Starting phenix.real_space_refine on Thu Feb 15 05:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2d_32965/02_2024/7x2d_32965_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2d_32965/02_2024/7x2d_32965.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/7x2d_32965/02_2024/7x2d_32965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2d_32965/02_2024/7x2d_32965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2d_32965/02_2024/7x2d_32965_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2d_32965/02_2024/7x2d_32965_updated.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= 0.002 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3052 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5215 2.51 5 N 1428 2.21 5 O 1502 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 132": "OE1" <-> "OE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8203 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2241 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 280, 2230 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 bond proxies already assigned to first conformer: 2274 Chain: "A" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1883 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2619 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Conformer: "B" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} bond proxies already assigned to first conformer: 2640 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'86W': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 6.73, per 1000 atoms: 0.82 Number of scatterers: 8203 At special positions: 0 Unit cell: (78.264, 97.83, 128.266, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 F 3 9.00 O 1502 8.00 N 1428 7.00 C 5215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 2.5 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 10 sheets defined 40.0% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'F' and resid 21 through 50 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 58 through 76 Processing helix chain 'F' and resid 78 through 87 Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.865A pdb=" N ALA F 101 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 Processing helix chain 'F' and resid 137 through 160 removed outlier: 3.875A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 204 through 237 Processing helix chain 'F' and resid 265 through 297 removed outlier: 4.092A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL F 282 " --> pdb=" O MET F 278 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 310 through 331 removed outlier: 4.798A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.714A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.562A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.575A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 277 removed outlier: 3.682A pdb=" N LEU A 266 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLN A 267 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 349 removed outlier: 4.023A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.204A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.756A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.969A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.785A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.839A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.808A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.480A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.938A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.042A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1046 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: 2.34 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1321 1.30 - 1.43: 2323 1.43 - 1.57: 4663 1.57 - 1.70: 0 1.70 - 1.83: 74 Bond restraints: 8381 Sorted by residual: bond pdb=" C19 86W F 502 " pdb=" C20 86W F 502 " ideal model delta sigma weight residual 1.359 1.479 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C24 86W F 502 " pdb=" N23 86W F 502 " ideal model delta sigma weight residual 1.372 1.465 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C24 86W F 502 " pdb=" N26 86W F 502 " ideal model delta sigma weight residual 1.380 1.467 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA SER F 191 " pdb=" C SER F 191 " ideal model delta sigma weight residual 1.524 1.478 0.045 1.26e-02 6.30e+03 1.28e+01 bond pdb=" CA CYS F 186 " pdb=" C CYS F 186 " ideal model delta sigma weight residual 1.530 1.493 0.036 1.10e-02 8.26e+03 1.10e+01 ... (remaining 8376 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.27: 161 106.27 - 113.22: 4515 113.22 - 120.17: 3132 120.17 - 127.12: 3465 127.12 - 134.07: 94 Bond angle restraints: 11367 Sorted by residual: angle pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" CB GLU D 42 " ideal model delta sigma weight residual 110.39 117.99 -7.60 1.66e+00 3.63e-01 2.09e+01 angle pdb=" C LYS A 233 " pdb=" N TRP A 234 " pdb=" CA TRP A 234 " ideal model delta sigma weight residual 121.94 112.86 9.08 2.00e+00 2.50e-01 2.06e+01 angle pdb=" N ILE F 125 " pdb=" CA ILE F 125 " pdb=" C ILE F 125 " ideal model delta sigma weight residual 113.53 109.20 4.33 9.80e-01 1.04e+00 1.95e+01 angle pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 122.07 128.37 -6.30 1.43e+00 4.89e-01 1.94e+01 angle pdb=" N ASN F 185 " pdb=" CA ASN F 185 " pdb=" C ASN F 185 " ideal model delta sigma weight residual 110.28 103.95 6.33 1.48e+00 4.57e-01 1.83e+01 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4513 17.96 - 35.91: 420 35.91 - 53.87: 90 53.87 - 71.82: 11 71.82 - 89.78: 9 Dihedral angle restraints: 5043 sinusoidal: 2025 harmonic: 3018 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual 93.00 4.29 88.71 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS F 96 " pdb=" SG CYS F 96 " pdb=" SG CYS F 186 " pdb=" CB CYS F 186 " ideal model delta sinusoidal sigma weight residual 93.00 173.69 -80.69 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CA PHE F 333 " pdb=" C PHE F 333 " pdb=" N ASN F 334 " pdb=" CA ASN F 334 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 974 0.055 - 0.111: 245 0.111 - 0.166: 40 0.166 - 0.221: 11 0.221 - 0.277: 5 Chirality restraints: 1275 Sorted by residual: chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLU D 42 " pdb=" N GLU D 42 " pdb=" C GLU D 42 " pdb=" CB GLU D 42 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ARG B 8 " pdb=" N ARG B 8 " pdb=" C ARG B 8 " pdb=" CB ARG B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1272 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 157 " 0.081 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO F 158 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO F 158 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO F 158 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 169 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C TRP B 169 " 0.056 2.00e-02 2.50e+03 pdb=" O TRP B 169 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 170 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 28 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C LYS A 28 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 28 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 29 " -0.015 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 42 2.47 - 3.08: 5657 3.08 - 3.68: 12526 3.68 - 4.29: 18728 4.29 - 4.90: 31022 Nonbonded interactions: 67975 Sorted by model distance: nonbonded pdb=" F16 86W F 502 " pdb=" O08 86W F 502 " model vdw 1.860 2.390 nonbonded pdb=" OG1 THR F 37 " pdb=" OG SER F 325 " model vdw 2.078 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.079 2.440 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.148 2.440 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.164 2.520 ... (remaining 67970 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=0.50 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 1.780 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 28.830 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 8381 Z= 0.342 Angle : 0.854 14.105 11367 Z= 0.474 Chirality : 0.053 0.277 1275 Planarity : 0.006 0.121 1440 Dihedral : 14.430 89.779 3076 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 0.68 % Favored : 98.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1021 helix: 0.60 (0.25), residues: 404 sheet: -0.57 (0.32), residues: 227 loop : -0.97 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.010 0.002 HIS A 220 PHE 0.032 0.002 PHE B 234 TYR 0.021 0.002 TYR A 253 ARG 0.006 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8926 (tp) cc_final: 0.8717 (tp) REVERT: F 157 ILE cc_start: 0.8838 (mm) cc_final: 0.8562 (mt) REVERT: A 386 MET cc_start: 0.7482 (ttp) cc_final: 0.7060 (ttm) REVERT: D 51 LEU cc_start: 0.7813 (tp) cc_final: 0.7431 (tp) REVERT: E 78 THR cc_start: 0.7646 (t) cc_final: 0.7315 (p) REVERT: E 117 TYR cc_start: 0.8412 (m-80) cc_final: 0.8179 (m-80) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.1913 time to fit residues: 49.6586 Evaluate side-chains 150 