Starting phenix.real_space_refine on Sat Mar 16 16:34:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/03_2024/6zqj_11366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/03_2024/6zqj_11366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/03_2024/6zqj_11366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/03_2024/6zqj_11366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/03_2024/6zqj_11366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/03_2024/6zqj_11366.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 9501 2.51 5 N 2625 2.21 5 O 2841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D GLU 180": "OE1" <-> "OE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D GLU 245": "OE1" <-> "OE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D ARG 410": "NH1" <-> "NH2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G GLU 245": "OE1" <-> "OE2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G GLU 248": "OE1" <-> "OE2" Residue "G GLU 277": "OE1" <-> "OE2" Residue "G ARG 317": "NH1" <-> "NH2" Residue "G GLU 321": "OE1" <-> "OE2" Residue "G GLU 330": "OE1" <-> "OE2" Residue "G GLU 368": "OE1" <-> "OE2" Residue "G ARG 410": "NH1" <-> "NH2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "B" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "D" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "G" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "H" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "I" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "F" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.13, per 1000 atoms: 0.54 Number of scatterers: 15096 At special positions: 0 Unit cell: (170.69, 179.14, 141.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 2841 8.00 N 2625 7.00 C 9501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 67 " distance=2.04 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 121 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 116 " distance=2.04 Simple disulfide: pdb=" SG CYS G 191 " - pdb=" SG CYS G 292 " distance=2.03 Simple disulfide: pdb=" SG CYS G 309 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 69 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 81 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 67 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 201 " - " ASN B 70 " " NAG E 201 " - " ASN E 70 " " NAG H 201 " - " ASN H 70 " Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.8 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 35 sheets defined 23.4% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.716A pdb=" N ALA A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.544A pdb=" N GLY A 104 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.608A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 220' Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.971A pdb=" N ALA A 242 " --> pdb=" O ASN A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.594A pdb=" N THR A 395 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 396 " --> pdb=" O GLY A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 396' Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 437 through 458 removed outlier: 5.782A pdb=" N SER A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.540A pdb=" N LEU A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.697A pdb=" N PHE A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.787A pdb=" N ALA D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.516A pdb=" N GLY D 104 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.525A pdb=" N HIS D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.600A pdb=" N THR D 395 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS D 396 " --> pdb=" O GLY D 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 392 through 396' Processing helix chain 'D' and resid 406 through 425 Processing helix chain 'D' and resid 437 through 458 removed outlier: 5.822A pdb=" N SER D 452 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA D 453 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 removed outlier: 3.527A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 502 removed outlier: 3.699A pdb=" N PHE D 489 " --> pdb=" O VAL D 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.801A pdb=" N ALA G 86 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 104 removed outlier: 3.505A pdb=" N GLY G 104 " --> pdb=" O TRP G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.666A pdb=" N HIS G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 220' Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 392 through 396 removed outlier: 3.598A pdb=" N THR G 395 " --> pdb=" O THR G 392 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS G 396 " --> pdb=" O GLY G 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 392 through 396' Processing helix chain 'G' and resid 406 through 425 Processing helix chain 'G' and resid 437 through 458 removed outlier: 5.801A pdb=" N SER G 452 " --> pdb=" O GLN G 448 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA G 453 " --> pdb=" O VAL G 449 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 479 removed outlier: 3.571A pdb=" N LEU G 468 " --> pdb=" O PHE G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 502 removed outlier: 3.690A pdb=" N PHE G 489 " --> pdb=" O VAL G 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 146 removed outlier: 3.565A pdb=" N ALA I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 165 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 146 removed outlier: 3.991A pdb=" N THR F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.986A pdb=" N THR C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.189A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.738A pdb=" N GLU A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.942A pdb=" N LYS A 291 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 64 removed outlier: 6.170A pdb=" N VAL A 56 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS A 128 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 58 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 126 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A 60 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A 124 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 62 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 274 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.682A pdb=" N ALA A 307 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.549A pdb=" N THR A 328 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 