Starting phenix.real_space_refine on Thu Feb 15 07:30:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmz_34905/02_2024/8hmz_34905_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.133 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: 6 Type Number sf(0) Gaussians P 82 5.49 5 Mg 6 5.21 5 S 31 5.16 5 C 6946 2.51 5 N 2085 2.21 5 O 2392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 273": "OD1" <-> "OD2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 497": "OD1" <-> "OD2" Residue "C PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 517": "OD1" <-> "OD2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 121": "OE1" <-> "OE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11542 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2602 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 16, 'TRANS': 296} Chain breaks: 2 Chain: "B" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2062 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 245} Chain breaks: 1 Chain: "C" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2263 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 18, 'TRANS': 266} Chain breaks: 1 Chain: "D" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 984 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "5" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 968 Classifications: {'RNA': 45} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 7, 'rna3p': 37} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "3" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 788 Classifications: {'RNA': 37} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 30} Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 1869 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 332} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 361} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1202 Unresolved non-hydrogen angles: 1543 Unresolved non-hydrogen dihedrals: 992 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 9, 'TYR:plan': 13, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 21, 'GLU:plan': 28, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 664 Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.21, per 1000 atoms: 0.62 Number of scatterers: 11542 At special positions: 0 Unit cell: (134.788, 123.918, 152.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 82 15.00 Mg 6 11.99 O 2392 8.00 N 2085 7.00 C 6946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.2 seconds 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 13 sheets defined 29.3% alpha, 16.2% beta 23 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 101 through 118 removed outlier: 4.067A pdb=" N LEU A 114 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.768A pdb=" N ARG A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 Processing helix chain 'A' and resid 327 through 335 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 442 Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.544A pdb=" N GLN B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 97 through 110 Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 215 through 229 Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 62 through 65 No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 97 through 100 removed outlier: 3.527A pdb=" N GLN C 100 " --> pdb=" O LYS C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 485 through 495 Processing helix chain 'D' and resid 44 through 52 removed outlier: 3.691A pdb=" N LEU D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'E' and resid 90 through 109 removed outlier: 4.096A pdb=" N MET E 103 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG E 105 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 141 Processing helix chain 'E' and resid 197 through 217 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 260 through 268 Processing helix chain 'E' and resid 290 through 305 Processing helix chain 'E' and resid 308 through 310 No H-bonds generated for 'chain 'E' and resid 308 through 310' Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing sheet with id= A, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.786A pdb=" N PHE A 40 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TYR A 317 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA A 42 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 49 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 257 through 261 Processing sheet with id= C, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.853A pdb=" N TYR A 380 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU A 417 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE A 383 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET A 419 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLU