Starting phenix.real_space_refine on Fri Dec 8 10:40:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/12_2023/7m42_23662.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/12_2023/7m42_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_23662/12_2023/7m42_23662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/12_2023/7m42_23662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/12_2023/7m42_23662.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m42_23662/12_2023/7m42_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.77, per 1000 atoms: 0.59 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 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: 2.29 Time building geometry restraints manager: 3.23 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 - 17.03: 4512 17.03 - 34.06: 346 34.06 - 51.09: 79 51.09 - 68.12: 10 68.12 - 85.15: 8 Dihedral angle restraints: 4955 sinusoidal: 1882 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 4952 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: 1.300 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: 5.930 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.080 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- 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 : 12.880 85.147 2965 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 : 0.793 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 136 average time/residue: 0.1683 time to fit residues: 32.6500 Evaluate side-chains 92 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0685 time to fit residues: 1.5343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 D 212 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8322 Z= 0.162 Angle : 0.517 10.899 11349 Z= 0.262 Chirality : 0.043 0.180 1271 Planarity : 0.004 0.044 1456 Dihedral : 4.046 44.534 1193 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 3.33 % Allowed : 14.44 % Favored : 82.22 % 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: -1.88 (0.24), residues: 1060 helix: -2.96 (0.47), residues: 68 sheet: -0.20 (0.24), residues: 439 loop : -1.94 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 53 HIS 0.003 0.001 HIS D 35 PHE 0.007 0.001 PHE E 377 TYR 0.026 0.001 TYR C 93 ARG 0.003 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 121 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.901 Fit side-chains outliers start: 30 outliers final: 20 residues processed: 114 average time/residue: 0.1561 time to fit residues: 26.6208 Evaluate side-chains 103 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0695 time to fit residues: 3.7981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.6537 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8322 Z= 0.232 Angle : 0.553 9.157 11349 Z= 0.279 Chirality : 0.044 0.187 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.381 40.448 1193 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 2.67 % Allowed : 17.22 % Favored : 80.11 % 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: -1.59 (0.24), residues: 1060 helix: -2.71 (0.47), residues: 70 sheet: 0.00 (0.25), residues: 440 loop : -1.74 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 53 HIS 0.003 0.001 HIS D 35 PHE 0.024 0.002 PHE A 143 TYR 0.013 0.001 TYR E 453 ARG 0.003 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 122 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.899 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.1529 time to fit residues: 26.2208 Evaluate side-chains 103 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0775 time to fit residues: 3.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 0.0770 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.1954 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= 0.206 Angle : 0.550 10.961 11349 Z= 0.277 Chirality : 0.044 0.192 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.418 39.926 1193 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 2.11 % Allowed : 19.00 % Favored : 78.89 % 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: -1.40 (0.25), residues: 1060 helix: -2.48 (0.50), residues: 70 sheet: 0.10 (0.24), residues: 437 loop : -1.60 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.023 0.001 PHE A 143 TYR 0.029 0.001 TYR C 93 ARG 0.003 0.000 ARG D 72 *********************** 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 106 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.802 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 100 average time/residue: 0.1621 time to fit residues: 24.0728 Evaluate side-chains 95 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0788 time to fit residues: 2.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 1 optimal weight: 0.0010 chunk 75 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.3424 ------------------------------------------------------------------------------- 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: 0.6495 moved from start: 0.1913 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= 0.116 Angle : 0.516 9.469 11349 Z= 0.259 Chirality : 0.043 0.189 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.198 38.694 1193 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 0.78 % Allowed : 21.56 % Favored : 77.67 % 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: -1.16 (0.25), residues: 1060 helix: -2.43 (0.50), residues: 76 sheet: 0.29 (0.24), residues: 444 loop : -1.45 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 50 HIS 0.002 0.000 HIS D 35 PHE 0.024 0.001 PHE A 143 TYR 0.024 0.001 TYR C 51 ARG 0.002 0.000 ARG D 16 *********************** 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 105 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.878 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 102 average time/residue: 0.1585 time to fit residues: 24.5432 Evaluate side-chains 89 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0967 time to fit residues: 1.8898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.6572 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8322 Z= 0.240 Angle : 0.560 9.109 11349 Z= 0.285 Chirality : 0.044 0.193 