Starting phenix.real_space_refine on Mon Aug 5 00:32:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/08_2024/8r3g_18864.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/08_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_18864/08_2024/8r3g_18864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/08_2024/8r3g_18864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/08_2024/8r3g_18864.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3g_18864/08_2024/8r3g_18864.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: 6 Type Number sf(0) Gaussians Se 48 7.20 5 P 82 5.49 5 S 8 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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 Time building chain proxies: 6.98, per 1000 atoms: 0.58 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: 4.67 Conformation dependent library (CDL) restraints added in 1.6 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: 3.97 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: 3.78 Time building geometry restraints manager: 5.14 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 3.040 nonbonded pdb=" OE2 GLU C 33 " pdb=" OH TYR C 78 " model vdw 2.243 3.040 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 3.040 nonbonded pdb=" OE2 GLU D 33 " pdb=" OH TYR D 78 " model vdw 2.259 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.110 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.230 Find NCS groups from input model: 0.290 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: 0.000 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: 40.900 ------------------------------------------------------------------------------- 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 : 11.87 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 : 1.301 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: 0.2825 time to fit residues: 151.4970 Evaluate side-chains 203 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.262 ------------------------------------------------------------------------------- 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: 6.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.5822 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12304 Z= 0.299 Angle : 0.747 8.859 16923 Z= 0.403 Chirality : 0.046 0.262 1980 Planarity : 0.006 0.102 1878 Dihedral : 20.703 178.013 2326 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 0.49 (0.22), residues: 1324 helix: 0.79 (0.18), residues: 760 sheet: -0.30 (0.36), residues: 144 loop : -0.07 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 122 HIS 0.007 0.002 HIS B 192 PHE 0.030 0.003 PHE D 139 TYR 0.020 0.002 TYR C 274 ARG 0.013 0.001 ARG B 49 *********************** 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 232 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.173 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: C 125 LYS cc_start: 0.7831 (mttm) cc_final: 0.7271 (tttt) REVERT: C 158 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7392 (mm-30) REVERT: C 201 TYR cc_start: 0.5111 (p90) cc_final: 0.4909 (p90) REVERT: C 203 LEU cc_start: 0.5600 (mt) cc_final: 0.5389 (mt) REVERT: A 114 SER cc_start: 0.8032 (m) cc_final: 0.7693 (t) REVERT: B 71 MSE cc_start: 0.6572 (mpp) cc_final: 0.5504 (mtm) REVERT: B 132 VAL cc_start: 0.8803 (t) cc_final: 0.7985 (p) REVERT: B 203 LEU cc_start: 0.5706 (mt) cc_final: 0.5436 (mt) REVERT: B 304 VAL cc_start: 0.8078 (t) cc_final: 0.7828 (m) REVERT: D 114 SER cc_start: 0.8045 (m) cc_final: 0.7741 (t) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2320 time to fit residues: 77.0259 Evaluate side-chains 150 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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: 0.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12304 Z= 0.184 Angle : 0.590 7.599 16923 Z= 0.323 Chirality : 0.041 0.208 1980 Planarity : 0.004 0.071 1878 Dihedral : 20.576 179.759 2326 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 0.92 (0.23), residues: 1324 helix: 1.27 (0.18), residues: 762 sheet: 0.11 (0.36), residues: 154 loop : -0.30 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 122 HIS 0.002 0.001 HIS B 283 PHE 0.021 0.002 PHE A 271 TYR 0.017 0.002 TYR B 201 ARG 0.004 0.001 ARG C 38 *********************** 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 198 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.257 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 156 VAL cc_start: 0.9079 (t) cc_final: 0.8711 (t) REVERT: C 203 LEU cc_start: 0.5346 (mt) cc_final: 0.4983 (mt) REVERT: C 247 MSE cc_start: -0.0222 (mmm) cc_final: -0.0524 (mmp) REVERT: A 114 SER cc_start: 0.8254 (m) cc_final: 0.7822 (t) REVERT: B 71 MSE cc_start: 0.6553 (mpp) cc_final: 0.5790 (mtm) REVERT: B 132 VAL cc_start: 0.8606 (t) cc_final: 0.7985 (p) REVERT: D 295 ILE cc_start: 0.8679 (pt) cc_final: 0.8292 (pt) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2234 time to fit residues: 64.8036 Evaluate side-chains 147 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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: 7.