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 292 ASN A 294 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8381 Z= 0.219 Angle : 0.552 7.602 11367 Z= 0.298 Chirality : 0.042 0.137 1275 Planarity : 0.005 0.082 1440 Dihedral : 5.589 40.637 1216 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.59 % Allowed : 10.34 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.25), residues: 1021 helix: 1.24 (0.24), residues: 408 sheet: -0.06 (0.32), residues: 211 loop : -0.61 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.006 0.001 HIS A 357 PHE 0.020 0.002 PHE B 253 TYR 0.010 0.001 TYR E 32 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8840 (tp) cc_final: 0.8634 (tp) REVERT: F 157 ILE cc_start: 0.8841 (mm) cc_final: 0.8565 (mt) REVERT: F 278 MET cc_start: 0.7416 (tpp) cc_final: 0.6999 (tpp) REVERT: A 307 LYS cc_start: 0.7243 (ptpp) cc_final: 0.6859 (pttt) REVERT: A 386 MET cc_start: 0.7521 (ttp) cc_final: 0.7162 (ttm) REVERT: B 153 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6871 (p0) REVERT: B 197 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7390 (mmp80) REVERT: B 226 GLU cc_start: 0.8062 (tt0) cc_final: 0.7804 (tt0) REVERT: B 325 MET cc_start: 0.7575 (mmm) cc_final: 0.7298 (tpp) REVERT: E 117 TYR cc_start: 0.8336 (m-80) cc_final: 0.8006 (m-80) outliers start: 11 outliers final: 8 residues processed: 160 average time/residue: 0.2005 time to fit residues: 44.4033 Evaluate side-chains 151 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8381 Z= 0.290 Angle : 0.565 8.039 11367 Z= 0.301 Chirality : 0.043 0.143 1275 Planarity : 0.004 0.070 1440 Dihedral : 5.739 47.446 1216 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.84 % Allowed : 11.70 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1021 helix: 1.50 (0.24), residues: 401 sheet: -0.11 (0.31), residues: 222 loop : -0.42 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.012 0.001 HIS A 220 PHE 0.020 0.002 PHE F 29 TYR 0.014 0.002 TYR F 214 ARG 0.009 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8846 (tp) cc_final: 0.8622 (tp) REVERT: F 157 ILE cc_start: 0.8868 (mm) cc_final: 0.8592 (mt) REVERT: F 333 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7292 (m-10) REVERT: A 307 LYS cc_start: 0.7360 (ptpp) cc_final: 0.6940 (pttt) REVERT: A 386 MET cc_start: 0.7569 (ttp) cc_final: 0.7214 (ttm) REVERT: B 197 ARG cc_start: 0.7751 (mmp80) cc_final: 0.7433 (mmp80) REVERT: E 31 ASN cc_start: 0.7929 (m-40) cc_final: 0.7725 (t0) outliers start: 22 outliers final: 17 residues processed: 166 average time/residue: 0.1889 time to fit residues: 43.9682 Evaluate side-chains 160 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8381 Z= 0.210 Angle : 0.502 6.620 11367 Z= 0.270 Chirality : 0.041 0.137 1275 Planarity : 0.004 0.061 1440 Dihedral : 5.570 47.634 1216 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.30 % Allowed : 12.84 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1021 helix: 1.64 (0.25), residues: 401 sheet: -0.09 (0.31), residues: 222 loop : -0.34 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.014 0.001 HIS A 220 PHE 0.019 0.002 PHE F 264 TYR 0.015 0.001 TYR B 105 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8849 (tp) cc_final: 0.8643 (tp) REVERT: F 157 ILE cc_start: 0.8863 (mm) cc_final: 0.8582 (mt) REVERT: A 307 LYS cc_start: 0.7321 (ptpp) cc_final: 0.6900 (pttt) REVERT: A 386 MET cc_start: 0.7561 (ttp) cc_final: 0.7188 (ttm) REVERT: B 37 ILE cc_start: 0.8546 (tp) cc_final: 0.8004 (pt) REVERT: B 197 ARG cc_start: 0.7768 (mmp80) cc_final: 0.7419 (mmp80) REVERT: B 220 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: E 111 THR cc_start: 0.7958 (m) cc_final: 0.7667 (m) outliers start: 26 outliers final: 22 residues processed: 159 average time/residue: 0.1940 time to fit residues: 42.7513 Evaluate side-chains 160 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8381 Z= 0.140 Angle : 0.459 6.565 11367 Z= 0.247 Chirality : 0.040 0.134 1275 Planarity : 0.004 0.055 1440 Dihedral : 5.079 41.428 1216 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.30 % Allowed : 14.