320 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.957A pdb=" N ARG A 358 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.137A pdb=" N TYR B 10 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 77 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N MET B 12 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLY B 79 " --> pdb=" O MET B 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.697A pdb=" N ASP D 10 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 32 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE D 43 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER D 142 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU D 45 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 140 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 47 " --> pdb=" O ARG D 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.697A pdb=" N ASP D 10 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 32 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 277 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.942A pdb=" N LYS D 291 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 226 through 228 removed outlier: 7.065A pdb=" N GLY D 127 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER D 58 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 125 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS D 60 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS D 123 " --> pdb=" O CYS D 60 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU D 62 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N CYS D 121 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU D 274 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 90 through 98 removed outlier: 6.675A pdb=" N MET D 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLU E 52 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER D 70 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR E 10 " --> pdb=" O TRP E 75 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL E 77 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N MET E 12 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY E 79 " --> pdb=" O MET E 12 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC1, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.616A pdb=" N ALA D 307 " --> pdb=" O LYS D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 312 through 315 removed outlier: 3.560A pdb=" N THR D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 320 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 312 through 315 removed outlier: 3.952A pdb=" N ARG D 358 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AC5, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.742A pdb=" N ASP G 10 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 32 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE G 43 " --> pdb=" O SER G 142 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER G 142 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU G 45 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 140 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR G 47 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.742A pdb=" N ASP G 10 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 32 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 277 " --> pdb=" O THR G 284 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 25 removed outlier: 3.959A pdb=" N LYS G 291 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 226 through 228 removed outlier: 5.904A pdb=" N VAL G 56 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS G 128 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER G 58 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR G 126 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS G 60 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS G 124 " --> pdb=" O CYS G 60 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU G 62 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 122 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU G 274 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 69 through 73 Processing sheet with id=AD2, first strand: chain 'G' and resid 244 through 246 Processing sheet with id=AD3, first strand: chain 'G' and resid 307 through 308 removed outlier: 6.692A pdb=" N ALA G 307 " --> pdb=" O LYS G 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 312 through 315 removed outlier: 3.593A pdb=" N THR G 328 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER G 320 " --> pdb=" O THR G 328 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 312 through 315 removed outlier: 4.044A pdb=" N ARG G 358 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 344 through 347 Processing sheet with id=AD7, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.451A pdb=" N TYR H 10 " --> pdb=" O TRP H 75 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL H 77 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET H 12 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY H 79 " --> pdb=" O MET H 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 22 through 26 629 hydrogen bonds defined for protein. 1740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4937 1.35 - 1.46: 3726 1.46 - 1.58: 6565 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 15432 Sorted by residual: bond pdb=" C1 NAG B 201 " pdb=" O5 NAG B 201 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG E 201 " pdb=" O5 NAG E 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG H 201 " pdb=" O5 NAG H 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C CYS G 74 " pdb=" N PRO G 75 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 bond pdb=" C CYS D 74 " pdb=" N PRO D 75 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 15427 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.25: 531 107.25 - 113.94: 8698 113.94 - 120.62: 5691 120.62 - 127.31: 5765 127.31 - 133.99: 201 Bond angle restraints: 20886 Sorted by residual: angle pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 114.40 124.58 -10.18 2.30e+00 1.89e-01 1.96e+01 angle pdb=" CA CYS D 116 " pdb=" CB CYS D 116 " pdb=" SG CYS D 116 " ideal model delta sigma weight residual 114.40 124.38 -9.98 2.30e+00 1.89e-01 1.88e+01 angle pdb=" CA CYS G 116 " pdb=" CB CYS G 116 " pdb=" SG CYS G 116 " ideal model delta sigma weight residual 114.40 124.33 -9.93 2.30e+00 1.89e-01 1.87e+01 angle pdb=" CA CYS D 92 " pdb=" CB CYS D 92 " pdb=" SG CYS D 92 " ideal model delta sigma weight residual 114.40 123.88 -9.48 2.30e+00 1.89e-01 1.70e+01 angle pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 114.40 123.72 -9.32 2.30e+00 1.89e-01 1.64e+01 ... (remaining 20881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8477 17.94 - 35.88: 552 35.88 - 53.82: 111 53.82 - 71.76: 13 71.76 - 89.70: 15 Dihedral angle restraints: 9168 sinusoidal: 3609 harmonic: 5559 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual 93.00 178.72 -85.72 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS D 74 " pdb=" SG CYS D 74 " pdb=" SG CYS D 105 " pdb=" CB CYS D 105 " ideal model delta sinusoidal sigma weight residual 93.00 175.19 -82.19 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS G 74 " pdb=" SG CYS G 74 " pdb=" SG CYS G 105 " pdb=" CB CYS G 105 " ideal model delta sinusoidal sigma weight residual 93.00 173.98 -80.98 1 1.00e+01 1.00e-02 8.09e+01 ... (remaining 9165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1662 0.039 - 0.077: 452 0.077 - 0.116: 163 0.116 - 0.155: 39 0.155 - 0.194: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CA CYS A 116 " pdb=" N CYS A 116 " pdb=" C CYS A 116 " pdb=" CB CYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA CYS D 116 " pdb=" N CYS D 116 " pdb=" C CYS D 116 " pdb=" CB CYS D 116 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA CYS G 116 " pdb=" N CYS G 116 " pdb=" C CYS G 116 " pdb=" CB CYS G 116 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 2316 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 111 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLY D 111 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY D 111 " 0.013 2.00e-02 2.50e+03 pdb=" N SER D 112 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 111 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C GLY G 111 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY G 111 " 0.012 2.00e-02 2.50e+03 pdb=" N SER G 112 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 51 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C TYR H 51 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR H 51 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU H 52 " -0.011 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4236 2.81 - 3.33: 13004 3.33 - 3.85: 22774 3.85 - 4.38: 24622 4.38 - 4.90: 44215 Nonbonded interactions: 108851 Sorted by model distance: nonbonded pdb=" OD1 ASP D 380 " pdb=" NH1 ARG D 403 " model vdw 2.286 2.520 nonbonded pdb=" OG SER G 348 " pdb=" NH2 ARG I 132 " model vdw 2.322 2.520 nonbonded pdb=" OD1 ASP G 380 " pdb=" NH1 ARG G 403 " model vdw 2.342 2.520 nonbonded pdb=" OD1 ASP A 380 " pdb=" NH1 ARG A 403 " model vdw 2.354 2.520 nonbonded pdb=" N ASN A 233 " pdb=" OD1 ASN A 233 " model vdw 2.370 2.520 ... (remaining 108846 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 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.550 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 40.110 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15432 Z= 0.134 Angle : 0.555 10.184 20886 Z= 0.314 Chirality : 0.042 0.194 2319 Planarity : 0.003 0.032 2661 Dihedral : 12.255 89.703 5541 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 4.03 % Favored : 94.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 1947 helix: -0.01 (0.24), residues: 396 sheet: -0.54 (0.21), residues: 564 loop : -2.64 (0.15), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.008 0.001 HIS B 83 PHE 0.012 0.001 PHE A 445 TYR 0.009 0.001 TYR E 51 ARG 0.009 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 739 time to evaluate : 1.636 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: A 23 ILE cc_start: 0.8763 (pt) cc_final: 0.8560 (mt) REVERT: A 36 ASN cc_start: 0.8293 (p0) cc_final: 0.7889 (p0) REVERT: A 118 LYS cc_start: 0.8792 (tttp) cc_final: 0.8159 (ttpt) REVERT: A 140 LEU cc_start: 0.9126 (mt) cc_final: 0.8920 (mt) REVERT: A 151 MET cc_start: 0.3263 (tpt) cc_final: 0.2885 (mmp) REVERT: A 207 MET cc_start: 0.7556 (ttt) cc_final: 0.7305 (tmm) REVERT: A 294 LEU cc_start: 0.8978 (mt) cc_final: 0.8351 (mp) REVERT: A 416 MET cc_start: 0.7953 (ttt) cc_final: 0.7302 (tpt) REVERT: A 489 PHE cc_start: 0.3431 (m-10) cc_final: 0.3020 (m-10) REVERT: B 12 MET cc_start: 0.8261 (mtm) cc_final: 0.8008 (mtp) REVERT: B 26 GLU cc_start: 0.8089 (tt0) cc_final: 0.7586 (tp30) REVERT: B 63 GLU cc_start: 0.6154 (tt0) cc_final: 0.5672 (tm-30) REVERT: B 93 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6643 (ptp90) REVERT: B 101 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5182 (m-70) REVERT: D 118 LYS cc_start: 0.8352 (tttp) cc_final: 0.8146 (tttt) REVERT: D 253 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7241 (pttp) REVERT: D 285 ILE cc_start: 0.8154 (mp) cc_final: 0.7699 (mp) REVERT: D 302 LYS cc_start: 0.7515 (tttt) cc_final: 0.7229 (tptt) REVERT: D 383 PHE cc_start: 0.8253 (m-80) cc_final: 0.7664 (m-10) REVERT: D 403 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8050 (ptm160) REVERT: D 447 HIS cc_start: 0.8068 (t-90) cc_final: 0.7504 (t-90) REVERT: D 487 MET cc_start: 0.2812 (mpp) cc_final: 0.2582 (tmm) REVERT: D 495 MET cc_start: 0.6537 (ttm) cc_final: 0.6221 (mmm) REVERT: E 44 MET cc_start: 0.6487 (tpp) cc_final: 0.5745 (tpp) REVERT: E 101 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.5527 (m-70) REVERT: G 27 HIS cc_start: 0.5741 (t-90) cc_final: 0.5282 (t-90) REVERT: G 53 MET cc_start: 0.7557 (mtm) cc_final: 0.7300 (mtm) REVERT: G 71 ASP cc_start: 0.8438 (t0) cc_final: 0.7432 (t0) REVERT: G 87 ASP cc_start: 0.6750 (t0) cc_final: 0.5697 (t0) REVERT: G 90 PHE cc_start: 0.8620 (m-80) cc_final: 0.8141 (m-80) REVERT: G 131 GLN cc_start: 0.8603 (mm110) cc_final: 0.8357 (mt0) REVERT: G 140 LEU cc_start: 0.8785 (mt) cc_final: 0.8572 (mt) REVERT: G 151 MET cc_start: 0.4884 (tpt) cc_final: 0.4056 (tpp) REVERT: G 207 MET cc_start: 0.8681 (ttt) cc_final: 0.8097 (tmm) REVERT: G 248 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7721 (pp20) REVERT: G 250 HIS cc_start: 0.6610 (t70) cc_final: 0.6223 (t-170) REVERT: G 294 LEU cc_start: 0.8230 (mt) cc_final: 0.7847 (mp) REVERT: G 302 LYS cc_start: 0.8546 (tttt) cc_final: 0.7956 (tptp) REVERT: G 313 PHE cc_start: 0.8367 (m-80) cc_final: 0.8164 (m-10) REVERT: G 341 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8347 (mtmm) REVERT: G 376 MET cc_start: 0.8754 (ttp) cc_final: 0.8180 (tmm) REVERT: G 383 PHE cc_start: 0.7201 (m-80) cc_final: 0.6898 (m-80) REVERT: G 422 MET cc_start: 0.9304 (tpp) cc_final: 0.9011 (mmm) REVERT: G 435 VAL cc_start: 0.7062 (p) cc_final: 0.6859 (p) REVERT: G 439 PHE cc_start: 0.7315 (m-80) cc_final: 0.6776 (p90) REVERT: G 440 ASN