A 385 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N CYS A 421 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL A 387 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU A 423 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 418 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 68 through 70 removed outlier: 6.510A pdb=" N VAL B 4 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B 11 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 233 through 236 removed outlier: 6.546A pdb=" N THR B 287 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLN B 261 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 289 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 80 through 83 Processing sheet with id= G, first strand: chain 'C' and resid 104 through 106 Processing sheet with id= H, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.511A pdb=" N PHE C 450 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.443A pdb=" N ILE D 90 " --> pdb=" O PRO D 107 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N SER D 138 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N VAL D 106 " --> pdb=" O SER D 138 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N THR D 140 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR D 108 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALA D 142 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 12 through 17 removed outlier: 3.971A pdb=" N GLN E 74 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E 36 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 62 through 67 removed outlier: 4.274A pdb=" N THR E 21 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 81 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 275 through 279 removed outlier: 7.074A pdb=" N CYS E 226 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL E 119 " --> pdb=" O CYS E 226 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE E 228 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N THR E 146 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN E 229 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL E 148 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 315 through 320 removed outlier: 3.769A pdb=" N SER E 391 " --> pdb=" O THR E 400 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 402 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL E 389 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY E 385 " --> pdb=" O VAL E 368 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 5.62 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: 1751 1.30 - 1.42: 3512 1.42 - 1.55: 6448 1.55 - 1.68: 164 1.68 - 1.81: 50 Bond restraints: 11925 Sorted by residual: bond pdb=" O2' A23 5 52 " pdb=" PC A23 5 52 " ideal model delta sigma weight residual 1.342 1.606 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C2' A23 5 52 " pdb=" C1' A23 5 52 " ideal model delta sigma weight residual 1.269 1.520 -0.251 2.00e-02 2.50e+03 1.57e+02 bond pdb=" O4' A23 5 52 " pdb=" C1' A23 5 52 " ideal model delta sigma weight residual 1.672 1.431 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" P A23 5 52 " pdb=" OP2 A23 5 52 " ideal model delta sigma weight residual 1.487 1.273 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" P A23 5 52 " pdb=" OP1 A23 5 52 " ideal model delta sigma weight residual 1.478 1.287 0.191 2.00e-02 2.50e+03 9.09e+01 ... (remaining 11920 not shown) Histogram of bond angle deviations from ideal: 95.40 - 104.61: 551 104.61 - 113.83: 6973 113.83 - 123.04: 7882 123.04 - 132.26: 1170 132.26 - 141.48: 31 Bond angle restraints: 16607 Sorted by residual: angle pdb=" C GLY C 412 " pdb=" N GLN C 413 " pdb=" CA GLN C 413 " ideal model delta sigma weight residual 121.54 141.48 -19.94 1.91e+00 2.74e-01 1.09e+02 angle pdb=" O4' C 5 51 " pdb=" C1' C 5 51 " pdb=" C2' C 5 51 " ideal model delta sigma weight residual 105.80 96.43 9.37 1.00e+00 1.00e+00 8.78e+01 angle pdb=" O ALA C 414 " pdb=" C ALA C 414 " pdb=" N SER C 415 " ideal model delta sigma weight residual 122.59 133.69 -11.10 1.33e+00 5.65e-01 6.96e+01 angle pdb=" C VAL C 420 " pdb=" N LEU C 421 " pdb=" CA LEU C 421 " ideal model delta sigma weight residual 121.54 137.43 -15.89 1.91e+00 2.74e-01 6.92e+01 angle pdb=" C VAL C 419 " pdb=" N VAL C 420 " pdb=" CA VAL C 420 " ideal model delta sigma weight residual 121.97 136.67 -14.70 1.80e+00 3.09e-01 6.67e+01 ... (remaining 16602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 6802 35.11 - 70.22: 433 70.22 - 105.33: 33 105.33 - 140.44: 0 140.44 - 175.55: 1 Dihedral angle restraints: 7269 sinusoidal: 3315 harmonic: 3954 Sorted by residual: dihedral pdb=" C VAL C 419 " pdb=" N VAL C 419 " pdb=" CA VAL C 419 " pdb=" CB VAL C 419 " ideal model delta harmonic sigma weight