Starting phenix.real_space_refine on Mon Mar 11 11:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/03_2024/7m42_23662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/03_2024/7m42_23662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/03_2024/7m42_23662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/03_2024/7m42_23662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/03_2024/7m42_23662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/03_2024/7m42_23662.pdb" } resolution = 3.3 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= 0.035 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 31 5.16 5 C 5110 2.51 5 N 1362 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 427": "OD1" <-> "OD2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "E GLU 484": "OE1" <-> "OE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 56": "NH1" <-> "NH2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8115 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1551 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 210} Chain: "E" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1572 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Chain: "D" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1700 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.67, per 1000 atoms: 0.58 Number of scatterers: 8115 At special positions: 0 Unit cell: (74.8, 114.75, 148.75, 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 31 16.00 O 1612 8.00 N 1362 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 199 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG F 1 " - " ASN E 343 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 25 sheets defined 8.7% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.764A pdb=" N ASP A 84 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.707A pdb=" N HIS A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.154A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.024A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.964A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 409 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 410' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'C' and resid 127 through 133 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.619A pdb=" N TRP C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.409A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP A 37 " --> pdb=" O MET A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.409A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.186A pdb=" N TYR A 176 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.186A pdb=" N TYR A 176 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.378A pdb=" N TRP A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.849A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 117 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 134 removed outlier: 6.107A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.661A pdb=" N SER B 142 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 164 removed outlier: 4.259A pdb=" N TYR B 204 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.822A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.725A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.725A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.253A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.253A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.497A pdb=" N TRP C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC4, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.920A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.311A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 146 through 147 removed outlier: 4.142A pdb=" N SER D 147 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.576A pdb=" N TYR D 209 " --> pdb=" O VAL D 226 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 870 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: 2.52 Time building geometry restraints manager: 3.06 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: 2583 1.34 - 1.46: 2120 1.46 - 1.58: 3581 1.58 - 1.70: 0 1.70 - 1.83: 38 Bond restraints: 8322 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.25e+00 ... (remaining 8317 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 304 106.87 - 113.65: 4538 113.65 - 120.43: 2908 120.43 - 127.21: 3498 127.21 - 133.99: 101 Bond angle restraints: 11349 Sorted by