cc_start: 0.7862 (t0) cc_final: 0.7554 (t0) REVERT: H 36 ILE cc_start: 0.7679 (mt) cc_final: 0.7433 (mt) REVERT: H 51 TYR cc_start: 0.8535 (p90) cc_final: 0.8232 (p90) REVERT: H 83 HIS cc_start: 0.6778 (m170) cc_final: 0.6171 (m170) REVERT: H 101 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6209 (m-70) REVERT: I 125 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8686 (mtmt) REVERT: I 128 ASN cc_start: 0.8098 (t0) cc_final: 0.7897 (t0) outliers start: 25 outliers final: 6 residues processed: 753 average time/residue: 0.2814 time to fit residues: 301.6827 Evaluate side-chains 482 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 472 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 236 HIS A 250 HIS A 363 ASN A 448 GLN B 83 HIS B 101 HIS D 147 GLN D 148 HIS D 400 HIS E 83 HIS G 131 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 363 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 15432 Z= 0.217 Angle : 0.646 13.955 20886 Z= 0.339 Chirality : 0.045 0.254 2319 Planarity : 0.004 0.035 2661 Dihedral : 4.975 82.712 2166 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.43 % Allowed : 4.90 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.18), residues: 1947 helix: 1.27 (0.27), residues: 399 sheet: -0.09 (0.21), residues: 591 loop : -2.08 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 129 HIS 0.012 0.001 HIS A 235 PHE 0.032 0.002 PHE C 157 TYR 0.026 0.001 TYR G 203 ARG 0.009 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 549 time to evaluate : 1.580 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: A 76 THR cc_start: 0.8473 (m) cc_final: 0.8210 (m) REVERT: A 85 MET cc_start: 0.7422 (mtm) cc_final: 0.7130 (ttm) REVERT: A 131 GLN cc_start: 0.7469 (mt0) cc_final: 0.6957 (mm-40) REVERT: A 133 GLU cc_start: 0.7707 (pm20) cc_final: 0.7489 (pm20) REVERT: A 147 GLN cc_start: 0.8337 (mt0) cc_final: 0.8041 (mt0) REVERT: A 156 THR cc_start: 0.8110 (p) cc_final: 0.7899 (t) REVERT: A 227 HIS cc_start: 0.8878 (p90) cc_final: 0.8645 (p90) REVERT: A 241 GLU cc_start: 0.8372 (mp0) cc_final: 0.8168 (mp0) REVERT: A 294 LEU cc_start: 0.8835 (mt) cc_final: 0.8493 (mp) REVERT: A 415 THR cc_start: 0.8774 (m) cc_final: 0.8521 (p) REVERT: A 416 MET cc_start: 0.7845 (ttt) cc_final: 0.7371 (tpt) REVERT: A 438 MET cc_start: 0.8769 (tpt) cc_final: 0.7074 (mpp) REVERT: B 5 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8676 (pttt) REVERT: B 26 GLU cc_start: 0.8068 (tt0) cc_final: 0.7647 (tp30) REVERT: B 27 THR cc_start: 0.6840 (p) cc_final: 0.6385 (p) REVERT: B 63 GLU cc_start: 0.6394 (tt0) cc_final: 0.5927 (tm-30) REVERT: B 77 VAL cc_start: 0.8800 (p) cc_final: 0.8280 (m) REVERT: D 26 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8178 (mm-30) REVERT: D 108 PHE cc_start: 0.6534 (m-10) cc_final: 0.6016 (m-10) REVERT: D 297 ASP cc_start: 0.7677 (p0) cc_final: 0.7337 (p0) REVERT: D 383 PHE cc_start: 0.8421 (m-80) cc_final: 0.8163 (m-10) REVERT: D 487 MET cc_start: 0.2963 (mpp) cc_final: 0.2461 (tmm) REVERT: D 495 MET cc_start: 0.6507 (ttm) cc_final: 0.5946 (mmm) REVERT: E 44 MET cc_start: 0.5704 (tpp) cc_final: 0.5454 (tpp) REVERT: E 68 TRP cc_start: 0.7170 (p90) cc_final: 0.6891 (p90) REVERT: G 44 GLU cc_start: 0.8142 (tt0) cc_final: 0.7687 (tt0) REVERT: G 68 MET cc_start: 0.8617 (mtt) cc_final: 0.8354 (mtt) REVERT: G 151 MET cc_start: 0.4951 (tpt) cc_final: 0.4568 (tpp) REVERT: G 160 HIS cc_start: 0.7111 (m-70) cc_final: 0.6790 (m-70) REVERT: G 250 HIS cc_start: 0.7157 (t70) cc_final: 0.6558 (t-170) REVERT: G 285 ILE cc_start: 0.8520 (mp) cc_final: 0.8253 (mt) REVERT: G 301 LEU cc_start: 0.9395 (tp) cc_final: 0.9113 (tp) REVERT: G 302 LYS cc_start: 0.8671 (tttt) cc_final: 0.8416 (tptp) REVERT: G 349 ASP cc_start: 0.8688 (t0) cc_final: 0.8186 (t0) REVERT: G 376 MET cc_start: 0.8679 (ttp) cc_final: 0.8012 (tmm) REVERT: G 383 PHE cc_start: 0.7322 (m-80) cc_final: 0.6951 (m-80) REVERT: G 422 MET cc_start: 0.9163 (tpp) cc_final: 0.8928 (mmm) REVERT: G 439 PHE cc_start: 0.7602 (m-80) cc_final: 0.6921 (p90) REVERT: H 66 ASP cc_start: 0.5445 (m-30) cc_final: 0.4811 (m-30) REVERT: I 125 LYS cc_start: 0.9182 (mtpt) cc_final: 0.8773 (mtmt) REVERT: F 153 GLN cc_start: 0.6463 (mp10) cc_final: 0.6058 (mp10) outliers start: 7 outliers final: 3 residues processed: 549 average time/residue: 0.2529 time to fit residues: 203.9478 Evaluate side-chains 442 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 439 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 177 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 144 HIS ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS A 250 HIS D 148 HIS D 164 ASN D 289 HIS D 448 GLN E 37 GLN G 37 ASN G 144 HIS G 159 GLN G 250 HIS G 254 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15432 Z= 0.287 Angle : 0.686 16.073 20886 Z= 0.362 Chirality : 0.046 0.262 2319 Planarity : 0.004 0.037 2661 Dihedral : 5.430 89.606 2166 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.37 % Allowed : 5.15 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1947 helix: 1.23 (0.26), residues: 417 sheet: -0.09 (0.21), residues: 624 loop : -1.97 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 68 HIS 0.010 0.001 HIS A 27 PHE 0.018 0.002 PHE C 157 TYR 0.021 0.002 TYR G 203 ARG 0.005 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 502 time to evaluate : 1.752 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: A 82 LEU cc_start: 0.9249 (tp) cc_final: 0.8819 (tp) REVERT: A 131 GLN cc_start: 0.7641 (mt0) cc_final: 0.7385 (mm-40) REVERT: A 207 MET cc_start: 0.8514 (tmm) cc_final: 0.7858 (ptm) REVERT: A 415 THR cc_start: 0.8849 (m) cc_final: 0.8597 (p) REVERT: A 416 MET cc_start: 0.7622 (ttt) cc_final: 0.7200 (mmm) REVERT: A 438 MET cc_start: 0.8406 (tpt) cc_final: 0.7031 (mpp) REVERT: B 5 LYS cc_start: 0.8994 (ptmt) cc_final: 0.8634 (pttt) REVERT: B 26 GLU cc_start: 0.8098 (tt0) cc_final: 0.7726 (tp30) REVERT: B 27 THR cc_start: 0.7243 (p) cc_final: 0.6964 (p) REVERT: B 63 GLU cc_start: 0.7002 (tt0) cc_final: 0.6734 (tm-30) REVERT: B 77 VAL cc_start: 0.8524 (p) cc_final: 0.8275 (m) REVERT: B 86 THR cc_start: 0.6907 (p) cc_final: 0.6691 (p) REVERT: D 20 TRP cc_start: 0.8615 (m100) cc_final: 0.8332 (m100) REVERT: D 26 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8161 (mm-30) REVERT: D 53 MET cc_start: 0.7453 (ptp) cc_final: 0.7219 (ptp) REVERT: D 245 GLU cc_start: 0.8290 (tt0) cc_final: 0.8072 (tt0) REVERT: D 297 ASP cc_start: 0.7688 (p0) cc_final: 0.7389 (p0) REVERT: D 383 PHE cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-10) REVERT: D 389 ILE