) REVERT: F 86 LYS cc_start: 0.8543 (tppp) cc_final: 0.8297 (tppt) outliers start: 134 outliers final: 82 residues processed: 375 average time/residue: 0.1816 time to fit residues: 97.1911 Evaluate side-chains 322 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 228 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 80 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8037 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9370 Z= 0.231 Angle : 0.759 9.545 12730 Z= 0.358 Chirality : 0.046 0.269 1528 Planarity : 0.005 0.097 1604 Dihedral : 10.931 59.261 1425 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 11.47 % Allowed : 27.06 % Favored : 61.47 % 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: -2.33 (0.23), residues: 1202 helix: -0.89 (0.19), residues: 648 sheet: -1.15 (0.62), residues: 62 loop : -2.44 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 195 HIS 0.004 0.001 HIS D 122 PHE 0.014 0.002 PHE B 65 TYR 0.019 0.002 TYR D 261 ARG 0.003 0.000 ARG C 77 *********************** 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 371 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 257 time to evaluate : 1.090 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: A 26 MET cc_start: 0.8704 (ppp) cc_final: 0.8491 (ppp) REVERT: A 89 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7445 (ppp) REVERT: A 90 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8736 (tm) REVERT: A 106 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7645 (mt) REVERT: A 191 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7788 (p0) REVERT: A 197 MET cc_start: 0.7541 (tpt) cc_final: 0.7105 (tpp) REVERT: A 198 ASP cc_start: 0.7746 (t0) cc_final: 0.7290 (t0) REVERT: B 58 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 89 MET cc_start: 0.7846 (tmm) cc_final: 0.7593 (ppp) REVERT: B 90 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8640 (tm) REVERT: B 133 GLU cc_start: 0.8445 (tt0) cc_final: 0.8035 (mt-10) REVERT: B 176 SER cc_start: 0.7710 (m) cc_final: 0.7256 (t) REVERT: B 197 MET cc_start: 0.7559 (tpp) cc_final: 0.7210 (tpp) REVERT: C 116 LEU cc_start: 0.9195 (tp) cc_final: 0.8827 (tp) REVERT: C 120 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8357 (tm) REVERT: C 130 GLU cc_start: 0.7586 (tp30) cc_final: 0.7230 (tp30) REVERT: C 207 GLU cc_start: 0.8107 (tp30) cc_final: 0.7812 (mm-30) REVERT: C 256 TYR cc_start: 0.8033 (t80) cc_final: 0.7516 (t80) REVERT: D 187 ILE cc_start: 0.9392 (pt) cc_final: 0.9132 (pt) REVERT: D 233 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8345 (tp-100) REVERT: E 44 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8692 (pp) REVERT: E 80 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8478 (mmmm) REVERT: E 86 LYS cc_start: 0.8540 (tppp) cc_final: 0.8306 (tppt) REVERT: F 5 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.6909 (tp) REVERT: F 80 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8386 (mmmm) REVERT: F 86 LYS cc_start: 0.8548 (tppp) cc_final: 0.8329 (tppt) outliers start: 114 outliers final: 82 residues processed: 337 average time/residue: 0.1894 time to fit residues: 90.2765 Evaluate side-chains 325 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 234 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** D 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9370 Z= 0.240 Angle : 0.736 9.542 12730 Z= 0.346 Chirality : 0.047 0.441 1528 Planarity : 0.005 0.094 1604 Dihedral : 10.166 59.678 1402 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 12.07 % Allowed : 26.96 % Favored : 60.97 % 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: -2.02 (0.23), residues: 1202 helix: -0.58 (0.20), residues: 646 sheet: -2.08 (0.54), residues: 80 loop : -2.18 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 195 HIS 0.004 0.001 HIS D 113 PHE 0.017 0.002 PHE A 65 TYR 0.014 0.002 TYR D 261 ARG 0.005 0.000 ARG F 46 *********************** 