Starting phenix.real_space_refine on Sat Jul 20 19:35:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/07_2024/8r3g_18864_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/07_2024/8r3g_18864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/07_2024/8r3g_18864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/07_2024/8r3g_18864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/07_2024/8r3g_18864_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/07_2024/8r3g_18864_neut.cif" } resolution = 4.4 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= 0.001 sd= 0.015 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: 5 Type Number sf(0) Gaussians P 82 5.49 5 S 56 5.16 5 C 7285 2.51 5 N 2090 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 33": "OE1" <-> "OE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11985 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 837 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "E" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 844 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Chain: "D" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2576 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 324} Chain breaks: 1 Number of resolved scattering type symbol conflicts: 48 Time building chain proxies: 8.19, per 1000 atoms: 0.68 Number of scatterers: 11985 At special positions: 0 Unit cell: (146.316, 130.698, 88.776, 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) Se 48 33.99 S 8 16.00 P 82 15.00 O 2472 8.00 N 2090 7.00 C 7285 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: 5.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 61.3% alpha, 13.1% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'C' and resid 1 through 12 Processing helix chain 'C' and resid 12 through 33 Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 47 through 61 Processing helix chain 'C' and resid 74 through 92 removed outlier: 5.160A pdb=" N ASP C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 Processing helix chain 'C' and resid 254 through 264 Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP C 296 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 310 through 318 Processing helix chain 'C' and resid 330 through 338 Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.683A pdb=" N LYS A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 33 Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 47 through 61 Processing helix chain 'A' and resid 74 through 92 removed outlier: 3.695A pdb=" N ASP A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.651A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP A 296 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 12 through 33 Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 47 through 61 Processing helix chain 'B' and resid 74 through 92 removed outlier: 5.159A pdb=" N ASP B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 105 Processing helix chain 'B' and resid 121 through 139 removed outlier: 4.160A pdb=" N LYS B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 160 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.705A pdb=" N VAL B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.705A pdb=" N ASP B 296 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.682A pdb=" N LYS D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 74 through 92 removed outlier: 3.695A pdb=" N ASP D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 removed outlier: 3.651A pdb=" N LEU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 139 removed outlier: 4.161A pdb=" N LYS D 125 " --> pdb=" O PRO D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 185 through 198 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 221 through 233 removed outlier: 3.704A pdb=" N VAL D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.704A pdb=" N ASP D 296 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 310 through 318 Processing helix chain 'D' and resid 330 through 338 Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 67 Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP C 109 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 328 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 111 