Starting phenix.real_space_refine on Sun Mar 17 07:54:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/03_2024/7b70_12063_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/03_2024/7b70_12063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/03_2024/7b70_12063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/03_2024/7b70_12063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/03_2024/7b70_12063_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b70_12063/03_2024/7b70_12063_neut.pdb" } resolution = 4.0 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= 0.002 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 95 5.16 5 C 10934 2.51 5 N 2914 2.21 5 O 3141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 31": "NH1" <-> "NH2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "G ARG 52": "NH1" <-> "NH2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "I ARG 358": "NH1" <-> "NH2" Residue "I GLU 374": "OE1" <-> "OE2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 508": "NH1" <-> "NH2" Residue "I GLU 537": "OE1" <-> "OE2" Residue "I ASP 539": "OD1" <-> "OD2" Residue "I TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 76": "OE1" <-> "OE2" Residue "J GLU 182": "OE1" <-> "OE2" Residue "J ARG 363": "NH1" <-> "NH2" Residue "J GLU 419": "OE1" <-> "OE2" Residue "J TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 446": "NH1" <-> "NH2" Residue "J GLU 514": "OE1" <-> "OE2" Residue "J PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 699": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17084 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "C" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1204 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1741 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 207} Chain: "E" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1177 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "F" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "G" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1363 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1089 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "I" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1710 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain breaks: 1 Chain: "J" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4904 Classifications: {'peptide': 614} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 592} Chain breaks: 4 Time building chain proxies: 9.08, per 1000 atoms: 0.53 Number of scatterers: 17084 At special positions: 0 Unit cell: (204.793, 283.946, 113.076, 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 95 16.00 O 3141 8.00 N 2914 7.00 C 10934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.44 Conformation dependent library (CDL) restraints added in 3.2 seconds 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 12 sheets defined 53.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 13 through 15 No H-bonds generated for 'chain 'A' and resid 13 through 15' Processing helix chain 'A' and resid 16 through 33 removed outlier: 3.783A pdb=" N LEU A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 62 removed outlier: 4.250A pdb=" N GLU A 56 " --> pdb=" O MET A 52 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 85 Processing helix chain 'A' and resid 126 through 140 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.318A pdb=" N PHE B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.699A pdb=" N ARG B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 115 removed outlier: 4.126A pdb=" N PHE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 103 through 109 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 104 through 121 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 166 through 182 Processing helix chain 'D' and resid 195 through 211 Processing helix chain 'E' and resid 26 through 55 removed outlier: 3.606A pdb=" N HIS E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 110 removed outlier: 3.890A pdb=" N ASN E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 Processing helix chain 'F' and resid 32 through 50 Processing helix chain 'F' and resid 52 through 78 removed outlier: 4.041A pdb=" N ARG F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.623A pdb=" N THR F 132 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'G' and resid 13 through 32 removed outlier: 3.554A pdb=" N LEU G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 61 removed outlier: 3.552A pdb=" N MET G 51 " --> pdb=" O TYR G 47 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG G 52 " --> pdb=" O ASN G 48 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU G 55 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 84 removed outlier: 3.605A pdb=" N THR G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 120 removed outlier: 3.705A pdb=" N THR G 120 " --> pdb=" O PRO G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 126 through 139 Processing helix chain 'G' and resid 150 through 154 removed outlier: 3.712A pdb=" N GLY G 154 " --> pdb=" O GLN G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.884A pdb=" N VAL H 95 " --> pdb=" O ARG H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'I' and resid 356 through 385 Proline residue: I 371 - end of helix Processing helix chain 'I' and resid 425 through 436 Processing helix chain 'I' and resid 440 through 453 Processing helix chain 'I' and resid 460 through 479 removed outlier: 4.142A pdb=" N TYR I 464 " --> pdb=" O ALA I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 482 through 492 Processing helix chain 'I' and resid 493 through 500 removed outlier: 3.519A pdb=" N THR I 498 " --> pdb=" O VAL I 494 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL I 499 " --> pdb=" O CYS I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 520 Processing