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 375 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 255 time to evaluate : 1.016 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: A 26 MET cc_start: 0.8711 (ppp) cc_final: 0.8508 (ppp) REVERT: A 56 MET cc_start: 0.7801 (ttp) cc_final: 0.7271 (ptt) REVERT: A 90 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8707 (tm) REVERT: A 106 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 133 GLU cc_start: 0.8482 (tt0) cc_final: 0.8204 (mt-10) REVERT: A 191 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7829 (p0) REVERT: A 195 TRP cc_start: 0.7350 (p90) cc_final: 0.7121 (p90) REVERT: A 197 MET cc_start: 0.7474 (tpt) cc_final: 0.6996 (tpp) REVERT: A 253 LEU cc_start: 0.8263 (tt) cc_final: 0.8050 (tt) REVERT: B 89 MET cc_start: 0.7883 (tmm) cc_final: 0.7567 (ppp) REVERT: B 90 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8686 (tm) REVERT: B 133 GLU cc_start: 0.8296 (tt0) cc_final: 0.8022 (mt-10) REVERT: B 176 SER cc_start: 0.7646 (m) cc_final: 0.7207 (t) REVERT: B 197 MET cc_start: 0.7426 (tpp) cc_final: 0.7198 (tpp) REVERT: C 116 LEU cc_start: 0.9168 (tp) cc_final: 0.8779 (tp) REVERT: C 120 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8325 (tm) REVERT: C 130 GLU cc_start: 0.7681 (tp30) cc_final: 0.7238 (tp30) REVERT: C 207 GLU cc_start: 0.8207 (tp30) cc_final: 0.7873 (mm-30) REVERT: C 256 TYR cc_start: 0.8020 (t80) cc_final: 0.7531 (t80) REVERT: D 187 ILE cc_start: 0.9400 (pt) cc_final: 0.9149 (pt) REVERT: D 233 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8212 (tp-100) REVERT: E 44 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8617 (pp) REVERT: E 86 LYS cc_start: 0.8532 (tppp) cc_final: 0.8316 (tppt) REVERT: F 79 ASP cc_start: 0.7927 (p0) cc_final: 0.7709 (p0) REVERT: F 80 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8370 (mmmm) REVERT: F 86 LYS cc_start: 0.8590 (tppp) cc_final: 0.8349 (tppt) outliers start: 120 outliers final: 83 residues processed: 341 average time/residue: 0.1820 time to fit residues: 88.3043 Evaluate side-chains 322 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 232 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 80 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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** F 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9370 Z= 0.214 Angle : 0.729 9.273 12730 Z= 0.342 Chirality : 0.046 0.361 1528 Planarity : 0.005 0.090 1604 Dihedral : 9.405 58.673 1387 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 10.87 % Allowed : 28.77 % Favored : 60.36 % 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: -1.96 (0.23), residues: 1202 helix: -0.48 (0.20), residues: 660 sheet: -2.32 (0.48), residues: 90 loop : -2.22 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 195 HIS 0.005 0.001 HIS D 113 PHE 0.022 0.002 PHE B 219 TYR 0.012 0.001 TYR D 261 ARG 0.008 0.000 ARG F 46 *********************** 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 357 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 249 time to evaluate : 1.448 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: A 56 MET cc_start: 0.7731 (ttp) cc_final: 0.7150 (ptt) REVERT: A 106 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7638 (mt) REVERT: A 191 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7803 (p0) REVERT: A 195 TRP cc_start: 0.7303 (p90) cc_final: 0.6669 (p90) REVERT: A 197 MET cc_start: 0.7508 (tpt) cc_final: 0.7046 (tpp) REVERT: B 89 MET cc_start: 0.7849 (tmm) cc_final: 0.7525 (ppp) REVERT: B 90 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8663 (tm) REVERT: B 106 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7621 (mt) REVERT: B 133 GLU cc_start: 0.8309 (tt0) cc_final: 0.8054 (mt-10) REVERT: B 176 SER cc_start: 0.7702 (m) cc_final: 0.7270 (t) REVERT: B 197 MET cc_start: 0.7304 (tpp) cc_final: 0.6969 (tpp) REVERT: C 91 PHE cc_start: 0.7642 (m-80) cc_final: 0.7092 (m-80) REVERT: C 116 LEU