residual -122.00 -147.16 25.16 0 2.50e+00 1.60e-01 1.01e+02 dihedral pdb=" N VAL C 419 " pdb=" C VAL C 419 " pdb=" CA VAL C 419 " pdb=" CB VAL C 419 " ideal model delta harmonic sigma weight residual 123.40 148.29 -24.89 0 2.50e+00 1.60e-01 9.91e+01 dihedral pdb=" O4' C 5 51 " pdb=" C1' C 5 51 " pdb=" N1 C 5 51 " pdb=" C2 C 5 51 " ideal model delta sinusoidal sigma weight residual 232.00 56.45 175.55 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 7266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 1939 0.182 - 0.365: 12 0.365 - 0.547: 4 0.547 - 0.730: 2 0.730 - 0.912: 1 Chirality restraints: 1958 Sorted by residual: chirality pdb=" CA VAL C 419 " pdb=" N VAL C 419 " pdb=" C VAL C 419 " pdb=" CB VAL C 419 " both_signs ideal model delta sigma weight residual False 2.44 1.53 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" C4' A23 5 52 " pdb=" C5' A23 5 52 " pdb=" O4' A23 5 52 " pdb=" C3' A23 5 52 " both_signs ideal model delta sigma weight residual False -2.55 -1.92 -0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" CG LEU C 421 " pdb=" CB LEU C 421 " pdb=" CD1 LEU C 421 " pdb=" CD2 LEU C 421 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 1955 not shown) Planarity restraints: 1869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 414 " -0.032 2.00e-02 2.50e+03 7.85e-02 6.16e+01 pdb=" C ALA C 414 " 0.135 2.00e-02 2.50e+03 pdb=" O ALA C 414 " -0.057 2.00e-02 2.50e+03 pdb=" N SER C 415 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 521 " 0.038 2.00e-02 2.50e+03 7.56e-02 5.71e+01 pdb=" C PRO C 521 " -0.131 2.00e-02 2.50e+03 pdb=" O PRO C 521 " 0.049 2.00e-02 2.50e+03 pdb=" N GLN C 522 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 412 " 0.031 2.00e-02 2.50e+03 6.86e-02 4.71e+01 pdb=" C GLY C 412 " -0.119 2.00e-02 2.50e+03 pdb=" O GLY C 412 " 0.046 2.00e-02 2.50e+03 pdb=" N GLN C 413 " 0.042 2.00e-02 2.50e+03 ... (remaining 1866 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 213 2.65 - 3.22: 9823 3.22 - 3.78: 17764 3.78 - 4.34: 24287 4.34 - 4.90: 37529 Nonbonded interactions: 89616 Sorted by model distance: nonbonded pdb=" O1C A23 5 52 " pdb=" O5' A 3 53 " model vdw 2.093 2.440 nonbonded pdb=" OE1 GLU B 62 " pdb=" OH TYR B 221 " model vdw 2.102 2.440 nonbonded pdb=" O2 U 5 36 " pdb=" N6 A 5 47 " model vdw 2.103 2.520 nonbonded pdb=" O2' U 5 16 " pdb=" OP1 A 5 19 " model vdw 2.113 2.440 nonbonded pdb=" O LEU C 440 " pdb=" OG SER C 443 " model vdw 2.124 2.440 ... (remaining 89611 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.240 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 39.190 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.008 0.264 11925 Z= 0.476 Angle : 0.940 20.215 16607 Z= 0.540 Chirality : 0.059 0.912 1958 Planarity : 0.007 0.080 1869 Dihedral : 20.298 175.552 4709 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.69 % Favored : 92.86 % Rotamer: Outliers : 5.96 % Allowed : 30.76 % Favored : 63.27 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.18), residues: 1345 helix: -2.18 (0.20), residues: 447 sheet: -1.89 (0.28), residues: 279 loop : -3.07 (0.19), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 110 HIS 0.010 0.001 HIS C 526 PHE 0.019 0.002 PHE A 391 TYR 0.019 0.002 TYR A 343 ARG 0.008 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 146 time to evaluate : 1.169 Fit side-chains REVERT: A 23 LEU cc_start: 0.3669 (OUTLIER) cc_final: 0.3226 (pp) REVERT: A 43 GLU cc_start: 0.7154 (mp0) cc_final: 0.6910 (mp0) REVERT: A 102 LYS cc_start: 0.3165 (OUTLIER) cc_final: 0.2273 (tppt) REVERT: A 285 ILE cc_start: 0.1135 (OUTLIER) cc_final: 0.0914 (pp) REVERT: A 327 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5500 (pttt) REVERT: A 438 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6025 (mp0) REVERT: B 42 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8531 (pp30) REVERT: B 100 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7296 (pt) REVERT: B 247 TYR cc_start: 0.8568 (m-80) cc_final: 0.8363 (m-80) REVERT: B 267 ASP cc_start: 0.7534 (m-30) cc_final: 0.7267 (m-30) REVERT: C 100 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: D 103 GLN cc_start: 0.7615 (mt0) cc_final: 0.7395 (mt0) outliers start: 51 outliers final: 21 residues processed: 186 average time/residue: 1.3777 time to fit residues: 274.7198 Evaluate side-chains 138 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 40.0000 chunk 106 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 110 optimal weight: 50.0000 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 128 optimal weight: 40.