helix chain 'I' and resid 522 through 535 removed outlier: 3.701A pdb=" N VAL I 526 " --> pdb=" O LEU I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 557 removed outlier: 3.557A pdb=" N THR I 556 " --> pdb=" O CYS I 552 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN I 557 " --> pdb=" O PHE I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 578 removed outlier: 3.519A pdb=" N LEU I 570 " --> pdb=" O PHE I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 580 through 598 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 33 through 46 removed outlier: 4.264A pdb=" N SER J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 94 removed outlier: 3.565A pdb=" N HIS J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 135 removed outlier: 5.248A pdb=" N GLU J 133 " --> pdb=" O ASN J 129 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ARG J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 154 through 169 Processing helix chain 'J' and resid 180 through 215 removed outlier: 5.077A pdb=" N GLY J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 239 Processing helix chain 'J' and resid 243 through 259 Processing helix chain 'J' and resid 265 through 287 removed outlier: 4.178A pdb=" N ILE J 269 " --> pdb=" O ASN J 265 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 308 removed outlier: 3.859A pdb=" N VAL J 308 " --> pdb=" O HIS J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 339 Processing helix chain 'J' and resid 341 through 347 removed outlier: 3.841A pdb=" N GLN J 346 " --> pdb=" O ALA J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 374 removed outlier: 4.324A pdb=" N HIS J 353 " --> pdb=" O GLY J 349 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS J 354 " --> pdb=" O ILE J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 422 Processing helix chain 'J' and resid 425 through 442 removed outlier: 4.036A pdb=" N ILE J 429 " --> pdb=" O SER J 425 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 463 Processing helix chain 'J' and resid 464 through 483 removed outlier: 3.605A pdb=" N ALA J 468 " --> pdb=" O ASP J 464 " (cutoff:3.500A) Proline residue: J 477 - end of helix Processing helix chain 'J' and resid 484 through 503 removed outlier: 3.883A pdb=" N THR J 489 " --> pdb=" O THR J 485 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS J 494 " --> pdb=" O ASP J 490 " (cutoff:3.500A) Processing helix chain 'J' and resid 504 through 518 removed outlier: 3.725A pdb=" N LEU J 518 " --> pdb=" O GLU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 539 Processing helix chain 'J' and resid 550 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.731A pdb=" N VAL A 163 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 161 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 160 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 164 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 145 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 166 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A 143 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.597A pdb=" N TYR B 86 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.908A pdb=" N ILE C 8 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR C 18 " --> pdb=" O LEU C 6 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 6 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN C 5 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR C 64 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C 63 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU D 135 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 143 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 8 " --> pdb=" O ILE D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.071A pdb=" N LYS D 30 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 96 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 65 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER D 99 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU D 63 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 71 " --> pdb=" O VAL D 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 40 through 43 Processing sheet with id=AA6, first strand: chain 'E' and resid 15 through 20 removed outlier: 3.583A pdb=" N TYR E 5 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 83 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS E 86 " --> pdb=" O PHE E 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 113 removed outlier: 3.509A pdb=" N ILE F 124 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 99 through 100 removed outlier: 3.505A pdb=" N PHE G 100 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 99 through 100 removed outlier: 3.505A pdb=" N PHE G 100 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU G 159 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLU G 142 " --> pdb=" O VAL G 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.677A pdb=" N TYR H 61 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY H 70 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU H 59 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL H 72 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU H 57 " --> pdb=" O VAL H 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 55 through 56 removed outlier: 4.271A pdb=" N VAL J 99 " --> pdb=" O LEU J 19 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL J 101 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 102 " --> pdb=" O CYS J 139 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL J 141 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N PHE J 176 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU J 140 " --> pdb=" O PHE J 176 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU J 178 " --> pdb=" O LEU J 140 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU J 142 " --> pdb=" O LEU J 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 602 through 603 removed outlier: 4.495A pdb=" N VAL J 602 " --> pdb=" O TYR J 678 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR J 678 " --> pdb=" O VAL J 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 900 hydrogen bonds defined for protein. 