cc_start: 0.9172 (tp) cc_final: 0.8826 (tp) REVERT: C 120 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8327 (tm) REVERT: C 130 GLU cc_start: 0.7615 (tp30) cc_final: 0.7123 (tp30) REVERT: C 256 TYR cc_start: 0.8032 (t80) cc_final: 0.7583 (t80) REVERT: D 91 PHE cc_start: 0.7625 (m-80) cc_final: 0.7396 (m-80) REVERT: D 166 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8825 (tt) REVERT: D 187 ILE cc_start: 0.9438 (pt) cc_final: 0.9191 (pt) REVERT: D 233 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8181 (tp-100) REVERT: E 9 GLN cc_start: 0.7364 (tt0) cc_final: 0.6351 (tp-100) REVERT: E 44 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8572 (pp) REVERT: E 86 LYS cc_start: 0.8606 (tppp) cc_final: 0.8356 (tppt) REVERT: F 33 GLU cc_start: 0.9031 (pm20) cc_final: 0.8387 (pm20) REVERT: F 79 ASP cc_start: 0.8006 (p0) cc_final: 0.7784 (p0) REVERT: F 80 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8357 (mmmm) REVERT: F 86 LYS cc_start: 0.8594 (tppp) cc_final: 0.8328 (tppt) outliers start: 108 outliers final: 78 residues processed: 325 average time/residue: 0.1843 time to fit residues: 84.8140 Evaluate side-chains 324 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 239 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7981 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9370 Z= 0.210 Angle : 0.743 9.928 12730 Z= 0.348 Chirality : 0.046 0.333 1528 Planarity : 0.005 0.089 1604 Dihedral : 8.965 59.293 1378 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 9.76 % Allowed : 30.38 % Favored : 59.86 % 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: -1.77 (0.24), residues: 1202 helix: -0.32 (0.20), residues: 662 sheet: -2.09 (0.48), residues: 90 loop : -2.19 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 195 HIS 0.006 0.001 HIS D 113 PHE 0.022 0.002 PHE B 219 TYR 0.011 0.001 TYR D 261 ARG 0.009 0.000 ARG F 46 *********************** 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 341 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 244 time to evaluate : 1.082 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: A 56 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7130 (ptt) REVERT: A 89 MET cc_start: 0.7556 (ppp) cc_final: 0.7221 (ppp) REVERT: A 106 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7710 (mt) REVERT: A 191 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7734 (p0) REVERT: A 197 MET cc_start: 0.7454 (tpt) cc_final: 0.6966 (tpp) REVERT: A 198 ASP cc_start: 0.7472 (m-30) cc_final: 0.7159 (m-30) REVERT: B 76 LEU cc_start: 0.8836 (mp) cc_final: 0.8411 (mt) REVERT: B 89 MET cc_start: 0.7803 (tmm) cc_final: 0.7488 (ppp) REVERT: B 90 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8703 (tm) REVERT: B 106 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7542 (mt) REVERT: B 133 GLU cc_start: 0.8290 (tt0) cc_final: 0.8074 (mt-10) REVERT: B 197 MET cc_start: 0.7288 (tpp) cc_final: 0.6902 (tpp) REVERT: C 80 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.7992 (tp) REVERT: C 91 PHE cc_start: 0.7300 (m-80) cc_final: 0.7069 (m-80) REVERT: C 113 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7153 (m90) REVERT: C 116 LEU cc_start: 0.9153 (tp) cc_final: 0.8763 (tp) REVERT: C 120 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8336 (tm) REVERT: C 130 GLU cc_start: 0.7573 (tp30) cc_final: 0.7265 (tp30) REVERT: C 256 TYR cc_start: 0.8000 (t80) cc_final: 0.7587 (t80) REVERT: D 187 ILE cc_start: 0.9414 (pt) cc_final: 0.9170 (pt) REVERT: D 233 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8138 (tp-100) REVERT: E 86 LYS cc_start: 0.8618 (tppp) cc_final: 0.8359 (tppt) REVERT: F 80 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8299 (mmmm) REVERT: F 86 LYS cc_start: 0.8595 (tppp) cc_final: 0.8319 (tppt) outliers start: 97 outliers final: 77 residues processed: 310 average time/residue: 0.1846 time to fit residues: 81.5470 Evaluate side-chains 317 