cc_start: 0.9288 (mp) cc_final: 0.8941 (tp) REVERT: D 487 MET cc_start: 0.2855 (mpp) cc_final: 0.2005 (tmm) REVERT: E 39 MET cc_start: 0.5823 (mmm) cc_final: 0.5157 (mmm) REVERT: E 41 ILE cc_start: 0.8975 (tt) cc_final: 0.8735 (mp) REVERT: E 44 MET cc_start: 0.5692 (tpp) cc_final: 0.5315 (tpp) REVERT: E 88 GLU cc_start: 0.7418 (mp0) cc_final: 0.7200 (mp0) REVERT: E 93 ARG cc_start: 0.8470 (ptp-110) cc_final: 0.8184 (ptp-170) REVERT: G 68 MET cc_start: 0.8570 (mtt) cc_final: 0.8238 (mtp) REVERT: G 151 MET cc_start: 0.4377 (tpt) cc_final: 0.3616 (tpp) REVERT: G 160 HIS cc_start: 0.7198 (m-70) cc_final: 0.6921 (m-70) REVERT: G 207 MET cc_start: 0.8851 (tmm) cc_final: 0.7687 (tmm) REVERT: G 254 GLN cc_start: 0.8299 (mt0) cc_final: 0.8081 (mm110) REVERT: G 306 TYR cc_start: 0.7582 (m-10) cc_final: 0.6952 (m-10) REVERT: G 349 ASP cc_start: 0.8477 (t0) cc_final: 0.7987 (t0) REVERT: G 378 GLU cc_start: 0.8588 (tt0) cc_final: 0.8314 (tt0) REVERT: G 380 ASP cc_start: 0.7589 (t0) cc_final: 0.7066 (p0) REVERT: G 387 TYR cc_start: 0.7892 (m-10) cc_final: 0.7660 (m-10) REVERT: G 439 PHE cc_start: 0.7763 (m-80) cc_final: 0.7280 (p90) REVERT: G 487 MET cc_start: 0.5614 (mtm) cc_final: 0.3725 (tmm) REVERT: H 21 LYS cc_start: 0.6348 (pttp) cc_final: 0.6115 (pttp) REVERT: H 88 GLU cc_start: 0.8873 (tp30) cc_final: 0.8667 (tp30) REVERT: I 125 LYS cc_start: 0.9332 (mtpt) cc_final: 0.8857 (mtmt) REVERT: C 161 LEU cc_start: 0.8689 (tp) cc_final: 0.8447 (tp) outliers start: 6 outliers final: 2 residues processed: 503 average time/residue: 0.2556 time to fit residues: 187.9297 Evaluate side-chains 407 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 405 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN A 164 ASN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS D 144 HIS D 254 GLN D 262 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 15432 Z= 0.536 Angle : 0.890 19.938 20886 Z= 0.470 Chirality : 0.052 0.317 2319 Planarity : 0.006 0.059 2661 Dihedral : 6.676 88.165 2166 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.37 % Allowed : 6.95 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.48 (0.18), residues: 1947 helix: 0.96 (0.26), residues: 411 sheet: -0.59 (0.20), residues: 660 loop : -2.28 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 475 HIS 0.017 0.003 HIS G 27 PHE 0.035 0.003 PHE A 219 TYR 0.031 0.003 TYR A 61 ARG 0.010 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 465 time to evaluate : 1.547 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: A 82 LEU cc_start: 0.8890 (tp) cc_final: 0.8607 (tp) REVERT: A 96 TYR cc_start: 0.8084 (m-80) cc_final: 0.7737 (m-80) REVERT: A 131 GLN cc_start: 0.7816 (mt0) cc_final: 0.7162 (mm-40) REVERT: A 133 GLU cc_start: 0.7739 (pm20) cc_final: 0.7401 (tm-30) REVERT: A 136 GLU cc_start: 0.8129 (mp0) cc_final: 0.7901 (mp0) REVERT: A 207 MET cc_start: 0.8443 (tmm) cc_final: 0.7859 (ptm) REVERT: A 349 ASP cc_start: 0.7704 (t0) cc_final: 0.7429 (t0) REVERT: A 415 THR cc_start: 0.8966 (m) cc_final: 0.8714 (p) REVERT: A 416 MET cc_start: 0.7156 (ttt) cc_final: 0.6027 (tpp) REVERT: A 495 MET cc_start: 0.6892 (mtp) cc_final: 0.6342 (mmp) REVERT: B 77 VAL cc_start: 0.8662 (p) cc_final: 0.8276 (m) REVERT: B 89 THR cc_start: 0.8901 (t) cc_final: 0.8655 (p) REVERT: D 26 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8006 (mt-10) REVERT: D 53 MET cc_start: 0.8203 (ptp) cc_final: 0.7922 (ptp) REVERT: D 73 ARG cc_start: 0.6722 (ttm170) cc_final: 0.6406 (ttm170) REVERT: D 108 PHE cc_start: 0.6820 (m-10) cc_final: 0.6353 (m-10) REVERT: D 202 LEU cc_start: 0.8641 (mt) cc_final: 0.8377 (mt) REVERT: D 245 GLU cc_start: 0.8276 (tt0) cc_final: 0.8032 (tt0) REVERT: D 297 ASP cc_start: 0.7974 (p0) cc_final: 0.7633 (p0) REVERT: D 389 ILE cc_start: 0.9381 (mp) cc_final: 0.9028 (tp) REVERT: D 400 HIS cc_start: 0.8049 (t70) cc_final: 0.7728 (t-90) REVERT: D 422 MET cc_start: 0.9397 (tpp) cc_final: 0.9025 (tpp) REVERT: D 425 LEU cc_start: 0.8842 (mm) cc_final: 0.8492 (mt) REVERT: D 487 MET cc_start: 0.4818 (mpp) cc_final: 0.3579 (tmm) REVERT: E 39 MET cc_start: 0.6081 (mmm) cc_final: 0.5783 (mmm) REVERT: E 51 TYR cc_start: 0.7792 (p90) cc_final: 0.7581 (p90) REVERT: E 63 GLU cc_start: 0.7223 (mp0) cc_final: 0.6875 (mp0) REVERT: E 64 ASP cc_start: 0.6698 (t0) cc_final: 0.6494 (t0) REVERT: E 88 GLU cc_start: 0.7119 (mp0) cc_final: 0.6684 (mp0) REVERT: G 68 MET cc_start: 0.8734 (mtt) cc_final: 0.8528 (mtp) REVERT: G 151 MET cc_start: 0.6101 (tpt) cc_final: 0.5381 (tpp) REVERT: G 207 MET cc_start: 0.8974 (tmm) cc_final: 0.7897 (tmm) REVERT: G 254 GLN cc_start: 0.8775 (tt0) cc_final: 0.8511 (tt0) REVERT: G 274 LEU cc_start: 0.9065 (tt) cc_final: 0.8559 (mp) REVERT: G 349 ASP cc_start: 0.8653 (t0) cc_final: 0.8223 (t0) REVERT: G 387 TYR cc_start: 0.8240 (m-10) cc_final: 0.7310 (m-10) REVERT: G 481 ARG cc_start: 0.6539 (pmt170) cc_final: 0.6326 (mpt180) REVERT: H 36 ILE cc_start: 0.7414 (mt) cc_final: 0.7181 (mt) REVERT: H 37 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7354 (mm-40) REVERT: I 125 LYS cc_start: 0.9483 (mtpt) cc_final: 0.8933 (mtmt) REVERT: I 161 LEU cc_start: 0.6703 (mm) cc_final: 0.6478 (tp) REVERT: F 147 LEU cc_start: 0.6576 (mt) cc_final: 0.6192 (mp) REVERT: C 161 LEU cc_start: 0.8580 (tp) cc_final: 0.8352 (tp) outliers start: 6 outliers final: 4 residues processed: 467 average time/residue: 0.2502 time to fit residues: 173.1317 Evaluate side-chains 380 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 376 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 144 HIS A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 262 GLN E 32 ASN ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 400 HIS G 479 ASN ** F 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15432 Z= 0.277 Angle : 0.719 20.424 20886 Z= 0.380 Chirality : 0.047 0.290 2319 Planarity : 0.004 0.041 2661 Dihedral : 6.081 85.879 2166 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.12 % Allowed : 3.48 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.19), residues: 1947 helix: 1.36 (0.27), residues: 411 sheet: -0.36 (0.20), residues: 627 loop : -2.13 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 129 HIS 0.013 0.001 HIS A 27 PHE 0.020 0.002 PHE A 445 TYR 0.023 0.002 TYR A 306 ARG 0.006 0.001 ARG G 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 470 time to evaluate : 1.655 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: A 82 LEU cc_start: 0.9062 (tp) cc_final: 0.8075 (tp) REVERT: A 131 GLN cc_start: 0.7685 (mt0) cc_final: 0.7041 (mm-40) REVERT: A 136 GLU cc_start: 