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.475 39.258 1193 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.98 % Favored : 92.92 % Rotamer: Outliers : 1.44 % Allowed : 22.67 % Favored : 75.89 % 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: -1.18 (0.25), residues: 1060 helix: -2.37 (0.51), residues: 70 sheet: 0.30 (0.25), residues: 430 loop : -1.47 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 53 HIS 0.004 0.001 HIS D 35 PHE 0.017 0.002 PHE A 143 TYR 0.022 0.001 TYR C 51 ARG 0.004 0.000 ARG D 72 *********************** 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 99 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.939 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 95 average time/residue: 0.1674 time to fit residues: 23.4385 Evaluate side-chains 92 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0732 time to fit residues: 2.2568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.1980 chunk 63 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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: 0.6501 moved from start: 0.2164 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= 0.124 Angle : 0.515 8.774 11349 Z= 0.259 Chirality : 0.043 0.191 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.214 40.044 1193 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.94 % Rotamer: Outliers : 0.89 % Allowed : 23.00 % 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: -0.92 (0.25), residues: 1060 helix: -2.34 (0.51), residues: 76 sheet: 0.48 (0.25), residues: 439 loop : -1.29 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 50 HIS 0.003 0.001 HIS B 210 PHE 0.023 0.001 PHE A 143 TYR 0.033 0.001 TYR C 93 ARG 0.002 0.000 ARG D 16 *********************** 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 97 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.944 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1671 time to fit residues: 23.5177 Evaluate side-chains 90 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0736 time to fit residues: 1.8097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8322 Z= 0.272 Angle : 0.589 13.007 11349 Z= 0.295 Chirality : 0.045 0.213 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.527 40.188 1193 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 0.89 % Allowed : 23.67 % Favored : 75.44 % 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: -1.04 (0.25), residues: 1060 helix: -2.19 (0.54), residues: 69 sheet: 0.39 (0.25), residues: 430 loop : -1.38 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.016 0.002 PHE A 143 TYR 0.027 0.002 TYR C 51 ARG 0.004 0.000 ARG D 72 *********************** 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 89 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.002 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.1766 time to fit residues: 22.2678 Evaluate side-chains 80 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0677 time to fit residues: 1.7149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 0.0000 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8322 Z= 0.263 Angle : 0.588 10.879 11349 Z= 0.295 Chirality : 0.045 0.216 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.667 41.276 1193 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.15 % Rotamer: Outliers : 0.89 % Allowed : 23.78 % Favored : 75.33 % 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: -1.09 (0.25), residues: 1060 helix: -2.33 (0.50), residues: 75 sheet: 0.35 (0.25), residues: 430 loop : -1.38 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 50 HIS 0.004 0.001 HIS D 35 PHE 0.018 0.002 PHE A 143 TYR 0.047 0.002 TYR C 93 ARG 0.004 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 89 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.926 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 0.1869 time to fit residues: 23.2640 Evaluate side-chains 84 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0652 time to fit residues: 1.8183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.6573 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8322 Z= 0.207 Angle : 0.572 11.791 11349 Z= 0.285 Chirality : 0.044 0.206 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.586 41.227 1193 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.85 % Favored : 94.06 % Rotamer: Outliers : 0.22 % Allowed : 23.89 % Favored : 75.89 % 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: -1.00 (0.25), residues: 1060 helix: -2.27 (0.51), residues: 75 sheet: 0.39 (0.25), residues: 430 loop : -1.30 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 50 HIS 0.003 0.001 HIS D 35 PHE 0.019 0.001 PHE A 143 TYR 0.028 0.001 TYR D 160 ARG 0.003 0.000 ARG D 72 ********************** REFINEMENT MACRO_CYCLE 10 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 84 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.919 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.1808 time to fit residues: 22.1103 Evaluate side-chains 81 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0804 time to fit residues: 1.4125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 4.9990 chunk 25 optimal weight: 0.0030 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.163126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.115124 restraints weight = 11279.994| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.68 r_work: 0.3277 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8322 Z= 0.130 Angle : 0.540 11.804 11349 Z= 0.266 Chirality : 0.044 0.202 1271 Planarity : 0.004 0.045 1456 Dihedral : 4.276 40.043 1193 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 0.22 % Allowed : 24.33 % Favored : 75.44 % 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: -0.75 (0.26), residues: 1060 helix: -2.16 (0.52), residues: 76 sheet: 0.57 (0.25), residues: 440 loop : -1.15 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 50 HIS 0.003 0.001 HIS B 210 PHE 0.023 0.001 PHE A 143 TYR 0.029 0.001 TYR D 160 ARG 0.002 0.000 ARG E 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.44 seconds wall clock time: 36 minutes 20.41 seconds (2180.41 seconds total)