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 232 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0370 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9370 Z= 0.210 Angle : 0.737 9.059 12730 Z= 0.345 Chirality : 0.046 0.292 1528 Planarity : 0.005 0.086 1604 Dihedral : 8.663 59.838 1374 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 10.26 % Allowed : 31.09 % Favored : 58.65 % 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: -1.68 (0.23), residues: 1202 helix: -0.25 (0.20), residues: 670 sheet: -2.01 (0.53), residues: 80 loop : -2.19 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 195 HIS 0.006 0.001 HIS D 113 PHE 0.023 0.002 PHE B 219 TYR 0.009 0.001 TYR D 261 ARG 0.008 0.000 ARG E 46 *********************** 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 342 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 240 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: A 56 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7120 (ptt) REVERT: A 134 MET cc_start: 0.8538 (tpt) cc_final: 0.8137 (mmt) REVERT: A 191 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 197 MET cc_start: 0.7395 (tpt) cc_final: 0.6890 (tpp) REVERT: B 76 LEU cc_start: 0.8827 (mp) cc_final: 0.8406 (mt) REVERT: B 89 MET cc_start: 0.7798 (tmm) cc_final: 0.7467 (ppp) REVERT: B 90 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8697 (tm) REVERT: B 106 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7554 (mt) REVERT: B 133 GLU cc_start: 0.8337 (tt0) cc_final: 0.8084 (mt-10) REVERT: B 197 MET cc_start: 0.7308 (tpp) cc_final: 0.6722 (tpp) REVERT: C 91 PHE cc_start: 0.7278 (m-80) cc_final: 0.7060 (m-80) REVERT: C 113 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7080 (m90) REVERT: C 116 LEU cc_start: 0.9140 (tp) cc_final: 0.8762 (tp) REVERT: C 120 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8395 (tm) REVERT: C 130 GLU cc_start: 0.7640 (tp30) cc_final: 0.7359 (tp30) REVERT: C 256 TYR cc_start: 0.7954 (t80) cc_final: 0.7584 (t80) REVERT: D 149 MET cc_start: 0.7840 (mtm) cc_final: 0.7598 (mtm) REVERT: D 187 ILE cc_start: 0.9403 (pt) cc_final: 0.9157 (pt) REVERT: D 233 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8115 (tp-100) REVERT: D 256 TYR cc_start: 0.7848 (t80) cc_final: 0.7520 (t80) REVERT: E 86 LYS cc_start: 0.8643 (tppp) cc_final: 0.8372 (tppt) REVERT: F 80 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8401 (mmmm) REVERT: F 82 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: F 86 LYS cc_start: 0.8668 (tppp) cc_final: 0.8392 (tppt) outliers start: 102 outliers final: 81 residues processed: 308 average time/residue: 0.1854 time to fit residues: 80.7949 Evaluate side-chains 320 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 232 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 0.0470 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- 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** C 226 HIS D 115 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 9370 Z= 0.314 Angle : 0.780 8.953 12730 Z= 0.373 Chirality : 0.047 0.230 1528 Planarity : 0.005 0.087 1604 Dihedral : 8.641 59.984 1369 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 10.66 % Allowed : 30.38 % Favored : 58.95 % 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: -1.61 (0.24), residues: 1202 helix: -0.24 (0.20), residues: 660 sheet: -1.81 (0.52), residues: 90 loop : -2.07 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 195 HIS 0.003 0.001 HIS D 113 PHE 0.037 0.002 PHE C 243 TYR 0.013 0.002 TYR C 261 ARG 0.007 0.001 ARG F 46 *********************** 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 340 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 234 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7578 (ppp) cc_final: 0.7268 (ppp) REVERT: A 134 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8341 (mmt) REVERT: A 191 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7678 (p0) REVERT: A 197 MET cc_start: 0.7543 (tpt) cc_final: 0.7233 (tpp) REVERT: B 76 LEU cc_start: 0.8802 (mp) cc_final: 0.8378 (mt) REVERT: B 106 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7696 (mt) REVERT: B 133 GLU cc_start: 0.8353 (tt0) cc_final: 0.8091 (mt-10) REVERT: B 197 MET cc_start: 0.7363 (tpp) cc_final: 0.7116 (tpp) REVERT: C 113 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7316 (m90) REVERT: C 116 LEU cc_start: 0.9194 (tp) cc_final: 0.8818 (tp) REVERT: C 120 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8517 (tm) REVERT: C 130 GLU cc_start: 0.7688 (tp30) cc_final: 0.7398 (tp30) REVERT: C 256 TYR cc_start: 0.8097 (t80) cc_final: 0.7686 (t80) REVERT: D 89 MET cc_start: 0.8004 (ttm) cc_final: 0.7760 (ttm) REVERT: D 187 ILE cc_start: 0.9429 (pt) cc_final: 0.9219 (pt) REVERT: D 233 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8191 (tp-100) REVERT: D 256 TYR cc_start: 0.7945 (t80) cc_final: 0.7635 (t80) REVERT: E 86 LYS cc_start: 0.8744 (tppp) cc_final: 0.8456 (tppt) REVERT: F 80 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8406 (mmmm) REVERT: F 82 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: F 86 LYS cc_start: 0.8730 (tppp) cc_final: 0.8441 (tppt) outliers start: 106 outliers final: 89 residues processed: 308 average time/residue: 0.1848 time to fit residues: 80.8646 Evaluate side-chains 318 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 223 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 MET Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 230 GLN Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9370 Z= 0.226 Angle : 0.781 8.985 12730 Z= 0.367 Chirality : 0.047 0.227 1528 Planarity : 0.005 0.083 1604 Dihedral : 8.432 59.026 1366 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 9.15 % Allowed : 32.29 % Favored : 58.55 % 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: -1.59 (0.24), residues: 1202 helix: -0.23 (0.20), residues: 672 sheet: -1.71 (0.53), residues: 90 loop : -2.12 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 195 HIS 0.015 0.001 HIS C 226 PHE 0.028 0.002 PHE B 219 TYR 0.012 0.002 TYR C 261 ARG 0.003 0.000 ARG E 46 *********************** 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 324 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 233 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7036 (ptt) REVERT: A 89 MET cc_start: 0.7497 (ppp) cc_final: 0.7172 (ppp) REVERT: A 191 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7653 (p0) REVERT: A 196 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.5548 (ttm170) REVERT: A 197 MET cc_start: 0.7578 (tpt) cc_final: 0.7307 (tpp) REVERT: B 76 LEU cc_start: 0.8777 (mp) cc_final: 0.8343 (mt) REVERT: B 106 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7637 (mt) REVERT: B 133 GLU cc_start: 0.8358 (tt0) cc_final: 0.8100 (mt-10) REVERT: B 197 MET cc_start: 0.7453 (tpp) cc_final: 0.7168 (tpp) REVERT: C 113 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.6955 (m90) REVERT: C 116 LEU cc_start: 0.9154 (tp) cc_final: 0.8841 (tp) REVERT: C 120 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (tm) REVERT: C 130 GLU cc_start: 0.7656 (tp30) cc_final: 0.7332 (tp30) REVERT: C 256 TYR cc_start: 0.8057 (t80) cc_final: 0.7655 (t80) REVERT: D 149 MET cc_start: 0.7843 (mtm) cc_final: 0.7588 (mtm) REVERT: D 187 ILE cc_start: 0.9410 (pt) cc_final: 0.9182 (pt) REVERT: D 233 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8164 (tp-100) REVERT: D 256 TYR cc_start: 0.7872 (t80) cc_final: 0.7536 (t80) REVERT: E 86 LYS cc_start: 0.8718 (tppp) cc_final: 0.8423 (tppt) REVERT: F 80 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8407 (mmmm) REVERT: F 82 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: F 86 LYS cc_start: 0.8731 (tppp) cc_final: 0.8447 (tppt) outliers start: 91 outliers final: 73 residues processed: 294 average time/residue: 0.1954 time to fit residues: 80.4494 Evaluate side-chains 303 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 