residual: angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 109.24 100.09 9.15 1.67e+00 3.59e-01 3.00e+01 angle pdb=" C ASP A 52 " pdb=" N VAL A 53 " pdb=" CA VAL A 53 " ideal model delta sigma weight residual 121.97 128.67 -6.70 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N VAL A 53 " pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 109.34 116.23 -6.89 2.08e+00 2.31e-01 1.10e+01 angle pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sigma weight residual 116.30 125.15 -8.85 3.50e+00 8.16e-02 6.39e+00 angle pdb=" CA GLU C 204 " pdb=" CB GLU C 204 " pdb=" CG GLU C 204 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.41e+00 ... (remaining 11344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.96: 4677 21.96 - 43.91: 243 43.91 - 65.87: 33 65.87 - 87.82: 17 87.82 - 109.78: 4 Dihedral angle restraints: 4974 sinusoidal: 1901 harmonic: 3073 Sorted by residual: dihedral pdb=" CB CYS D 155 " pdb=" SG CYS D 155 " pdb=" SG CYS D 211 " pdb=" CB CYS D 211 " ideal model delta sinusoidal sigma weight residual 93.00 44.21 48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 56.19 36.81 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS C 140 " pdb=" SG CYS C 140 " pdb=" SG CYS C 199 " pdb=" CB CYS C 199 " ideal model delta sinusoidal sigma weight residual 93.00 58.27 34.73 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 4971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1044 0.052 - 0.103: 176 0.103 - 0.155: 44 0.155 - 0.206: 5 0.206 - 0.258: 2 Chirality restraints: 1271 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS D 221 " pdb=" N LYS D 221 " pdb=" C LYS D 221 " pdb=" CB LYS D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1268 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 97 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ALA D 97 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA D 97 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS D 98 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " -0.019 2.00e-02 2.50e+03 1.79e-02 4.02e+00 pdb=" CG ASN E 343 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 163 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 164 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 136 2.68 - 3.24: 7148 3.24 - 3.79: 11566 3.79 - 4.35: 15577 4.35 - 4.90: 26834 Nonbonded interactions: 61261 Sorted by model distance: nonbonded pdb=" O ASP A 52 " pdb=" N SER A 54 " model vdw 2.128 2.520 nonbonded pdb=" OG SER A 65 " pdb=" OG1 THR A 76 " model vdw 2.135 2.440 nonbonded pdb=" OG SER D 52 " pdb=" OG SER D 57 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR B 155 " pdb=" OE2 GLU B 158 " model vdw 2.217 2.440 nonbonded pdb=" O HIS A 201 " pdb=" OG SER A 204 " model vdw 2.270 2.440 ... (remaining 61256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.010 Extract box with map and model: 6.070 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 24.400 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.002 0.033 8322 Z= 0.130 Angle : 0.557 9.147 11349 Z= 0.296 Chirality : 0.045 0.258 1271 Planarity : 0.004 0.042 1456 Dihedral : 13.897 109.779 2984 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.22 % Allowed : 10.33 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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: -2.65 (0.23), residues: 1060 helix: -3.74 (0.36), residues: 72 sheet: -0.76 (0.23), residues: 438 loop : -2.36 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.001 0.000 HIS B 210 PHE 0.008 0.001 PHE C 145 TYR 0.019 0.001 TYR E 351 ARG 0.007 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.913 Fit side-chains REVERT: E 458 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8286 (mttp) REVERT: C 55 ASN cc_start: 0.8319 (m-40) cc_final: 0.8099 (m110) REVERT: C 83 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7361 (tm-30) outliers start: 11 outliers final: 3 residues processed: 136 average time/residue: 0.1726 time to fit residues: 33.4969 Evaluate side-chains 93 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 192 HIS A 198 GLN E 370 ASN E 493 GLN C 16 GLN C 28 ASN C 194 HIS D 170 ASN D 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8322 Z= 0.147 Angle : 0.515 10.934 11349 Z= 0.259 Chirality : 0.044 0.179 1271 Planarity : 0.004 0.043 1456 Dihedral : 6.108 60.429 1216 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 3.44 % Allowed : 14.44 