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 301 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 327 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA C 303 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP C 329 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 237 " --> pdb=" O ILE C 302 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 304 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS C 239 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 242 through 243 removed outlier: 6.768A pdb=" N PHE C 275 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 269 " --> pdb=" O TYR C 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN C 276 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C 281 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 64 through 67 Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP A 109 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 328 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE A 111 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 301 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL A 327 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 303 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASP A 329 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 237 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 304 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS A 239 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE A 275 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 269 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN A 276 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 281 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 113 removed outlier: 6.555A pdb=" N ASP B 109 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B 328 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 111 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B 301 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 327 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 303 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ASP B 329 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 237 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL B 304 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N HIS B 239 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE B 275 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 269 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASN B 276 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 281 " --> pdb=" O ASN B 276 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 67 Processing sheet with id=AB2, first strand: chain 'D' and resid 109 through 113 removed outlier: 6.556A pdb=" N ASP D 109 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 328 " --> pdb=" O ASP D 109 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 111 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 301 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL D 327 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA D 303 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP D 329 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU D 237 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL D 304 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS D 239 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 242 through 243 removed outlier: 6.767A pdb=" N PHE D 275 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU D 269 " --> pdb=" O TYR D 273 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN D 276 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 281 " --> pdb=" O ASN D 276 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 4.21 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3703 1.35 - 1.51: 3821 1.51 - 1.67: 4676 1.67 - 1.84: 8 1.84 - 2.00: 96 Bond restraints: 12304 Sorted by residual: bond pdb=" N VAL D 206 " pdb=" CA VAL D 206 " ideal model delta sigma weight residual 1.460 1.494 -0.035 7.50e-03 1.78e+04 2.13e+01 bond pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.10e+01 bond pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.99e+01 bond pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.50e-03 1.78e+04 1.99e+01 bond pdb=" N LEU B 107 " pdb=" CA