223 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** C 226 HIS D 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4861 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= 0.216 Angle : 0.810 11.641 12730 Z= 0.375 Chirality : 0.048 0.258 1528 Planarity : 0.005 0.077 1604 Dihedral : 8.356 59.875 1364 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 7.75 % Allowed : 33.90 % Favored : 58.35 % 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: -1.34 (0.24), residues: 1202 helix: 0.00 (0.20), residues: 662 sheet: -1.60 (0.55), residues: 90 loop : -2.02 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 195 HIS 0.007 0.001 HIS D 113 PHE 0.039 0.002 PHE C 243 TYR 0.013 0.001 TYR C 261 ARG 0.005 0.000 ARG D 151 ********************** 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 318 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 241 time to evaluate : 1.014 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: A 56 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.6996 (ptt) REVERT: A 89 MET cc_start: 0.7474 (ppp) cc_final: 0.7144 (ppp) REVERT: A 191 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7630 (p0) REVERT: A 196 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.5465 (ttm170) REVERT: A 197 MET cc_start: 0.7572 (tpt) cc_final: 0.7345 (tpp) REVERT: A 198 ASP cc_start: 0.7540 (p0) cc_final: 0.7174 (p0) REVERT: B 76 LEU cc_start: 0.8769 (mp) cc_final: 0.8324 (mt) REVERT: B 133 GLU cc_start: 0.8382 (tt0) cc_final: 0.8110 (mt-10) REVERT: C 91 PHE cc_start: 0.7371 (m-80) cc_final: 0.6982 (m-80) REVERT: C 113 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7109 (m90) REVERT: C 116 LEU cc_start: 0.9126 (tp) cc_final: 0.8833 (tp) REVERT: C 130 GLU cc_start: 0.7620 (tp30) cc_final: 0.7320 (tp30) REVERT: C 256 TYR cc_start: 0.8052 (t80) cc_final: 0.7645 (t80) REVERT: D 149 MET cc_start: 0.7819 (mtm) cc_final: 0.7564 (mtm) REVERT: D 187 ILE cc_start: 0.9375 (pt) cc_final: 0.9131 (pt) REVERT: D 233 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8117 (tp-100) REVERT: D 256 TYR cc_start: 0.7858 (t80) cc_final: 0.7492 (t80) REVERT: E 86 LYS cc_start: 0.8709 (tppp) cc_final: 0.8417 (tppt) REVERT: F 82 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: F 86 LYS cc_start: 0.8724 (tppp) cc_final: 0.8432 (tppt) outliers start: 77 outliers final: 66 residues processed: 289 average time/residue: 0.1924 time to fit residues: 77.9582 Evaluate side-chains 304 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 233 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 113 HIS Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 71 ASN Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 82 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 201 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 226 HIS D 57 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.088795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075519 restraints weight = 27170.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077590 restraints weight = 15675.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078642 restraints weight = 10647.625| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4993 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= 0.220 Angle : 0.818 11.740 12730 Z= 0.378 Chirality : 0.047 0.229 1528 Planarity : 0.005 0.078 1604 Dihedral : 8.081 58.412 1352 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 7.44 % Allowed : 34.00 % Favored : 58.55 % 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: -1.21 (0.24), residues: 1202 helix: 0.13 (0.20), residues: 660 sheet: -1.57 (0.56), residues: 90 loop : -1.97 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 195 HIS 0.012 0.001 HIS C 226 PHE 0.041 0.002 PHE A 219 TYR 0.012 0.001 TYR C 261 ARG 0.004 0.000 ARG F 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.05 seconds wall clock time: 41 minutes 28.09 seconds (2488.09 seconds total)