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.81 (0.24), residues: 1060 helix: -2.87 (0.48), residues: 68 sheet: -0.14 (0.24), residues: 440 loop : -1.91 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 53 HIS 0.002 0.000 HIS D 35 PHE 0.011 0.001 PHE E 377 TYR 0.024 0.001 TYR C 93 ARG 0.004 0.000 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.880 Fit side-chains REVERT: E 335 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.4489 (tt) REVERT: E 354 ASN cc_start: 0.8083 (t0) cc_final: 0.7799 (t0) REVERT: E 458 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8281 (mttp) REVERT: E 471 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: C 83 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7362 (tm-30) outliers start: 31 outliers final: 20 residues processed: 118 average time/residue: 0.1463 time to fit residues: 26.1805 Evaluate side-chains 105 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8322 Z= 0.177 Angle : 0.528 10.717 11349 Z= 0.263 Chirality : 0.044 0.188 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.631 39.554 1214 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 3.89 % Allowed : 17.00 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.45 (0.24), residues: 1060 helix: -2.76 (0.46), residues: 76 sheet: 0.16 (0.25), residues: 433 loop : -1.65 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.026 0.001 PHE A 143 TYR 0.014 0.001 TYR C 93 ARG 0.002 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 0.766 Fit side-chains REVERT: A 56 ARG cc_start: 0.7883 (ptt-90) cc_final: 0.7561 (ptp90) REVERT: E 335 LEU cc_start: 0.4773 (OUTLIER) cc_final: 0.4531 (tt) REVERT: E 354 ASN cc_start: 0.8182 (t0) cc_final: 0.7877 (t0) REVERT: E 420 ASP cc_start: 0.7630 (m-30) cc_final: 0.7315 (m-30) REVERT: E 458 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8236 (mttp) REVERT: C 55 ASN cc_start: 0.8687 (m110) cc_final: 0.8325 (m110) REVERT: C 83 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7315 (tm-30) REVERT: C 93 TYR cc_start: 0.8475 (t80) cc_final: 0.8207 (t80) REVERT: D 43 LYS cc_start: 0.7860 (mmmm) cc_final: 0.7393 (mmtm) outliers start: 35 outliers final: 27 residues processed: 122 average time/residue: 0.1503 time to fit residues: 26.9137 Evaluate side-chains 116 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 101 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8322 Z= 0.128 Angle : 0.508 9.766 11349 Z= 0.253 Chirality : 0.043 0.185 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.265 39.592 1214 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer: Outliers : 3.67 % Allowed : 17.67 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.22 (0.25), residues: 1060 helix: -2.50 (0.53), residues: 64 sheet: 0.25 (0.24), residues: 437 loop : -1.51 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.003 0.000 HIS D 35 PHE 0.021 0.001 PHE A 143 TYR 0.012 0.001 TYR D 95 ARG 0.002 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.951 Fit side-chains REVERT: A 56 ARG cc_start: 0.7863 (ptt-90) cc_final: 0.7521 (ptp90) REVERT: E 335 LEU cc_start: 0.4706 (OUTLIER) cc_final: 0.4464 (tt) REVERT: E 354 ASN cc_start: 0.8182 (t0) cc_final: 0.7821 (t0) REVERT: E 420 ASP cc_start: 0.7657 (m-30) cc_final: 0.7338 (m-30) REVERT: E 458 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8236 (mttp) REVERT: C 55 ASN cc_start: 0.8662 (m110) cc_final: 0.8296 (m110) REVERT: C 83 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 43 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7455 (mmtm) outliers start: 33 outliers final: 25 residues processed: 120 average time/residue: 0.1641 time to fit residues: 28.8846 Evaluate side-chains 113 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 87 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 1 optimal weight: 0.0370 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 51 optimal weight: 0.0870 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8322 Z= 0.113 Angle : 0.510 12.420 11349 Z= 0.249 Chirality : 0.042 0.190 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.139 38.572 1214 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 3.11 % Allowed : 19.44 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.25), residues: 1060 helix: -2.47 (0.51), residues: 70 sheet: 0.49 (0.24), residues: 439 loop : -1.36 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.002 0.001 HIS D 35 PHE 0.022 0.001 PHE A 143 TYR 0.033 0.001 TYR C 93 ARG 