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 120 GLN B 78 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS C 51 GLN C 69 GLN C 138 GLN ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN C 465 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 11925 Z= 0.454 Angle : 0.762 13.091 16607 Z= 0.383 Chirality : 0.048 0.197 1958 Planarity : 0.006 0.086 1869 Dihedral : 17.902 158.117 2800 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 8.89 % Allowed : 29.24 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.35 (0.21), residues: 1345 helix: -0.56 (0.23), residues: 443 sheet: -1.26 (0.30), residues: 283 loop : -2.45 (0.21), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 110 HIS 0.006 0.002 HIS C 113 PHE 0.017 0.003 PHE B 233 TYR 0.021 0.003 TYR A 309 ARG 0.006 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 109 time to evaluate : 1.157 Fit side-chains REVERT: A 19 TYR cc_start: 0.2917 (OUTLIER) cc_final: 0.1695 (p90) REVERT: A 23 LEU cc_start: 0.4877 (OUTLIER) cc_final: 0.4004 (pp) REVERT: A 43 GLU cc_start: 0.7315 (mp0) cc_final: 0.7005 (mp0) REVERT: A 102 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2236 (tppt) REVERT: A 281 ARG cc_start: 0.1009 (OUTLIER) cc_final: 0.0192 (mtm-85) REVERT: A 285 ILE cc_start: 0.1273 (OUTLIER) cc_final: 0.0957 (pp) REVERT: A 438 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: B 42 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: B 80 SER cc_start: 0.7081 (OUTLIER) cc_final: 0.6796 (p) REVERT: B 100 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7215 (pt) REVERT: B 267 ASP cc_start: 0.7481 (m-30) cc_final: 0.7267 (m-30) REVERT: C 100 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: C 494 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: C 500 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8546 (tp) REVERT: D 146 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7801 (p) outliers start: 76 outliers final: 30 residues processed: 170 average time/residue: 1.1851 time to fit residues: 218.4650 Evaluate side-chains 144 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 101 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 146 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 50.0000 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 128 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 114 optimal weight: 50.0000 chunk 127 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11925 Z= 0.338 Angle : 0.666 12.350 16607 Z= 0.334 Chirality : 0.045 0.186 1958 Planarity : 0.005 0.081 1869 Dihedral : 17.581 161.689 2784 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 8.77 % Allowed : 29.24 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.60 (0.22), residues: 1345 helix: 0.15 (0.25), residues: 445 sheet: -0.89 (0.29), residues: 296 loop : -2.08 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 110 HIS 0.004 0.001 HIS B 255 PHE 0.019 0.002 PHE C 43 TYR 0.019 0.002 TYR A 132 ARG 0.006 0.001 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 112 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 19 TYR cc_start: 0.3099 (OUTLIER) cc_final: 0.2431 (m-10) REVERT: A 23 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4061 (pp) REVERT: A 43 GLU cc_start: 0.7292 (mp0) cc_final: 0.6901 (mp0) REVERT: A 102 LYS cc_start: 0.3300 (OUTLIER) cc_final: 0.2296 (tppt) REVERT: A 281 ARG cc_start: 0.0952 (OUTLIER) cc_final: 0.0158 (mtm-85) REVERT: A 438 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: B 42 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8470 (pp30) REVERT: B 196 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8198 (ttmm) REVERT: B 198 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7503 (ptt90) REVERT: B 267 ASP cc_start: 0.7507 (m-30) cc_final: 0.7276 (m-30) REVERT: C 100 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: C 428 GLN cc_start: 0.7579 (mp10) cc_final: 0.6962 (mm-40) REVERT: C 492 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8456 (m) REVERT: C 522 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6218 (tt0) REVERT: D 146 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7836 (p) outliers start: 75 outliers final: 36 residues processed: 175 average time/residue: 1.1848 time to fit residues: 224.9244 Evaluate side-chains 153 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 106 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 19 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 511 SER Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 146 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 0.0970 chunk 86 optimal weight: 0.0980 chunk 128 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN A 336 GLN A 347 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11925 Z= 0.144 Angle : 0.538 11.249 16607 Z= 0.271 Chirality : 0.040 0.191 1958 Planarity : 0.004 0.081 1869 Dihedral : 17.239 165.994 2778 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 5.61 % Allowed : 31.81 % Favored : 62.