LEU B 107 " ideal model delta sigma weight residual 1.455 1.507 -0.052 1.25e-02 6.40e+03 1.75e+01 ... (remaining 12299 not shown) Histogram of bond angle deviations from ideal: 93.90 - 101.93: 93 101.93 - 109.97: 3074 109.97 - 118.00: 7059 118.00 - 126.04: 6381 126.04 - 134.07: 316 Bond angle restraints: 16923 Sorted by residual: angle pdb=" C PHE C 205 " pdb=" N VAL C 206 " pdb=" CA VAL C 206 " ideal model delta sigma weight residual 122.59 114.90 7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE B 205 " pdb=" N VAL B 206 " pdb=" CA VAL B 206 " ideal model delta sigma weight residual 122.59 114.90 7.69 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C PHE D 205 " pdb=" N VAL D 206 " pdb=" CA VAL D 206 " ideal model delta sigma weight residual 122.59 116.43 6.16 7.20e-01 1.93e+00 7.31e+01 angle pdb=" C PHE A 205 " pdb=" N VAL A 206 " pdb=" CA VAL A 206 " ideal model delta sigma weight residual 122.59 116.46 6.13 7.20e-01 1.93e+00 7.24e+01 angle pdb=" N ARG B 175 " pdb=" CA ARG B 175 " pdb=" C ARG B 175 " ideal model delta sigma weight residual 110.53 99.79 10.74 1.32e+00 5.74e-01 6.62e+01 ... (remaining 16918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6931 35.97 - 71.93: 435 71.93 - 107.90: 18 107.90 - 143.87: 0 143.87 - 179.84: 2 Dihedral angle restraints: 7386 sinusoidal: 3546 harmonic: 3840 Sorted by residual: dihedral pdb=" C4' DC E 19 " pdb=" C3' DC E 19 " pdb=" O3' DC E 19 " pdb=" P DA E 20 " ideal model delta sinusoidal sigma weight residual 220.00 40.16 179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC F 19 " pdb=" C3' DC F 19 " pdb=" O3' DC F 19 " pdb=" P DC F 20 " ideal model delta sinusoidal sigma weight residual 220.00 43.75 176.25 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C MSE D 88 " pdb=" N MSE D 88 " pdb=" CA MSE D 88 " pdb=" CB MSE D 88 " ideal model delta harmonic sigma weight residual -122.60 -132.12 9.52 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 7383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1275 0.084 - 0.169: 549 0.169 - 0.253: 107 0.253 - 0.337: 38 0.337 - 0.422: 11 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA VAL D 325 " pdb=" N VAL D 325 " pdb=" C VAL D 325 " pdb=" CB VAL D 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA VAL A 325 " pdb=" N VAL A 325 " pdb=" C VAL A 325 " pdb=" CB VAL A 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA VAL C 325 " pdb=" N VAL C 325 " pdb=" C VAL C 325 " pdb=" CB VAL C 325 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1977 not shown) Planarity restraints: 1878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 87 " 0.022 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C THR D 87 " -0.083 2.00e-02 2.50e+03 pdb=" O THR D 87 " 0.032 2.00e-02 2.50e+03 pdb=" N MSE D 88 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 87 " -0.022 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C THR A 87 " 0.083 2.00e-02 2.50e+03 pdb=" O THR A 87 " -0.032 2.00e-02 2.50e+03 pdb=" N MSE A 88 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 174 " 0.019 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA A 174 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A 174 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 175 " 0.024 2.00e-02 2.50e+03 ... (remaining 1875 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1547 2.77 - 3.31: 11645 3.31 - 3.84: 20868 3.84 - 4.37: 26612 4.37 - 4.90: 39448 Nonbonded interactions: 100120 Sorted by model distance: nonbonded pdb=" OE2 GLU B 33 " pdb=" OH TYR B 78 " model vdw 2.243 2.440 nonbonded pdb=" OE2 GLU C 33 " pdb=" OH TYR C 78 " model vdw 2.243 2.440 nonbonded pdb=" NH2 ARG C 49 " pdb=" N6 DA E 28 " model vdw 2.253 3.200 nonbonded pdb=" OE2 GLU A 33 " pdb=" OH TYR A 78 " model vdw 2.259 2.440 nonbonded pdb=" OE2 GLU D 33 " pdb=" OH TYR D 78 " model vdw 2.259 2.440 ... (remaining 100115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 39.990 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5193 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 : 0.013 0.099 12304 Z= 0.863 Angle : 1.540 10.744 16923 Z= 1.061 Chirality : 0.100 0.422 1980 Planarity : 0.007 0.048 1878 Dihedral : 19.042 179.837 4906 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.18 % Allowed : 5.16 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1324 helix: -0.91 (0.16), residues: 732 sheet: -0.59 (0.35), residues: 156 loop : -0.21 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.005 TRP C 122 HIS 0.015 0.005 HIS C 239 PHE 0.028 0.006 PHE B 57 TYR 0.049 0.010 TYR A 317 ARG 0.011 0.002 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 393 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 20 GLN cc_start: 0.8013 (mt0) cc_final: 0.7503 (mm-40) REVERT: C 132 VAL cc_start: 0.8206 (t) cc_final: 0.7907 (p) REVERT: C 152 THR cc_start: 0.8581 (m) cc_final: 0.8272 (p) REVERT: C 173 PRO cc_start: 0.6274 (Cg_endo) cc_final: 0.5881 (Cg_exo) REVERT: C 304 VAL cc_start: 0.7403 (t) cc_final: 0.7123 (m) REVERT: A 145 VAL cc_start: 0.7381 (t) cc_final: 0.6907 (t) REVERT: B 29 ILE cc_start: 0.8635 (mt) cc_final: 0.8279 (mm) REVERT: B 35 ILE cc_start: 0.8725 (tt) cc_final: 0.8216 (tp) REVERT: B 101 LEU cc_start: 0.7635 (tp) cc_final: 0.7323 (tp) REVERT: B 132 VAL cc_start: 0.8259 (t) cc_final: 0.7993 (p) REVERT: B 152 THR cc_start: 0.8727 (m) cc_final: 0.8385 (p) REVERT: B 304 VAL cc_start: 0.7346 (t) cc_final: 0.7090 (m) REVERT: D 12 LEU cc_start: 0.8142 (mt) cc_final: 0.6583 (mt) REVERT: D 19 MSE cc_start: 0.5088 (mtp) cc_final: 0.4762 (ttp) REVERT: D 145 VAL cc_start: 0.7443 (t) cc_final: 0.7094 (t) REVERT: D 295 ILE cc_start: 0.8004 (pt) cc_final: 0.7693 (pt) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.2898 time to fit residues: 155.1492 Evaluate side-chains 203 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 8 GLN A 252 ASN B 3 GLN B 6 GLN D 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12304 Z= 0.260 Angle : 0.710 9.396 16923 Z= 0.383 Chirality : 0.045 0.260 1980 Planarity : 0.005 0.071 1878 Dihedral : 20.675 178.638 2326 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1324 helix: 0.90 (0.18), residues: 762 sheet: -0.11 (0.36), residues: 152 loop : -0.02 (0.33), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 122 HIS 0.005 0.001 HIS B 192 PHE 0.032 0.003 PHE D 139 TYR 0.020 0.002 TYR C 274 ARG 0.005 0.001 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8728 (mp) cc_final: 0.8044 (mp) REVERT: C 35 ILE cc_start: 0.8007 (mm) cc_final: 0.7689 (mm) REVERT: C 125 LYS cc_start: 0.7826 (mttm) cc_final: 0.7342 (tttt) REVERT: C 132 VAL cc_start: 0.8687 (t) cc_final: 0.8051 (p) REVERT: C 158 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7121 (mm-30) REVERT: C 203 LEU cc_start: 0.5615 (mt) cc_final: 0.5384 (mt) REVERT: B 132 VAL cc_start: 0.8756 (t) cc_final: 0.8148 (p) REVERT: B 156 VAL cc_start: 0.8933 (t) cc_final: 0.8533 (t) REVERT: B 203 LEU cc_start: 0.5668 (mt) cc_final: 0.5223 (mt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2410 time to fit residues: 85.8474 Evaluate side-chains 166 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12304 Z= 0.182 Angle : 0.588 7.491 16923 Z= 0.319 Chirality : 0.041 0.176 1980 Planarity : 0.004 0.066 1878 Dihedral : 20.536 179.617 2326 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1324 helix: 1.45 (0.19), residues: 760 sheet: 0.13 (0.36), residues: 156 loop : -0.11 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 122 HIS 0.002 0.001 HIS B 283 PHE 0.022 0.002 PHE D 271 TYR 0.016 0.002 TYR B 201 ARG 0.004 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8523 (mp) cc_final: 0.7842 (mp) REVERT: C 46 ILE cc_start: 0.7791 (tp) cc_final: 0.7406 (mm) REVERT: C 132 VAL cc_start: 0.8577 (t) cc_final: 0.8096 (p) REVERT: C 156 VAL cc_start: 0.9072 (t) cc_final: 0.8564 (t) REVERT: C 247 MSE cc_start: -0.0337 (mmm) cc_final: -0.0597 (mmp) REVERT: A 12 LEU cc_start: 0.8408 (mp) cc_final: 0.8196 (mt) REVERT: B 15 LEU cc_start: 0.8535 (mp) cc_final: 0.7656 (mm) REVERT: B 132 VAL cc_start: 0.8597 (t) cc_final: 0.8020 (p) REVERT: D 237 LEU cc_start: 0.8715 (tp) cc_final: 0.8513 (tt) REVERT: D 290 MSE cc_start: 0.5448 (mmp) cc_final: 0.4987 (mmt) REVERT: D 295 ILE cc_start: 0.8641 (pt) cc_final: 0.8285 (pt) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2630 time to fit residues: 80.9029 Evaluate side-chains 153 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 127 optimal weight: 0.0060 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12304 