0.002 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.018 Fit side-chains REVERT: A 56 ARG cc_start: 0.7774 (ptt-90) cc_final: 0.7448 (ptp90) REVERT: E 335 LEU cc_start: 0.4564 (OUTLIER) cc_final: 0.4338 (tt) REVERT: E 354 ASN cc_start: 0.8156 (t0) cc_final: 0.7794 (t0) REVERT: E 420 ASP cc_start: 0.7729 (m-30) cc_final: 0.7391 (m-30) REVERT: E 458 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8224 (mttp) REVERT: C 55 ASN cc_start: 0.8654 (m110) cc_final: 0.8289 (m110) REVERT: C 83 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7248 (tm-30) REVERT: D 43 LYS cc_start: 0.7778 (mmmm) cc_final: 0.7287 (mmtm) outliers start: 28 outliers final: 20 residues processed: 113 average time/residue: 0.1637 time to fit residues: 27.5902 Evaluate side-chains 108 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 53 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8322 Z= 0.133 Angle : 0.511 11.355 11349 Z= 0.251 Chirality : 0.042 0.185 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.129 36.586 1214 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 3.44 % Allowed : 19.11 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.25), residues: 1060 helix: -2.43 (0.51), residues: 70 sheet: 0.58 (0.25), residues: 432 loop : -1.26 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.018 0.001 PHE A 143 TYR 0.022 0.001 TYR C 93 ARG 0.003 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 0.894 Fit side-chains REVERT: E 335 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4350 (tt) REVERT: E 354 ASN cc_start: 0.8173 (t0) cc_final: 0.7804 (m-40) REVERT: E 420 ASP cc_start: 0.7747 (m-30) cc_final: 0.7405 (m-30) REVERT: E 458 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8225 (mttp) REVERT: C 83 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7235 (tm-30) REVERT: D 43 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7338 (mmtm) outliers start: 31 outliers final: 26 residues processed: 113 average time/residue: 0.1591 time to fit residues: 26.7699 Evaluate side-chains 112 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 63 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8322 Z= 0.111 Angle : 0.506 12.570 11349 Z= 0.246 Chirality : 0.042 0.190 1271 Planarity : 0.004 0.044 1456 Dihedral : 4.030 35.133 1214 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.56 % Allowed : 19.67 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1060 helix: -2.38 (0.51), residues: 70 sheet: 0.71 (0.25), residues: 439 loop : -1.19 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.003 0.000 HIS D 35 PHE 0.020 0.001 PHE A 143 TYR 0.019 0.001 TYR C 93 ARG 0.002 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.905 Fit side-chains REVERT: E 335 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.4344 (tt) REVERT: E 354 ASN cc_start: 0.8168 (t0) cc_final: 0.7813 (t0) REVERT: E 390 LEU cc_start: 0.7367 (tp) cc_final: 0.7092 (tp) REVERT: E 458 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8225 (mttp) REVERT: C 83 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 43 LYS cc_start: 0.7746 (mmmm) cc_final: 0.7285 (mmtm) REVERT: D 80 TYR cc_start: 0.7793 (m-80) cc_final: 0.6985 (m-80) outliers start: 32 outliers final: 25 residues processed: 117 average time/residue: 0.1495 time to fit residues: 26.1681 Evaluate side-chains 115 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 0.0770 chunk 96 optimal weight: 0.1980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8322 Z= 0.128 Angle : 0.512 12.568 11349 Z= 0.250 Chirality : 0.043 0.197 1271 Planarity : 0.004 0.044 1456 Dihedral : 4.035 34.266 1214 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.00 % Allowed : 19.89 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1060 helix: -2.13 (0.56), residues: 64 sheet: 0.82 (0.25), residues: 437 loop : -1.18 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.002 0.000 HIS D 35 PHE 0.020 0.001 PHE A 143 TYR 0.016 0.001 TYR C 93 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.933 Fit side-chains REVERT: E 335 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4388 (tt) REVERT: E 354 ASN cc_start: 0.8204 (t0) cc_final: 0.7860 (t0) REVERT: E 406 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: E 458 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8226 (mttp) REVERT: C 55 ASN cc_start: 0.8757 (m110) cc_final: 0.8389 (m110) REVERT: C 83 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 