0.8193 (mp0) cc_final: 0.7953 (mp0) REVERT: A 206 THR cc_start: 0.9560 (m) cc_final: 0.9264 (p) REVERT: A 207 MET cc_start: 0.8570 (tmm) cc_final: 0.7859 (ptm) REVERT: A 349 ASP cc_start: 0.7610 (t0) cc_final: 0.7384 (t0) REVERT: A 415 THR cc_start: 0.8900 (m) cc_final: 0.8600 (p) REVERT: A 416 MET cc_start: 0.7122 (ttt) cc_final: 0.5972 (tpp) REVERT: D 53 MET cc_start: 0.8042 (ptp) cc_final: 0.7751 (ptp) REVERT: D 73 ARG cc_start: 0.7022 (ttm170) cc_final: 0.6613 (ttm170) REVERT: D 108 PHE cc_start: 0.6985 (m-10) cc_final: 0.6566 (m-10) REVERT: D 195 SER cc_start: 0.8217 (p) cc_final: 0.7955 (p) REVERT: D 202 LEU cc_start: 0.8621 (mt) cc_final: 0.8396 (mt) REVERT: D 245 GLU cc_start: 0.8279 (tt0) cc_final: 0.7993 (tt0) REVERT: D 289 HIS cc_start: 0.8071 (p-80) cc_final: 0.7742 (p-80) REVERT: D 297 ASP cc_start: 0.7875 (p0) cc_final: 0.7491 (p0) REVERT: D 349 ASP cc_start: 0.8065 (t0) cc_final: 0.7703 (t0) REVERT: D 422 MET cc_start: 0.9423 (tpp) cc_final: 0.9198 (tpp) REVERT: D 487 MET cc_start: 0.4541 (mpp) cc_final: 0.3199 (tmm) REVERT: D 495 MET cc_start: 0.6951 (ttm) cc_final: 0.6592 (tmm) REVERT: E 16 LYS cc_start: 0.7158 (tttt) cc_final: 0.6950 (tttp) REVERT: E 63 GLU cc_start: 0.7194 (mp0) cc_final: 0.6874 (mp0) REVERT: E 64 ASP cc_start: 0.6806 (t0) cc_final: 0.6573 (t0) REVERT: E 68 TRP cc_start: 0.7281 (p90) cc_final: 0.6401 (p90) REVERT: E 88 GLU cc_start: 0.7645 (mp0) cc_final: 0.7413 (mp0) REVERT: G 13 GLU cc_start: 0.8113 (mp0) cc_final: 0.7829 (mp0) REVERT: G 42 ASP cc_start: 0.8470 (m-30) cc_final: 0.8121 (t0) REVERT: G 151 MET cc_start: 0.6015 (tpt) cc_final: 0.5225 (tpp) REVERT: G 203 TYR cc_start: 0.8546 (m-80) cc_final: 0.8338 (m-80) REVERT: G 207 MET cc_start: 0.8900 (tmm) cc_final: 0.7891 (tmm) REVERT: G 301 LEU cc_start: 0.9104 (tp) cc_final: 0.8658 (tt) REVERT: G 349 ASP cc_start: 0.8815 (t0) cc_final: 0.8449 (t0) REVERT: H 36 ILE cc_start: 0.7771 (mt) cc_final: 0.7378 (mt) REVERT: H 37 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7528 (mp10) REVERT: H 88 GLU cc_start: 0.8829 (tp30) cc_final: 0.8515 (tp30) REVERT: I 125 LYS cc_start: 0.9490 (mtpt) cc_final: 0.8985 (mtmt) REVERT: I 132 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7977 (tpp80) REVERT: F 147 LEU cc_start: 0.6781 (mt) cc_final: 0.6479 (mp) REVERT: C 147 LEU cc_start: 0.7948 (mt) cc_final: 0.7592 (mt) REVERT: C 161 LEU cc_start: 0.8601 (tp) cc_final: 0.8399 (tp) outliers start: 2 outliers final: 0 residues processed: 470 average time/residue: 0.2496 time to fit residues: 172.6750 Evaluate side-chains 385 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 131 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS E 32 ASN E 43 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 15432 Z= 0.318 Angle : 0.739 18.830 20886 Z= 0.389 Chirality : 0.048 0.317 2319 Planarity : 0.004 0.041 2661 Dihedral : 6.063 86.589 2166 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.22 (0.19), residues: 1947 helix: 1.38 (0.27), residues: 411 sheet: -0.43 (0.20), residues: 627 loop : -2.17 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 226 HIS 0.007 0.001 HIS G 27 PHE 0.018 0.002 PHE G 458 TYR 0.019 0.002 TYR C 122 ARG 0.008 0.001 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 1.522 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: A 206 THR cc_start: 0.9593 (m) cc_final: 0.9303 (p) REVERT: A 207 MET cc_start: 0.8451 (tmm) cc_final: 0.7620 (ptm) REVERT: A 349 ASP cc_start: 0.7636 (t0) cc_final: 0.7396 (t0) REVERT: A 415 THR cc_start: 0.8865 (m) cc_final: 0.8581 (p) REVERT: A 416 MET cc_start: 0.7104 (ttt) cc_final: 0.5875 (tpp) REVERT: D 53 MET cc_start: 0.8089 (ptp) cc_final: 0.7763 (ptp) REVERT: D 73 ARG cc_start: 0.6988 (ttm170) cc_final: 0.6567 (ttm170) REVERT: D 108 PHE cc_start: 0.6900 (m-10) cc_final: 0.6410 (m-10) REVERT: D 245 GLU cc_start: 0.8292 (tt0) cc_final: 0.8040 (tt0) REVERT: D 297 ASP cc_start: 0.7925 (p0) cc_final: 0.7563 (p0) REVERT: D 349 ASP cc_start: 0.7954 (t0) cc_final: 0.7606 (t0) REVERT: D 466 GLN cc_start: 0.7314 (mp10) cc_final: 0.6860 (mp10) REVERT: D 487 MET cc_start: 0.4609 (mpp) cc_final: 0.3251 (tmm) REVERT: D 495 MET cc_start: 0.7076 (ttm) cc_final: 0.6733 (tmm) REVERT: E 16 LYS cc_start: 0.7646 (tttt) cc_final: 0.7384 (tttp) REVERT: E 63 GLU cc_start: 0.6909 (mp0) cc_final: 0.6648 (mp0) REVERT: E 68 TRP cc_start: 0.7322 (p90) cc_final: 0.6483 (p90) REVERT: E 88 GLU cc_start: 0.7591 (mp0) cc_final: 0.7171 (mp0) REVERT: G 13 GLU cc_start: 0.8311 (mp0) cc_final: 0.8011 (mp0) REVERT: G 82 LEU cc_start: 0.7324 (tp) cc_final: 0.7036 (tt) REVERT: G 151 MET cc_start: 0.6252 (tpt) cc_final: 0.5459 (tpp) REVERT: G 207 MET cc_start: 0.9126 (tmm) cc_final: 0.8254 (tmm) REVERT: G 301 LEU cc_start: 0.9101 (tp) cc_final: 0.8656 (tt) REVERT: G 304 MET cc_start: 0.8140 (pmm) cc_final: 0.7916 (pmm) REVERT: G 349 ASP cc_start: 0.8813 (t0) cc_final: 0.8324 (t70) REVERT: G 466 GLN cc_start: 0.8385 (mp10) cc_final: 0.7750 (mp10) REVERT: H 36 ILE cc_start: 0.7445 (mt) cc_final: 0.7001 (mt) REVERT: H 37 GLN cc_start: 0.8413 (mm110) cc_final: 0.7983 (mp10) REVERT: H 88 GLU cc_start: 0.8788 (tp30) cc_final: 0.8575 (tp30) REVERT: I 132 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7998 (tpp80) REVERT: I 161 LEU cc_start: 0.6275 (mm) cc_final: 0.5908 (tp) REVERT: C 129 TRP cc_start: 0.7896 (t60) cc_final: 0.7524 (t60) REVERT: C 168 TYR cc_start: 0.6825 (t80) cc_final: 0.6621 (t80) outliers start: 1 outliers final: 0 residues processed: 459 average time/residue: 0.2671 time to fit residues: 179.8086 Evaluate side-chains 389 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 235 HIS E 32 ASN E 43 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15432 Z= 0.193 Angle : 0.693 19.801 20886 Z= 0.362 Chirality : 0.046 0.319 2319 Planarity : 0.004 0.041 2661 Dihedral : 5.692 87.023 2166 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.19), residues: 1947 helix: 1.70 (0.27), residues: 411 sheet: -0.34 (0.20), residues: 627 loop : -2.07 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 68 HIS 0.010 0.001 HIS D 27 PHE 0.021 0.002 PHE A 454 TYR 0.018 0.001 TYR C 122 ARG 0.005 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 1.796 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: A 96 TYR cc_start: 0.8084 (m-80) cc_final: 0.7656 (m-10) REVERT: A 206 THR cc_start: 0.9542 (m) cc_final: 0.9246 (p) REVERT: A 207 MET cc_start: 0.8576 (tmm) cc_final: 0.7871 (ptm) REVERT: A 302 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8536 (tttm) REVERT: A 304 MET cc_start: 0.8406 (ppp) cc_final: 