Z= 0.177 Angle : 0.562 6.378 16923 Z= 0.309 Chirality : 0.040 0.177 1980 Planarity : 0.004 0.062 1878 Dihedral : 20.443 177.066 2326 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1324 helix: 1.53 (0.19), residues: 758 sheet: 0.33 (0.36), residues: 156 loop : -0.34 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 122 HIS 0.002 0.001 HIS C 239 PHE 0.023 0.002 PHE D 139 TYR 0.011 0.002 TYR B 201 ARG 0.004 0.000 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8792 (mp) cc_final: 0.8173 (mp) REVERT: C 59 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8193 (ttmm) REVERT: C 132 VAL cc_start: 0.8582 (t) cc_final: 0.8070 (p) REVERT: A 290 MSE cc_start: 0.5032 (mmp) cc_final: 0.4637 (mmt) REVERT: A 295 ILE cc_start: 0.8737 (pt) cc_final: 0.8371 (pt) REVERT: B 46 ILE cc_start: 0.7892 (pt) cc_final: 0.7674 (pt) REVERT: B 201 TYR cc_start: 0.5171 (p90) cc_final: 0.4946 (p90) REVERT: D 290 MSE cc_start: 0.5077 (mmp) cc_final: 0.4618 (mmt) REVERT: D 295 ILE cc_start: 0.8848 (pt) cc_final: 0.8438 (pt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2223 time to fit residues: 63.5242 Evaluate side-chains 143 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 6 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12304 Z= 0.186 Angle : 0.546 6.132 16923 Z= 0.302 Chirality : 0.039 0.162 1980 Planarity : 0.004 0.065 1878 Dihedral : 20.395 177.960 2326 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1324 helix: 1.59 (0.19), residues: 762 sheet: 0.16 (0.36), residues: 152 loop : -0.47 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 122 HIS 0.003 0.001 HIS B 192 PHE 0.028 0.003 PHE A 139 TYR 0.016 0.002 TYR B 201 ARG 0.007 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8749 (mp) cc_final: 0.8549 (mp) REVERT: C 120 SER cc_start: 0.6627 (p) cc_final: 0.6407 (m) REVERT: C 132 VAL cc_start: 0.8433 (t) cc_final: 0.8061 (p) REVERT: C 156 VAL cc_start: 0.9080 (t) cc_final: 0.8794 (t) REVERT: A 288 VAL cc_start: 0.7866 (m) cc_final: 0.7665 (m) REVERT: A 295 ILE cc_start: 0.8825 (pt) cc_final: 0.8487 (pt) REVERT: B 132 VAL cc_start: 0.8335 (t) cc_final: 0.8039 (t) REVERT: B 156 VAL cc_start: 0.8972 (t) cc_final: 0.8697 (t) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2255 time to fit residues: 61.8969 Evaluate side-chains 148 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 239 HIS ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12304 Z= 0.174 Angle : 0.559 8.406 16923 Z= 0.306 Chirality : 0.039 0.132 1980 Planarity : 0.004 0.065 1878 Dihedral : 20.323 177.912 2326 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1324 helix: 1.52 (0.19), residues: 766 sheet: 0.34 (0.37), residues: 152 loop : -0.53 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 122 HIS 0.002 0.000 HIS C 192 PHE 0.026 0.002 PHE D 139 TYR 0.012 0.002 TYR D 201 ARG 0.005 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 THR cc_start: 0.6781 (t) cc_final: 0.5128 (t) REVERT: A 236 MSE cc_start: 0.3116 (mtt) cc_final: 0.2575 (mtt) REVERT: B 207 PRO cc_start: 0.6323 (Cg_exo) cc_final: 0.6058 (Cg_endo) REVERT: D 200 THR cc_start: 0.6782 (t) cc_final: 0.5266 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2171 time to fit residues: 57.9294 Evaluate side-chains 131 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.0070 chunk 62 optimal weight: 0.0020 chunk 83 optimal weight: 0.8980 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN B 6 GLN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.7121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12304 Z= 0.157 Angle : 0.552 5.656 16923 Z= 0.300 Chirality : 0.039 0.133 1980 Planarity : 0.004 0.065 1878 Dihedral : 20.252 178.083 2326 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1324 helix: 1.60 (0.19), residues: 762 sheet: 0.24 (0.38), residues: 156 loop : -0.49 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 122 HIS 0.002 0.000 HIS D 192 PHE 0.021 0.002 PHE A 271 TYR 0.010 0.001 TYR D 274 ARG 0.004 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 ILE cc_start: 0.7634 (pt) cc_final: 0.7375 (pt) REVERT: D 201 TYR cc_start: 0.6797 (p90) cc_final: 0.6597 (p90) REVERT: D 290 MSE cc_start: 0.4978 (mmp) cc_final: 0.4454 (mmt) REVERT: D 295 ILE cc_start: 0.8767 (pt) cc_final: 0.8456 (pt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2199 time to fit residues: 56.5089 Evaluate side-chains 131 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.0370 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS B 6 GLN D 62 ASN D 286 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12304 Z= 0.164 Angle : 0.577 6.662 16923 Z= 0.311 Chirality : 0.039 0.157 1980 Planarity : 0.004 0.067 1878 Dihedral : 20.224 177.670 2326 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1324 helix: 1.57 (0.19), residues: 766 sheet: 0.22 (0.38), residues: 156 loop : -0.54 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 122 HIS 0.001 0.000 HIS B 192 PHE 0.018 0.002 PHE D 271 TYR 0.011 0.001 TYR D 274 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 SER cc_start: 0.6090 (p) cc_final: 0.5767 (m) REVERT: C 132 VAL cc_start: 0.8534 (t) cc_final: 0.8300 (t) REVERT: A 295 ILE cc_start: 0.8870 (pt) cc_final: 0.8513 (pt) REVERT: B 46 ILE cc_start: 0.7474 (pt) cc_final: 0.7234 (pt) REVERT: B 59 LYS cc_start: 0.8158 (ttmm) cc_final: 0.7766 (mttm) REVERT: D 295 ILE cc_start: 0.8721 (pt) cc_final: 0.8370 (pt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2353 time to fit residues: 57.3141 Evaluate side-chains 131 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12304 Z= 0.180 Angle : 0.595 7.567 16923 Z= 0.323 Chirality : 0.039 0.145 1980 Planarity : 0.004 0.070 1878 Dihedral : 20.192 177.484 2326 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1324 helix: 1.51 (0.19), residues: 764 sheet: 0.34 (0.38), residues: 152 loop : -0.58 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 122 HIS 0.005 0.001 HIS A 286 PHE 0.026 0.003 PHE D 139 TYR 0.010 0.001 TYR A 317 ARG 0.009 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 SER cc_start: 0.6125 (p) cc_final: 0.5748 (m) REVERT: A 295 ILE cc_start: 0.8857 (pt) cc_final: 0.8626 (pt) REVERT: B 46 ILE cc_start: 0.7465 (pt) cc_final: 0.7233 (pt) REVERT: B 59 LYS cc_start: 0.8241 (ttmm) cc_final: 0.7867 (mttm) REVERT: D 295 ILE cc_start: 0.8756 (pt) cc_final: 0.8510 (pt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2169 time to fit residues: 52.7859 Evaluate side-chains 130 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 286 HIS B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12304 Z= 0.208 Angle : 0.615 9.016 16923 Z= 0.335 Chirality : 0.039 0.175 1980 Planarity : 0.004 0.076 1878 Dihedral : 20.229 177.695 2326 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1324 helix: 1.54 (0.19), residues: 762 sheet: -0.16 (0.37), residues: 162 loop : -0.62 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 122 HIS 0.004 0.001 HIS A 286 PHE 0.022 0.003 PHE D 271 TYR 0.012 0.001 TYR B 28 ARG 0.010 0.001 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ILE cc_start: 0.7614 (pt) cc_final: 0.7394 (pt) REVERT: B 132 VAL cc_start: 0.8688 (t) cc_final: 0.8383 (p) REVERT: D 295 ILE cc_start: 0.8758 (pt) cc_final: 0.8523 (pt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2117 time to fit residues: 51.5924 Evaluate side-chains 127 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 0.0010 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 HIS A 192 HIS A 209 GLN A 291 GLN B 6 GLN D 192 HIS D 291 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.078122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062033 restraints weight = 58089.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.064383 restraints weight = 35750.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.066148 restraints weight = 24900.865| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.8369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12304 Z= 0.243 Angle : 0.657 11.514 16923 Z= 0.356 Chirality : 0.040 0.182 1980 Planarity : 0.005 0.078 1878 Dihedral : 20.325 177.887 2326 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1324 helix: 1.36 (0.19), residues: 774 sheet: 0.04 (0.39), residues: 146 loop : -1.07 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 122 HIS 0.009 0.002 HIS D 286 PHE 0.033 0.003 PHE A 23 TYR 0.012 0.002 TYR C 273 ARG 0.009 0.001 ARG C 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2458.77 seconds wall clock time: 45 minutes 19.52 seconds (2719.52 seconds total)