43 LYS cc_start: 0.7775 (mmmm) cc_final: 0.7320 (mmtm) REVERT: D 80 TYR cc_start: 0.7805 (m-80) cc_final: 0.6996 (m-80) REVERT: D 115 MET cc_start: 0.7871 (mtt) cc_final: 0.7619 (mtt) outliers start: 27 outliers final: 24 residues processed: 110 average time/residue: 0.1599 time to fit residues: 26.1896 Evaluate side-chains 115 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8322 Z= 0.246 Angle : 0.561 12.301 11349 Z= 0.281 Chirality : 0.044 0.210 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.429 36.222 1214 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.96 % Rotamer: Outliers : 3.56 % Allowed : 20.33 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.25), residues: 1060 helix: -2.39 (0.52), residues: 69 sheet: 0.71 (0.25), residues: 432 loop : -1.23 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 53 HIS 0.003 0.001 HIS D 35 PHE 0.019 0.002 PHE E 515 TYR 0.015 0.001 TYR C 93 ARG 0.003 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 0.869 Fit side-chains REVERT: E 335 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4323 (tt) REVERT: E 354 ASN cc_start: 0.8269 (t0) cc_final: 0.7906 (t0) REVERT: E 458 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8256 (mttp) REVERT: C 83 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7224 (tm-30) REVERT: C 93 TYR cc_start: 0.8486 (t80) cc_final: 0.8188 (t80) REVERT: D 43 LYS cc_start: 0.7666 (mmmm) cc_final: 0.7257 (mmtm) REVERT: D 65 LYS cc_start: 0.8152 (tptt) cc_final: 0.7898 (tttm) REVERT: D 76 LYS cc_start: 0.7863 (mptt) cc_final: 0.7464 (mmtp) REVERT: D 115 MET cc_start: 0.8123 (mtt) cc_final: 0.7912 (mtt) outliers start: 32 outliers final: 26 residues processed: 115 average time/residue: 0.1587 time to fit residues: 26.7222 Evaluate side-chains 116 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9811 > 50: distance: 27 - 224: 29.690 distance: 30 - 221: 19.665 distance: 44 - 201: 7.015 distance: 47 - 198: 14.565 distance: 81 - 231: 16.931 distance: 84 - 228: 20.053 distance: 93 - 213: 13.146 distance: 96 - 210: 12.424 distance: 149 - 155: 21.870 distance: 155 - 156: 33.544 distance: 156 - 157: 42.555 distance: 157 - 158: 26.284 distance: 157 - 159: 34.763 distance: 158 - 170: 40.642 distance: 159 - 160: 13.545 distance: 160 - 161: 14.112 distance: 160 - 163: 10.115 distance: 161 - 162: 20.763 distance: 161 - 166: 7.966 distance: 163 - 164: 14.984 distance: 163 - 165: 24.003 distance: 166 - 167: 10.212 distance: 167 - 168: 22.135 distance: 168 - 169: 23.702 distance: 168 - 170: 29.636 distance: 170 - 171: 14.515 distance: 171 - 172: 15.971 distance: 171 - 174: 16.820 distance: 172 - 173: 48.895 distance: 172 - 182: 15.030 distance: 174 - 175: 20.287 distance: 175 - 176: 9.711 distance: 175 - 177: 19.002 distance: 176 - 178: 10.529 distance: 177 - 179: 26.896 distance: 178 - 180: 21.319 distance: 179 - 180: 21.683 distance: 180 - 181: 13.536 distance: 182 - 183: 17.391 distance: 183 - 184: 30.680 distance: 183 - 186: 28.781 distance: 184 - 185: 8.550 distance: 184 - 191: 15.700 distance: 186 - 187: 32.742 distance: 187 - 188: 31.437 distance: 188 - 189: 26.566 distance: 188 - 190: 20.076 distance: 191 - 192: 9.993 distance: 191 - 197: 4.295 distance: 192 - 193: 10.140 distance: 192 - 195: 20.715 distance: 193 - 194: 7.783 distance: 193 - 198: 9.147 distance: 195 - 196: 20.787 distance: 196 - 197: 16.611 distance: 198 - 199: 15.285 distance: 199 - 200: 10.450 distance: 199 - 202: 6.731 distance: 200 - 201: 9.571 distance: 200 - 210: 5.174 distance: 202 - 203: 5.812 distance: 203 - 204: 9.403 distance: 203 - 205: 12.059 distance: 204 - 206: 11.722 distance: 205 - 207: 10.768 distance: 206 - 208: 7.364 distance: 207 - 208: 15.283 distance: 208 - 209: 7.897 distance: 210 - 211: 8.672 distance: 211 - 212: 13.962 distance: 211 - 214: 12.465 distance: 212 - 213: 18.767 distance: 212 - 221: 21.060 distance: 214 - 215: 20.860 distance: 215 - 216: 18.657 distance: 216 - 217: 7.540 distance: 217 - 218: 13.679 distance: 218 - 219: 15.450 distance: 218 - 220: 15.832 distance: 221 - 222: 24.913 distance: 222 - 223: 10.783 distance: 222 - 225: 11.985 distance: 223 - 224: 47.779 distance: 223 - 228: 38.514 distance: 225 - 226: 16.933 distance: 225 - 227: 13.809 distance: 228 - 229: 16.371 distance: 229 - 230: 9.366 distance: 229 - 232: 10.384 distance: 230 - 231: 24.551 distance: 230 - 235: 5.587 distance: 232 - 233: 27.094 distance: 232 - 234: 22.426