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1021 helix: 1.86 (0.25), residues: 407 sheet: 0.03 (0.31), residues: 222 loop : -0.22 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.012 0.001 HIS A 220 PHE 0.022 0.001 PHE F 29 TYR 0.010 0.001 TYR F 194 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8816 (tp) cc_final: 0.8602 (tp) REVERT: F 157 ILE cc_start: 0.8875 (mm) cc_final: 0.8588 (mt) REVERT: F 278 MET cc_start: 0.7268 (mmm) cc_final: 0.6994 (tpp) REVERT: F 333 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: A 307 LYS cc_start: 0.7257 (ptpp) cc_final: 0.6797 (pttt) REVERT: A 386 MET cc_start: 0.7534 (ttp) cc_final: 0.7169 (ttm) REVERT: B 37 ILE cc_start: 0.8473 (tp) cc_final: 0.7923 (pt) REVERT: B 153 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6970 (p0) REVERT: B 197 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7409 (mmp80) REVERT: E 60 TYR cc_start: 0.8793 (m-80) cc_final: 0.8523 (m-80) REVERT: E 117 TYR cc_start: 0.8338 (m-80) cc_final: 0.8098 (m-80) outliers start: 26 outliers final: 20 residues processed: 156 average time/residue: 0.2110 time to fit residues: 45.5909 Evaluate side-chains 158 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 30.0000 chunk 93 optimal weight: 0.0770 chunk 10 optimal weight: 2.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8381 Z= 0.148 Angle : 0.465 6.572 11367 Z= 0.248 Chirality : 0.039 0.133 1275 Planarity : 0.004 0.050 1440 Dihedral : 4.812 38.561 1216 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.61 % Allowed : 15.00 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1021 helix: 1.93 (0.25), residues: 407 sheet: 0.12 (0.31), residues: 222 loop : -0.16 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.013 0.001 HIS A 220 PHE 0.017 0.001 PHE F 264 TYR 0.009 0.001 TYR F 194 ARG 0.008 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8834 (tp) cc_final: 0.8619 (tp) REVERT: F 278 MET cc_start: 0.7405 (mmm) cc_final: 0.7111 (tpp) REVERT: F 333 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7492 (m-10) REVERT: A 253 TYR cc_start: 0.8206 (m-80) cc_final: 0.7532 (m-80) REVERT: A 307 LYS cc_start: 0.7252 (ptpp) cc_final: 0.6802 (pttt) REVERT: A 386 MET cc_start: 0.7549 (ttp) cc_final: 0.7184 (ttm) REVERT: B 37 ILE cc_start: 0.8487 (tp) cc_final: 0.7908 (pt) REVERT: B 153 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7017 (p0) REVERT: B 197 ARG cc_start: 0.7641 (mmp80) cc_final: 0.7378 (mmp80) REVERT: B 325 MET cc_start: 0.7545 (tpp) cc_final: 0.7320 (tpp) REVERT: E 31 ASN cc_start: 0.7729 (m-40) cc_final: 0.7494 (t0) REVERT: E 117 TYR cc_start: 0.8319 (m-80) cc_final: 0.8096 (m-80) outliers start: 20 outliers final: 15 residues processed: 152 average time/residue: 0.2075 time to fit residues: 43.2025 Evaluate side-chains 148 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8381 Z= 0.171 Angle : 0.470 6.599 11367 Z= 0.250 Chirality : 0.040 0.134 1275 Planarity : 0.004 0.049 1440 Dihedral : 4.668 37.299 1216 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.52 % Allowed : 14.55 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1021 helix: 1.92 (0.25), residues: 407 sheet: 0.16 (0.31), residues: 228 loop : -0.10 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.012 0.001 HIS A 220 PHE 0.022 0.001 PHE F 29 TYR 0.010 0.001 TYR F 214 ARG 0.009 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8841 (tp) cc_final: 0.8620 (tp) REVERT: F 278 MET cc_start: 0.7448 (mmm) cc_final: 0.7172 (tpp) REVERT: F 333 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: F 338 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7360 (mtm180) REVERT: A 253 TYR cc_start: 0.8230 (m-80) cc_final: 0.7528 (m-80) REVERT: A 307 LYS cc_start: 0.7261 (ptpp) cc_final: 0.6830 (pttt) REVERT: A 386 MET cc_start: 0.7562 (ttp) cc_final: 0.7188 (ttm) REVERT: B 37 ILE cc_start: 0.8479 (tp) cc_final: 0.7914 (pt) REVERT: B 197 ARG cc_start: 0.7597 (mmp80) cc_final: 0.7374 (mmp80) REVERT: B 325 MET cc_start: 0.7548 (tpp) cc_final: 0.7323 (tpp) REVERT: E 31 ASN cc_start: 0.7855 (m-40) cc_final: 0.7604 (t0) REVERT: E 87 LYS cc_start: 0.7713 (mmtp) cc_final: 0.7403 (mptt) REVERT: E 117 TYR cc_start: 0.8345 (m-80) cc_final: 0.8062 (m-80) outliers start: 28 outliers final: 23 residues processed: 149 average time/residue: 0.2063 time to fit residues: 41.8651 Evaluate side-chains 154 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.0470 chunk 92 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 0.0870 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8381 Z= 0.143 Angle : 0.461 6.522 11367 Z= 0.244 Chirality : 0.039 0.139 1275 Planarity : 0.004 0.046 1440 Dihedral : 4.382 32.831 1216 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.95 % Allowed : 15.23 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1021 helix: 1.97 (0.25), residues: 413 sheet: 0.31 (0.31), residues: 222 loop : -0.12 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.011 0.001 HIS