0.8120 (tmm) REVERT: A 415 THR cc_start: 0.8885 (m) cc_final: 0.8640 (p) REVERT: A 416 MET cc_start: 0.7727 (ttt) cc_final: 0.6430 (tpp) REVERT: A 438 MET cc_start: 0.8355 (tpt) cc_final: 0.6814 (mpp) REVERT: A 476 MET cc_start: 0.8535 (tmm) cc_final: 0.7703 (tpt) REVERT: B 5 LYS cc_start: 0.8114 (mttt) cc_final: 0.7834 (mtpt) REVERT: B 89 THR cc_start: 0.8628 (t) cc_final: 0.8405 (p) REVERT: D 53 MET cc_start: 0.7613 (ptp) cc_final: 0.7366 (ptp) REVERT: D 108 PHE cc_start: 0.7103 (m-10) cc_final: 0.6719 (m-10) REVERT: D 245 GLU cc_start: 0.8285 (tt0) cc_final: 0.8052 (tt0) REVERT: D 297 ASP cc_start: 0.7852 (p0) cc_final: 0.7459 (p0) REVERT: D 349 ASP cc_start: 0.7868 (t0) cc_final: 0.7623 (t0) REVERT: D 476 MET cc_start: 0.7782 (tmm) cc_final: 0.7502 (tmm) REVERT: D 487 MET cc_start: 0.5260 (mpp) cc_final: 0.3901 (tmm) REVERT: D 495 MET cc_start: 0.6924 (ttm) cc_final: 0.6566 (tmm) REVERT: E 16 LYS cc_start: 0.7747 (tttt) cc_final: 0.7508 (tttp) REVERT: E 49 MET cc_start: 0.9252 (ttt) cc_final: 0.8141 (tmm) REVERT: E 51 TYR cc_start: 0.7858 (p90) cc_final: 0.6767 (p90) REVERT: E 68 TRP cc_start: 0.7274 (p90) cc_final: 0.6387 (p90) REVERT: G 151 MET cc_start: 0.6010 (tpt) cc_final: 0.5156 (tpp) REVERT: G 201 ASP cc_start: 0.7917 (t0) cc_final: 0.7631 (t0) REVERT: G 207 MET cc_start: 0.9103 (tmm) cc_final: 0.8241 (tmm) REVERT: G 349 ASP cc_start: 0.8453 (t0) cc_final: 0.8027 (t70) REVERT: G 466 GLN cc_start: 0.8380 (mp10) cc_final: 0.7753 (mp10) REVERT: H 36 ILE cc_start: 0.7414 (mt) cc_final: 0.7037 (mt) REVERT: H 37 GLN cc_start: 0.8349 (mm110) cc_final: 0.7864 (mp10) REVERT: F 147 LEU cc_start: 0.6562 (mt) cc_final: 0.6348 (mp) REVERT: C 129 TRP cc_start: 0.7883 (t60) cc_final: 0.7499 (t60) REVERT: C 130 ILE cc_start: 0.8230 (pt) cc_final: 0.8015 (pt) REVERT: C 134 PRO cc_start: 0.7046 (Cg_endo) cc_final: 0.6818 (Cg_exo) REVERT: C 168 TYR cc_start: 0.6622 (t80) cc_final: 0.6377 (t80) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.2477 time to fit residues: 167.4121 Evaluate side-chains 400 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN E 32 ASN ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15432 Z= 0.312 Angle : 0.763 22.135 20886 Z= 0.399 Chirality : 0.049 0.343 2319 Planarity : 0.004 0.045 2661 Dihedral : 5.901 87.563 2166 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.19), residues: 1947 helix: 1.59 (0.27), residues: 411 sheet: -0.48 (0.20), residues: 630 loop : -2.15 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 68 HIS 0.009 0.001 HIS D 27 PHE 0.021 0.002 PHE A 445 TYR 0.019 0.002 TYR C 122 ARG 0.011 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 1.825 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: A 96 TYR cc_start: 0.8138 (m-80) cc_final: 0.7796 (m-10) REVERT: A 167 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7649 (mtp85) REVERT: A 206 THR cc_start: 0.9603 (m) cc_final: 0.9313 (p) REVERT: A 207 MET cc_start: 0.8449 (tmm) cc_final: 0.7721 (ptm) REVERT: A 349 ASP cc_start: 0.7542 (t0) cc_final: 0.7336 (t0) REVERT: A 415 THR cc_start: 0.8928 (m) cc_final: 0.8698 (p) REVERT: A 416 MET cc_start: 0.7107 (ttt) cc_final: 0.5855 (tpp) REVERT: A 476 MET cc_start: 0.8528 (tmm) cc_final: 0.7698 (tpt) REVERT: B 5 LYS cc_start: 0.8183 (mttt) cc_final: 0.7896 (mtpt) REVERT: B 64 ASP cc_start: 0.7428 (m-30) cc_final: 0.7151 (m-30) REVERT: D 53 MET cc_start: 0.7720 (ptp) cc_final: 0.7388 (ptp) REVERT: D 101 TRP cc_start: 0.7310 (m100) cc_final: 0.7083 (m100) REVERT: D 245 GLU cc_start: 0.8235 (tt0) cc_final: 0.7996 (tt0) REVERT: D 297 ASP cc_start: 0.7920 (p0) cc_final: 0.7547 (p0) REVERT: D 300 ARG cc_start: 0.7021 (ttt180) cc_final: 0.6782 (ttt180) REVERT: D 349 ASP cc_start: 0.8117 (t0) cc_final: 0.7815 (t0) REVERT: D 487 MET cc_start: 0.5419 (mpp) cc_final: 0.4021 (tmm) REVERT: E 1 VAL cc_start: 0.6678 (m) cc_final: 0.6458 (p) REVERT: E 12 MET cc_start: 0.8297 (ppp) cc_final: 0.8039 (ppp) REVERT: E 16 LYS cc_start: 0.8279 (tttt) cc_final: 0.8036 (tttp) REVERT: E 68 TRP cc_start: 0.7351 (p90) cc_final: 0.6502 (p90) REVERT: G 46 VAL cc_start: 0.8352 (m) cc_final: 0.8086 (p) REVERT: G 140 LEU cc_start: 0.9050 (mp) cc_final: 0.8604 (mp) REVERT: G 151 MET cc_start: 0.6144 (tpt) cc_final: 0.5465 (tpp) REVERT: G 207 MET cc_start: 0.9114 (tmm) cc_final: 0.8283 (tmm) REVERT: G 290 LEU cc_start: 0.8827 (tp) cc_final: 0.8579 (tp) REVERT: G 301 LEU cc_start: 0.9088 (tp) cc_final: 0.8794 (tt) REVERT: G 349 ASP cc_start: 0.8666 (t0) cc_final: 0.8281 (t70) REVERT: G 466 GLN cc_start: 0.8388 (mp10) cc_final: 0.7773 (mp10) REVERT: H 37 GLN cc_start: 0.8460 (mm110) cc_final: 0.7989 (mp10) REVERT: I 131 LEU cc_start: 0.9074 (mm) cc_final: 0.8794 (mm) REVERT: F 147 LEU cc_start: 0.6434 (mt) cc_final: 0.6137 (mp) REVERT: C 129 TRP cc_start: 0.7853 (t60) cc_final: 0.7492 (t60) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.2499 time to fit residues: 165.1439 Evaluate side-chains 394 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN E 32 ASN G 250 HIS ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN I 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15432 Z= 0.276 Angle : 0.755 23.050 20886 Z= 0.392 Chirality : 0.048 0.350 2319 Planarity : 0.004 0.040 2661 Dihedral : 5.794 89.337 2166 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.19), residues: 1947 helix: 1.73 (0.27), residues: 408 sheet: -0.49 (0.20), residues: 621 loop : -2.18 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 68 HIS 0.006 0.001 HIS G 27 PHE 0.020 0.002 PHE A 445 TYR 0.020 0.002 TYR C 122 ARG 0.005 0.001 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 1.689 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: A 96 TYR cc_start: 0.8127 (m-80) cc_final: 0.7776 (m-10) REVERT: A 206 THR cc_start: 0.9570 (m) cc_final: 0.9294 (p) REVERT: A 207 MET cc_start: 0.8471 (tmm) cc_final: 0.7779 (ptm) REVERT: A 415 THR cc_start: 0.8930 (m) cc_final: 0.8678 (p) REVERT: A 416 MET cc_start: 0.7091 (ttt) cc_final: 0.5834 (tpp) REVERT: A 438 MET cc_start: 0.8480 (tpt) cc_final: 0.7092 (mpp) REVERT: A 476 MET cc_start: 0.8490 (tmm) cc_final: 0.7645 (tpt) REVERT: B 9 THR cc_start: 0.9070 (t) cc_final: 0.8775 (t) REVERT: B 64 ASP cc_start: 0.7758 (m-30) cc_final: 0.7550 (m-30) REVERT: D 53 MET cc_start: 0.7740 (ptp) cc_final: 0.7436 (ptp) REVERT: D 178 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6626 (tm-30) REVERT: D 195 SER cc_start: 0.8551 (p) cc_final: 0.8325 (p) REVERT: D 245 GLU cc_start: 0.8280 (tt0) cc_final: 0.8041 (tt0) REVERT: D 289 HIS cc_start: 0.7978 (p-80) cc_final: 0.7587 (p-80) REVERT: D 297 ASP cc_start: 0.7971 (p0) cc_final: 0.7568 (p0) REVERT: D 349 ASP cc_start: 0.8068 (t0) cc_final: 0.7736 (t0) REVERT: D 487 MET cc_start: 0.5837 (mpp) cc_final: 0.4271 (tmm) REVERT: E 4 THR cc_start: 0.7156 (t) cc_final: 0.6680 (t) REVERT: E 16 LYS cc_start: 0.8297 (tttt) cc_final: 0.8050 (tttp) REVERT: E 68 TRP cc_start: 0.7459 (p90) cc_final: 0.6505 (p90) REVERT: G 42 ASP cc_start: 0.8883 (m-30) cc_final: 0.8144 (m-30) REVERT: G 151 MET cc_start: 0.6196 (tpt) cc_final: 0.5535 (tpp) REVERT: G 167 ARG cc_start: 0.8542 (mtp85) cc_final: 0.7777 (mtp-110) REVERT: G 201 ASP cc_start: 0.8006 (t0) cc_final: 0.7569 (t0) REVERT: G 207 MET cc_start: 0.9109 (tmm) cc_final: 0.8304 (tmm) REVERT: G 301 LEU cc_start: 0.9099 (tp) cc_final: 0.8830 (tt) REVERT: G 349 ASP cc_start: 0.8335 (t0) cc_final: 0.8092 (t70) REVERT: G 375 MET cc_start: 0.7618 (ppp) cc_final: 0.7345 (ppp) REVERT: G 466 GLN cc_start: 0.8424 (mp10) cc_final: 0.7795 (mp10) REVERT: H 37 GLN cc_start: 0.8513 (mm110) cc_final: 0.8132 (mp10) REVERT: I 127 GLU cc_start: 0.8940 (tp30) cc_final: 0.8522 (tp30) REVERT: I 131 LEU cc_start: 0.9182 (mm) cc_final: 0.8952 (mm) REVERT: F 147 LEU cc_start: 0.6236 (mt) cc_final: 0.5980 (mp) REVERT: C 129 TRP cc_start: 0.7832 (t60) cc_final: 0.7310 (t60) REVERT: C 157 PHE cc_start: 0.8022 (t80) cc_final: 0.7503 (t80) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.2538 time to fit residues: 168.0163 Evaluate side-chains 387 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 178 optimal weight: 0.0370 chunk 154 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 94 optimal weight: 0.0040 chunk 122 optimal weight: 3.9990 overall best weight: 0.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS A 250 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 144 HIS E 32 ASN H 43 HIS F 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15432 Z= 0.158 Angle : 0.731 24.002 20886 Z= 0.372 Chirality : 0.047 0.335 2319 Planarity : 0.004 0.042 2661 Dihedral : 5.396 89.884 2166 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.91 (0.19), residues: 1947 helix: 1.93 (0.28), residues: 408 sheet: -0.28 (0.21), residues: 609 loop : -2.07 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 68 HIS 0.007 0.001 HIS A 27 PHE 0.029 0.001 PHE A 454 TYR 0.018 0.001 TYR C 122 ARG 0.009 0.001 ARG F 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 1.987 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 23 ILE cc_start: 0.9101 (pt) cc_final: 0.8778 (pt) REVERT: A 96 TYR cc_start: 0.8084 (m-80) cc_final: 0.7690 (m-10) REVERT: A 116 CYS cc_start: 0.5635 (p) cc_final: 0.5421 (p) REVERT: A 151 MET cc_start: 0.3346 (mmp) cc_final: 0.3071 (mmp) REVERT: A 203 TYR cc_start: 0.8839 (m-10) cc_final: 0.8526 (m-10) REVERT: A 207 MET cc_start: 0.8440 (tmm) cc_final: 0.7884 (ptm) REVERT: A 367 THR cc_start: 0.8821 (p) cc_final: 0.8185 (p) REVERT: A 415 THR cc_start: 0.8849 (m) cc_final: 0.8638 (p) REVERT: A 416 MET cc_start: 0.7962 (ttt) cc_final: 0.7424 (mmm) REVERT: A 438 MET cc_start: 0.8348 (tpt) cc_final: 0.6867 (mpp) REVERT: A 476 MET cc_start: 0.8491 (tmm) cc_final: 0.7586 (tpt) REVERT: B 68 TRP cc_start: 0.8233 (p90) cc_final: 0.7509 (p90) REVERT: D 26 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7509 (mt-10) REVERT: D 53 MET cc_start: 0.7729 (ptp) cc_final: 0.7410 (ptp) REVERT: D 178 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6763 (tm-30) REVERT: D 201 ASP cc_start: 0.8640 (m-30) cc_final: 0.8283 (m-30) REVERT: D 245 GLU cc_start: 0.8283 (tt0) cc_final: 0.8052 (tt0) REVERT: D 289 HIS cc_start: 0.7972 (p-80) cc_final: 0.7473 (p-80) REVERT: D 297 ASP cc_start: 0.7825 (p0) cc_final: 0.7357 (p0) REVERT: D 403 ARG cc_start: 0.8373 (ttt180) cc_final: 0.8075 (ttt180) REVERT: D 466 GLN cc_start: 0.6809 (mp10) cc_final: 0.6513 (mp10) REVERT: D 487 MET cc_start: 0.5634 (mpp) cc_final: 0.4320 (tmm) REVERT: E 4 THR cc_start: 0.7744 (t) cc_final: 0.7422 (t) REVERT: E 16 LYS cc_start: 0.8307 (tttt) cc_final: 0.8055 (tttp) REVERT: E 68 TRP cc_start: 0.7545 (p90) cc_final: 0.6421 (p90) REVERT: G 42 ASP cc_start: 0.8915 (m-30) cc_final: 0.8577 (t0) REVERT: G 67 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7726 (mp0) REVERT: G 68 MET cc_start: 0.8432 (mtt) cc_final: 0.7880 (mtt) REVERT: G 151 MET cc_start: 0.5625 (tpt) cc_final: 0.5199 (tpp) REVERT: G 160 HIS cc_start: 0.7184 (m-70) cc_final: 0.6861 (m-70) REVERT: G 201 ASP cc_start: 0.7964 (t0) cc_final: 0.7692 (t0) REVERT: G 207 MET cc_start: 0.9095 (tmm) cc_final: 0.8309 (tmm) REVERT: G 301 LEU cc_start: 0.9109 (tp) cc_final: 0.8760 (tt) REVERT: G 349 ASP cc_start: 0.8141 (t0) cc_final: 0.7928 (t70) REVERT: G 375 MET cc_start: 0.7438 (ppp) cc_final: 0.7167 (ppp) REVERT: G 378 GLU cc_start: 0.8586 (tt0) cc_final: 0.7947 (tt0) REVERT: G 438 MET cc_start: 0.7021 (mmm) cc_final: 0.6714 (mmp) REVERT: G 466 GLN cc_start: 0.8443 (mp10) cc_final: 0.7720 (mp10) REVERT: H 36 ILE cc_start: 0.8006 (mt) cc_final: 0.7706 (mt) REVERT: I 125 LYS cc_start: 0.9377 (mtpt) cc_final: 0.8987 (mtmt) REVERT: I 127 GLU cc_start: 0.8773 (tp30) cc_final: 0.8235 (tp30) REVERT: I 131 LEU cc_start: 0.9133 (mm) cc_final: 0.8825 (mm) REVERT: C 129 TRP cc_start: 0.7792 (t60) cc_final: 0.7386 (t60) REVERT: C 157 PHE cc_start: 0.7971 (t80) cc_final: 0.7706 (t80) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.2448 time to fit residues: 166.2632 Evaluate side-chains 399 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 142 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 89 GLN ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 144 HIS E 32 ASN E 83 HIS G 37 ASN ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN H 43 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116721 restraints weight = 29687.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119532 restraints weight = 18684.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121499 restraints weight = 13456.172| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15432 Z= 0.306 Angle : 0.780 23.043 20886 Z= 0.405 Chirality : 0.049 0.343 2319 Planarity : 0.004 0.044 2661 Dihedral : 5.632 86.729 2166 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 1947 helix: 1.77 (0.27), residues: 408 sheet: -0.42 (0.21), residues: 621 loop : -2.12 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 68 HIS 0.007 0.001 HIS G 447 PHE 0.033 0.002 PHE F 157 TYR 0.020 0.002 TYR C 122 ARG 0.007 0.001 ARG F 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.41 seconds wall clock time: 67 minutes 9.55 seconds (4029.55 seconds total)