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 GLN B 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.6602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12304 Z= 0.291 Angle : 0.651 6.544 16923 Z= 0.361 Chirality : 0.042 0.191 1980 Planarity : 0.005 0.071 1878 Dihedral : 20.598 176.889 2326 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 0.55 (0.23), residues: 1324 helix: 0.99 (0.18), residues: 768 sheet: 0.08 (0.37), residues: 154 loop : -0.57 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 122 HIS 0.004 0.001 HIS B 192 PHE 0.021 0.003 PHE D 271 TYR 0.022 0.003 TYR C 201 ARG 0.007 0.001 ARG D 175 *********************** 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 167 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 LEU cc_start: 0.8827 (mp) cc_final: 0.8305 (mp) REVERT: A 114 SER cc_start: 0.8332 (m) cc_final: 0.7859 (t) REVERT: B 247 MSE cc_start: 0.0120 (mmm) cc_final: -0.0138 (mmp) REVERT: D 236 MSE cc_start: 0.3994 (mtp) cc_final: 0.3740 (mtp) REVERT: D 288 VAL cc_start: 0.7883 (m) cc_final: 0.7607 (m) REVERT: D 295 ILE cc_start: 0.8899 (pt) cc_final: 0.8696 (pt) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2129 time to fit residues: 55.3043 Evaluate side-chains 131 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12304 Z= 0.184 Angle : 0.567 9.053 16923 Z= 0.314 Chirality : 0.039 0.160 1980 Planarity : 0.004 0.070 1878 Dihedral : 20.537 178.970 2326 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 0.83 (0.23), residues: 1324 helix: 1.32 (0.19), residues: 760 sheet: -0.16 (0.36), residues: 162 loop : -0.49 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 122 HIS 0.003 0.001 HIS D 286 PHE 0.022 0.002 PHE A 271 TYR 0.007 0.001 TYR A 215 ARG 0.005 0.000 ARG D 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 178 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.190 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 66 ILE cc_start: 0.7967 (mp) cc_final: 0.7750 (mp) REVERT: A 114 SER cc_start: 0.8439 (m) cc_final: 0.7874 (t) REVERT: A 295 ILE cc_start: 0.8699 (pt) cc_final: 0.8455 (pt) REVERT: B 120 SER cc_start: 0.6707 (p) cc_final: 0.6325 (m) REVERT: B 247 MSE cc_start: -0.0103 (mmm) cc_final: -0.0359 (mmp) REVERT: D 295 ILE cc_start: 0.8827 (pt) cc_final: 0.8588 (pt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2145 time to fit residues: 56.5446 Evaluate side-chains 139 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12304 Z= 0.227 Angle : 0.590 9.263 16923 Z= 0.328 Chirality : 0.040 0.163 1980 Planarity : 0.004 0.072 1878 Dihedral : 20.528 177.622 2326 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.74 (0.23), residues: 1324 helix: 1.31 (0.18), residues: 756 sheet: -0.36 (0.35), residues: 162 loop : -0.59 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 122 HIS 0.004 0.001 HIS A 286 PHE 0.026 0.003 PHE A 139 TYR 0.012 0.001 TYR A 317 ARG 0.004 0.000 ARG D 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 163 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.214 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: 0.7816 (pt) cc_final: 0.7613 (pt) REVERT: A 19 MSE cc_start: 0.5019 (ptm) cc_final: 0.4629 (ptm) REVERT: A 236 MSE cc_start: 0.3650 (mtt) cc_final: 0.3175 (mtt) REVERT: B 24 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 120 SER cc_start: 0.6574 (p) cc_final: 0.6205 (m) REVERT: B 247 MSE cc_start: 0.0052 (mmm) cc_final: -0.0591 (mmp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2021 time to fit residues: 49.7739 Evaluate side-chains 126 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12304 Z= 0.237 Angle : 0.610 8.185 16923 Z= 0.336 Chirality : 0.040 0.152 1980 Planarity : 0.005 0.076 1878 Dihedral : 20.573 178.368 2326 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 0.66 (0.23), residues: 1324 helix: 1.31 (0.18), residues: 756 sheet: -0.59 (0.34), residues: 166 loop : -0.66 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 122 HIS 0.004 0.001 HIS B 283 PHE 0.025 0.003 PHE A 271 TYR 0.014 0.002 TYR C 28 ARG 0.006 0.001 ARG B 250 *********************** 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 161 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.220 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: C 88 MSE cc_start: 0.6947 (tpp) cc_final: 