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.88 (0.23), residues: 1345 helix: 0.80 (0.25), residues: 444 sheet: -0.40 (0.30), residues: 288 loop : -1.72 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 110 HIS 0.002 0.000 HIS C 130 PHE 0.014 0.001 PHE A 391 TYR 0.019 0.001 TYR A 132 ARG 0.006 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.4960 (OUTLIER) cc_final: 0.4171 (pp) REVERT: A 43 GLU cc_start: 0.7244 (mp0) cc_final: 0.6867 (mp0) REVERT: A 118 GLN cc_start: 0.2569 (OUTLIER) cc_final: 0.2328 (mt0) REVERT: A 285 ILE cc_start: 0.1057 (OUTLIER) cc_final: 0.0770 (pp) REVERT: A 375 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5782 (m-10) REVERT: A 438 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: B 196 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8223 (ttmm) REVERT: B 208 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: B 267 ASP cc_start: 0.7450 (m-30) cc_final: 0.7215 (m-30) REVERT: C 57 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6980 (mtm110) REVERT: C 85 GLU cc_start: 0.6587 (pm20) cc_final: 0.6159 (pm20) REVERT: C 86 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6791 (mp0) REVERT: C 100 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: C 428 GLN cc_start: 0.7545 (mp10) cc_final: 0.6949 (mm-40) REVERT: C 511 SER cc_start: 0.8820 (p) cc_final: 0.8609 (p) outliers start: 48 outliers final: 21 residues processed: 145 average time/residue: 1.3297 time to fit residues: 207.8045 Evaluate side-chains 134 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 94 optimal weight: 0.0870 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11925 Z= 0.255 Angle : 0.597 10.139 16607 Z= 0.298 Chirality : 0.042 0.197 1958 Planarity : 0.005 0.078 1869 Dihedral : 17.244 164.201 2765 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 7.02 % Allowed : 30.99 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.61 (0.23), residues: 1345 helix: 1.01 (0.26), residues: 444 sheet: -0.18 (0.31), residues: 294 loop : -1.61 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 110 HIS 0.003 0.001 HIS B 255 PHE 0.014 0.002 PHE D 139 TYR 0.015 0.002 TYR A 343 ARG 0.007 0.001 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 106 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.4979 (OUTLIER) cc_final: 0.4224 (pp) REVERT: A 43 GLU cc_start: 0.7282 (mp0) cc_final: 0.6928 (mp0) REVERT: A 281 ARG cc_start: 0.1017 (OUTLIER) cc_final: 0.0281 (mtm-85) REVERT: A 285 ILE cc_start: 0.1028 (OUTLIER) cc_final: 0.0770 (pp) REVERT: A 327 LYS cc_start: 0.6336 (OUTLIER) cc_final: 0.6000 (pttt) REVERT: A 334 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7597 (p) REVERT: B 196 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8243 (ttmm) REVERT: B 267 ASP cc_start: 0.7527 (m-30) cc_final: 0.7313 (m-30) REVERT: C 57 ARG cc_start: 0.7315 (mtp85) cc_final: 0.6939 (mtm110) REVERT: C 100 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: C 428 GLN cc_start: 0.7547 (mp10) cc_final: 0.6926 (mm-40) REVERT: C 494 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8042 (mt0) outliers start: 60 outliers final: 32 residues processed: 156 average time/residue: 1.2603 time to fit residues: 212.4646 Evaluate side-chains 142 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.0670 chunk 122 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11925 Z= 0.250 Angle : 0.584 10.048 16607 Z= 0.294 Chirality : 0.042 0.200 1958 Planarity : 0.005 0.076 1869 Dihedral : 17.197 164.336 2761 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.54 % Rotamer: Outliers : 6.55 % Allowed : 31.35 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.43 (0.23), residues: 1345 helix: 1.17 (0.26), residues: 444 sheet: -0.05 (0.31), residues: 296 loop : -1.53 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 110 HIS 0.003 0.001 HIS B 255 PHE 0.014 0.002 PHE A 391 TYR 0.015 0.002 TYR B 247 ARG 0.006 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 100 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4103 (pp) REVERT: A 43 GLU cc_start: 0.7319 (mp0) cc_final: 0.6934 (mp0) REVERT: A 281 ARG cc_start: 0.1285 (OUTLIER) cc_final: 0.0561 (mtm-85) REVERT: A 285 ILE cc_start: 0.1046 (OUTLIER) cc_final: 0.0795 (pp) REVERT: A 327 LYS cc_start: 0.6309 (OUTLIER) cc_final: 0.6040 (pttt) REVERT: A 334 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 458 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: B 196 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8224 (ttmm) REVERT: B 198 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7380 (ptt90) REVERT: B 208 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: B 267 ASP cc_start: 0.7583 (m-30) cc_final: 0.7377 (m-30) REVERT: C 57 ARG cc_start: 0.7338 (mtp85) cc_final: 0.7112 (ttp-170) REVERT: C 100 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: C 427 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 428 GLN cc_start: 0.7499 (mp10) cc_final: 0.6918 (mm-40) REVERT: C 522 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6172 (tt0) outliers start: 56 outliers final: 33 residues processed: 147 average time/residue: 1.1876 time to fit residues: 190.0728 Evaluate side-chains 143 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 99 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 327 LYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 138 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 40.0000 chunk 85 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11925 Z= 0.220 Angle : 0.565 9.742 16607 Z= 0.284 Chirality : 0.041 0.202 1958 Planarity : 0.004 0.072 1869 Dihedral : 17.175 164.774 2761 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 6.20 % Allowed : 32.05 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.28 (0.23), residues: 1345 helix: 1.30 (0.26), residues: 443 sheet: 0.07 (0.31), residues: 296 loop : -1.48 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 110 HIS 0.003 0.001 HIS B 255 PHE 0.014 0.001 PHE A 391 TYR 0.013 0.002 TYR A 343 ARG 0.007 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 103 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4038 (pp) REVERT: A 43 GLU cc_start: 0.7330 (mp0) cc_final: 0.6943 (mp0) REVERT: A 281 ARG cc_start: 0.1330 (OUTLIER) cc_final: 0.0593 (mtm-85) REVERT: A 285 ILE cc_start: 0.1033 (OUTLIER) cc_final: 0.0795 (pp) REVERT: A 334 VAL cc_start: 0.7936 (OUTLIER) cc_final: 0.7587 (p) REVERT: A 458 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 196 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8229 (ttmm) REVERT: B 208 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6818 (m-30) REVERT: B 267 ASP cc_start: 0.7548 (m-30) cc_final: 0.7316 (m-30) REVERT: C 57 ARG cc_start: 0.7389 (mtp85) cc_final: 0.7168 (ttp-170) REVERT: C 100 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: C 427 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8297 (mt) REVERT: C 428 GLN cc_start: 0.7498 (mp10) cc_final: 0.6916 (mm-40) REVERT: C 522 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.6180 (tt0) outliers start: 53 outliers final: 33 residues processed: 148 average time/residue: 1.2351 time to fit residues: 198.7450 Evaluate side-chains 142 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 100 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 522 GLN Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 154 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.0470 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 118 optimal weight: 50.0000 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11925 Z= 0.157 Angle : 0.519 9.885 16607 Z= 0.263 Chirality : 0.040 0.203 1958 Planarity : 0.004 0.073 1869 Dihedral : 17.097 167.838 2761 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.91 % Allowed : 33.22 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.06 (0.23), residues: 1345 helix: 1.49 (0.26), residues: 444 sheet: 0.23 (0.31), residues: 290 loop : -1.37 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 110 HIS 0.002 0.001 HIS B 255 PHE 0.013 0.001 PHE A 391 TYR 0.015 0.001 TYR B 247 ARG 0.009 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 109 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.4774 (OUTLIER) cc_final: 0.4050 (pp) REVERT: A 43 GLU cc_start: 0.7335 (mp0) cc_final: 0.6957 (mp0) REVERT: A 285 ILE cc_start: 0.1053 (OUTLIER) cc_final: 0.0803 (pp) REVERT: A 334 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7530 (p) REVERT: A 458 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: B 196 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8189 (ttmm) REVERT: B 208 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: B 267 ASP cc_start: 0.7455 (m-30) cc_final: 0.7209 (m-30) REVERT: C 85 GLU cc_start: 0.6662 (pm20) cc_final: 0.6347 (pm20) REVERT: C 86 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6688 (mp0) REVERT: C 100 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: C 427 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8281 (mt) REVERT: C 428 GLN cc_start: 0.7522 (mp10) cc_final: 0.6934 (mm-40) outliers start: 42 outliers final: 26 residues processed: 143 average time/residue: 1.2495 time to fit residues: 193.3873 Evaluate side-chains 137 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 146 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 76 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 114 optimal weight: 40.0000 chunk 119 optimal weight: 50.0000 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 50.0000 chunk 81 optimal weight: 0.7980 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11925 