A 220 PHE 0.017 0.001 PHE F 264 TYR 0.009 0.001 TYR F 214 ARG 0.007 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 154 ILE cc_start: 0.8825 (tp) cc_final: 0.8606 (tp) REVERT: F 278 MET cc_start: 0.7406 (mmm) cc_final: 0.7143 (tpp) REVERT: F 333 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: A 253 TYR cc_start: 0.8232 (m-80) cc_final: 0.7544 (m-80) REVERT: A 307 LYS cc_start: 0.7262 (ptpp) cc_final: 0.6849 (pttt) REVERT: A 386 MET cc_start: 0.7559 (ttp) cc_final: 0.7194 (ttm) REVERT: B 37 ILE cc_start: 0.8469 (tp) cc_final: 0.7893 (pt) REVERT: B 325 MET cc_start: 0.7576 (tpp) cc_final: 0.7292 (tpp) REVERT: E 31 ASN cc_start: 0.7820 (m-40) cc_final: 0.7538 (t0) REVERT: E 117 TYR cc_start: 0.8320 (m-80) cc_final: 0.8079 (m-80) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.2048 time to fit residues: 41.7863 Evaluate side-chains 147 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8381 Z= 0.285 Angle : 0.525 7.040 11367 Z= 0.279 Chirality : 0.042 0.188 1275 Planarity : 0.004 0.046 1440 Dihedral : 4.754 39.891 1216 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.30 % Allowed : 15.57 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1021 helix: 1.78 (0.25), residues: 414 sheet: -0.08 (0.30), residues: 234 loop : 0.02 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 281 HIS 0.013 0.002 HIS A 220 PHE 0.021 0.002 PHE F 29 TYR 0.014 0.002 TYR F 214 ARG 0.007 0.000 ARG F 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 157 ILE cc_start: 0.8916 (mm) cc_final: 0.8625 (mt) REVERT: F 160 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7874 (mp10) REVERT: F 278 MET cc_start: 0.7597 (mmm) cc_final: 0.7384 (tpp) REVERT: F 333 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7409 (m-10) REVERT: A 253 TYR cc_start: 0.8298 (m-80) cc_final: 0.7546 (m-80) REVERT: A 307 LYS cc_start: 0.7282 (ptpp) cc_final: 0.6872 (pttt) REVERT: A 386 MET cc_start: 0.7596 (ttp) cc_final: 0.7229 (ttm) REVERT: A 392 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7699 (mm-30) REVERT: E 31 ASN cc_start: 0.7932 (m-40) cc_final: 0.7635 (t0) REVERT: E 87 LYS cc_start: 0.7747 (mmtp) cc_final: 0.7455 (mptt) outliers start: 26 outliers final: 23 residues processed: 150 average time/residue: 0.2015 time to fit residues: 41.6002 Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 41 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8381 Z= 0.169 Angle : 0.486 6.554 11367 Z= 0.257 Chirality : 0.040 0.137 1275 Planarity : 0.004 0.047 1440 Dihedral : 4.532 37.685 1216 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.95 % Allowed : 15.91 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1021 helix: 1.87 (0.25), residues: 414 sheet: 0.22 (0.30), residues: 224 loop : -0.10 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 281 HIS 0.013 0.001 HIS A 220 PHE 0.016 0.001 PHE F 264 TYR 0.010 0.001 TYR E 60 ARG 0.007 0.000 ARG F 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 157 ILE cc_start: 0.8904 (mm) cc_final: 0.8615 (mt) REVERT: F 160 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7914 (mp10) REVERT: F 333 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: A 253 TYR cc_start: 0.8251 (m-80) cc_final: 0.7548 (m-80) REVERT: A 307 LYS cc_start: 0.7268 (ptpp) cc_final: 0.6868 (pttt) REVERT: A 386 MET cc_start: 0.7568 (ttp) cc_final: 0.7209 (ttm) REVERT: A 392 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7700 (mm-30) REVERT: E 31 ASN cc_start: 0.7824 (m-40) cc_final: 0.7520 (t0) outliers start: 23 outliers final: 21 residues processed: 151 average time/residue: 0.2113 time to fit residues: 43.9817 Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 118 SER Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119537 restraints weight = 24638.990| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.47 r_work: 0.3083 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8381 Z= 0.155 Angle : 0.477 6.453 11367 Z= 0.252 Chirality : 0.040 0.136 1275 Planarity : 0.004 0.046 1440 Dihedral : 4.283 33.174 1216 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.84 % Allowed : 16.25 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1021 helix: 1.95 (0.25), residues: 415 sheet: 0.26 (0.30), residues: 223 loop : -0.04 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 281 HIS 0.013 0.001 HIS A 220 PHE 0.021 0.001 PHE F 29 TYR 0.007 0.001 TYR F 194 ARG 0.009 0.000 ARG F 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.48 seconds wall clock time: 37 minutes 25.43 seconds (2245.43 seconds total)