0.6349 (tpt) REVERT: B 120 SER cc_start: 0.6588 (p) cc_final: 0.6175 (m) REVERT: D 236 MSE cc_start: 0.3265 (mtt) cc_final: 0.2981 (mtt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1995 time to fit residues: 49.1766 Evaluate side-chains 131 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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: 3.9990 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12304 Z= 0.181 Angle : 0.583 7.062 16923 Z= 0.318 Chirality : 0.039 0.168 1980 Planarity : 0.004 0.076 1878 Dihedral : 20.453 178.525 2326 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.85 (0.23), residues: 1324 helix: 1.53 (0.19), residues: 760 sheet: -0.48 (0.36), residues: 152 loop : -0.78 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 122 HIS 0.003 0.000 HIS B 283 PHE 0.018 0.002 PHE A 271 TYR 0.012 0.001 TYR A 274 ARG 0.003 0.000 ARG D 175 *********************** 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 168 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8238 (ttmm) REVERT: A 114 SER cc_start: 0.8453 (m) cc_final: 0.8024 (t) REVERT: D 19 MSE cc_start: 0.4870 (ptm) cc_final: 0.4668 (ptm) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2150 time to fit residues: 54.2402 Evaluate side-chains 134 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.8417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12304 Z= 0.267 Angle : 0.667 8.558 16923 Z= 0.364 Chirality : 0.041 0.163 1980 Planarity : 0.005 0.077 1878 Dihedral : 20.472 176.972 2326 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.46 (0.23), residues: 1324 helix: 1.17 (0.18), residues: 774 sheet: -0.49 (0.37), residues: 148 loop : -0.99 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 122 HIS 0.005 0.001 HIS B 283 PHE 0.028 0.003 PHE A 139 TYR 0.013 0.002 TYR B 273 ARG 0.005 0.001 ARG C 250 *********************** 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 158 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 GLU cc_start: 0.6143 (mm-30) cc_final: 0.5852 (mm-30) REVERT: C 236 MSE cc_start: 0.2096 (tpp) cc_final: 0.1646 (mmm) REVERT: B 120 SER cc_start: 0.6593 (p) cc_final: 0.6060 (m) REVERT: B 132 VAL cc_start: 0.8685 (t) cc_final: 0.7295 (t) REVERT: D 19 MSE cc_start: 0.5133 (ptm) cc_final: 0.4804 (ptm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2041 time to fit residues: 48.7799 Evaluate side-chains 134 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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: 5.9990 chunk 63 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.8790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12304 Z= 0.280 Angle : 0.667 8.892 16923 Z= 0.366 Chirality : 0.041 0.161 1980 Planarity : 0.005 0.084 1878 Dihedral : 20.528 178.022 2326 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.38 (0.23), residues: 1324 helix: 1.08 (0.18), residues: 762 sheet: -0.72 (0.37), residues: 146 loop : -0.82 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP C 122 HIS 0.004 0.001 HIS B 283 PHE 0.037 0.003 PHE A 139 TYR 0.015 0.002 TYR A 317 ARG 0.005 0.001 ARG B 30 ********************** 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 159 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 MSE cc_start: 0.2152 (tpp) cc_final: 0.1835 (mmm) REVERT: B 88 MSE cc_start: 0.6749 (tpp) cc_final: 0.6421 (tpp) REVERT: B 132 VAL cc_start: 0.8402 (t) cc_final: 0.7681 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1996 time to fit residues: 48.0205 Evaluate side-chains 126 residues out of total 1124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 0.9990 chunk 102 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 0.0470 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.078248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.062104 restraints weight = 57022.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.064553 restraints weight = 34694.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.066462 restraints weight = 23666.212| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.8877 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= 0.187 Angle : 0.617 8.264 16923 Z= 0.333 Chirality : 0.040 0.162 1980 Planarity : 0.004 0.075 1878 Dihedral : 20.411 178.303 2326 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.63 (0.23), residues: 1324 helix: 1.41 (0.19), residues: 756 sheet: -0.75 (0.38), residues: 144 loop : -0.89 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 122 HIS 0.004 0.001 HIS B 283 PHE 0.028 0.002 PHE D 139 TYR 0.010 0.001 TYR A 317 ARG 0.003 0.000 ARG D 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2273.47 seconds wall clock time: 41 minutes 45.73 seconds (2505.73 seconds total)