Z= 0.281 Angle : 0.599 10.083 16607 Z= 0.298 Chirality : 0.042 0.205 1958 Planarity : 0.005 0.069 1869 Dihedral : 17.168 164.316 2760 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.80 % Allowed : 32.98 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: -0.07 (0.23), residues: 1345 helix: 1.46 (0.26), residues: 442 sheet: 0.28 (0.31), residues: 300 loop : -1.40 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 110 HIS 0.003 0.001 HIS C 423 PHE 0.014 0.002 PHE D 139 TYR 0.015 0.002 TYR A 343 ARG 0.007 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 102 time to evaluate : 1.233 Fit side-chains REVERT: A 43 GLU cc_start: 0.7316 (mp0) cc_final: 0.6944 (mp0) REVERT: A 281 ARG cc_start: 0.1523 (OUTLIER) cc_final: 0.0625 (mtm-85) REVERT: A 285 ILE cc_start: 0.1075 (OUTLIER) cc_final: 0.0829 (pp) REVERT: A 458 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: B 118 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.3907 (tm-30) REVERT: B 196 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8236 (ttmm) REVERT: B 208 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: B 267 ASP cc_start: 0.7526 (m-30) cc_final: 0.7282 (m-30) REVERT: C 86 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6758 (mp0) REVERT: C 100 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: C 427 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8060 (mp) REVERT: C 428 GLN cc_start: 0.7483 (mp10) cc_final: 0.6896 (mm-40) outliers start: 41 outliers final: 29 residues processed: 136 average time/residue: 1.2039 time to fit residues: 177.5381 Evaluate side-chains 134 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 111 optimal weight: 50.0000 chunk 11 optimal weight: 0.0570 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN A 120 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11925 Z= 0.166 Angle : 0.538 9.722 16607 Z= 0.271 Chirality : 0.040 0.203 1958 Planarity : 0.004 0.071 1869 Dihedral : 17.119 166.108 2760 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.98 % Allowed : 33.80 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 0.04 (0.23), residues: 1345 helix: 1.54 (0.26), residues: 443 sheet: 0.37 (0.31), residues: 302 loop : -1.35 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 110 HIS 0.002 0.001 HIS B 255 PHE 0.014 0.001 PHE A 391 TYR 0.014 0.001 TYR A 343 ARG 0.008 0.000 ARG A 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2690 Ramachandran restraints generated. 1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 1.342 Fit side-chains REVERT: A 281 ARG cc_start: 0.1416 (OUTLIER) cc_final: 0.0569 (mtm-85) REVERT: A 285 ILE cc_start: 0.1073 (OUTLIER) cc_final: 0.0830 (pp) REVERT: A 334 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 458 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 196 LYS cc_start: 0.8465 (mtpt) cc_final: 0.8221 (ttmm) REVERT: B 208 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: B 267 ASP cc_start: 0.7448 (m-30) cc_final: 0.7203 (m-30) REVERT: C 85 GLU cc_start: 0.6730 (pm20) cc_final: 0.6504 (pm20) REVERT: C 86 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6742 (mp0) REVERT: C 100 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: C 427 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 428 GLN cc_start: 0.7490 (mp10) cc_final: 0.6924 (mm-40) outliers start: 34 outliers final: 26 residues processed: 136 average time/residue: 1.2764 time to fit residues: 187.7459 Evaluate side-chains 138 residues out of total 1187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 HIS Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 427 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 115 optimal weight: 40.0000 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 47 ASN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.213040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167975 restraints weight = 12307.763| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.56 r_work: 0.3300 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 11925 Z= 0.251 Angle : 0.800 59.181 16607 Z= 0.461 Chirality : 0.045 0.800 1958 Planarity : 0.004 0.071 1869 Dihedral : 17.118 166.117 2760 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.33 % Allowed : 33.45 % Favored : 62.22 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.67 % 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: 0.05 (0.23), residues: 1345 helix: 1.54 (0.26), residues: 443 sheet: 0.38 (0.31), residues: 302 loop : -1.33 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 110 HIS 0.003 0.001 HIS B 255 PHE 0.014 0.001 PHE A 391 TYR 0.014 0.001 TYR A 343 ARG 0.007 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3962.00 seconds wall clock time: 71 minutes 9.72 seconds (4269.72 seconds total)