2634 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: 4.99 Time building geometry restraints manager: 8.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4504 1.33 - 1.45: 3567 1.45 - 1.58: 9213 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 17436 Sorted by residual: bond pdb=" N VAL H 39 " pdb=" CA VAL H 39 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.08e-02 8.57e+03 1.59e+01 bond pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 1.334 1.292 0.042 1.11e-02 8.12e+03 1.41e+01 bond pdb=" N GLN I 557 " pdb=" CA GLN I 557 " ideal model delta sigma weight residual 1.455 1.487 -0.032 9.60e-03 1.09e+04 1.12e+01 bond pdb=" C HIS D 61 " pdb=" N VAL D 62 " ideal model delta sigma weight residual 1.334 1.292 0.041 1.24e-02 6.50e+03 1.11e+01 bond pdb=" C TRP C 115 " pdb=" N THR C 116 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.09e+01 ... (remaining 17431 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.53: 222 104.53 - 111.98: 8294 111.98 - 119.42: 6328 119.42 - 126.87: 8549 126.87 - 134.31: 186 Bond angle restraints: 23579 Sorted by residual: angle pdb=" N GLU H 40 " pdb=" CA GLU H 40 " pdb=" C GLU H 40 " ideal model delta sigma weight residual 112.54 103.73 8.81 1.22e+00 6.72e-01 5.21e+01 angle pdb=" N VAL H 39 " pdb=" CA VAL H 39 " pdb=" C VAL H 39 " ideal model delta sigma weight residual 113.42 105.30 8.12 1.17e+00 7.31e-01 4.81e+01 angle pdb=" N VAL I 569 " pdb=" CA VAL I 569 " pdb=" C VAL I 569 " ideal model delta sigma weight residual 111.00 104.39 6.61 1.09e+00 8.42e-01 3.68e+01 angle pdb=" N LEU H 44 " pdb=" CA LEU H 44 " pdb=" C LEU H 44 " ideal model delta sigma weight residual 113.15 106.07 7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" N ILE E 40 " pdb=" CA ILE E 40 " pdb=" C ILE E 40 " ideal model delta sigma weight residual 111.44 104.39 7.05 1.34e+00 5.57e-01 2.76e+01 ... (remaining 23574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9261 17.82 - 35.64: 967 35.64 - 53.46: 229 53.46 - 71.28: 55 71.28 - 89.10: 15 Dihedral angle restraints: 10527 sinusoidal: 4286 harmonic: 6241 Sorted by residual: dihedral pdb=" CA ILE D 214 " pdb=" C ILE D 214 " pdb=" N SER D 215 " pdb=" CA SER D 215 " ideal model delta harmonic sigma weight residual 180.00 140.32 39.68 0 5.00e+00 4.00e-02 6.30e+01 dihedral pdb=" CA ILE F 134 " pdb=" C ILE F 134 " pdb=" N SER F 135 " pdb=" CA SER F 135 " ideal model delta harmonic sigma weight residual 180.00 -141.08 -38.92 0 5.00e+00 4.00e-02 6.06e+01 dihedral pdb=" C VAL H 38 " pdb=" N VAL H 38 " pdb=" CA VAL H 38 " pdb=" CB VAL H 38 " ideal model delta harmonic sigma weight residual -122.00 -137.89 15.89 0 2.50e+00 1.60e-01 4.04e+01 ... (remaining 10524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2231 0.083 - 0.165: 368 0.165 - 0.248: 37 0.248 - 0.331: 8 0.331 - 0.414: 6 Chirality restraints: 2650 Sorted by residual: chirality pdb=" CB ILE F 134 " pdb=" CA ILE F 134 " pdb=" CG1 ILE F 134 " pdb=" CG2 ILE F 134 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CG LEU D 197 " pdb=" CB LEU D 197 " pdb=" CD1 LEU D 197 " pdb=" CD2 LEU D 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA HIS I 567 " pdb=" N HIS I 567 " pdb=" C HIS I 567 " pdb=" CB HIS I 567 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 ... (remaining 2647 not shown) Planarity restraints: 3009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 41 " -0.028 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C ALA E 41 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA E 41 " -0.039 2.00e-02 2.50e+03 pdb=" N HIS E 42 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 117 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO A 118 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 136 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO F 137 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO F 137 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 137 " -0.041 5.00e-02 4.00e+02 ... (remaining 3006 not shown) Histogram of nonbonded interaction distances: 0.46 - 1.35: 11 1.35 - 2.24: 78 2.24 - 3.13: 15948 3.13 - 4.01: 49640 4.01 - 4.90: 85044 Warning: very small nonbonded interaction distances. Nonbonded interactions: 150721 Sorted by model distance: nonbonded pdb=" NE2 HIS H 31 " pdb=" N ILE J 487 " model vdw 0.463 3.200 nonbonded pdb=" CE1 HIS H 31 " pdb=" CA ILE J 487 " model vdw 0.862 3.690 nonbonded pdb=" CB ALA H 34 " pdb=" CZ2 TRP J 484 " model vdw 0.934 3.760 nonbonded pdb=" CA ALA H 34 " pdb=" CH2 TRP J 484 " model vdw 1.025 3.770 nonbonded pdb=" CE1 HIS H 31 " pdb=" N ILE J 487 " model vdw 1.048 3.340 ... (remaining 150716 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 'G' and resid 9 through 173) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.080 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 47.090 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 17436 Z= 0.502 Angle : 1.130 14.570 23579 Z= 0.691 Chirality : 0.064 0.414 2650 Planarity : 0.006 0.076 3009 Dihedral : 15.939 89.102 6469 Min Nonbonded Distance : 0.463 Molprobity Statistics. All-atom Clashscore : 43.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.91 % Favored : 87.85 % Rotamer: Outliers : 4.66 % Allowed : 2.52 % Favored : 92.82 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.44 (0.17), residues: 2082 helix: -0.89 (0.15), residues: 1038 sheet: -1.65 (0.34), residues: 226 loop : -2.49 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 147 HIS 0.017 0.003 HIS F 113 PHE 0.037 0.004 PHE F 133 TYR 0.041 0.003 TYR J 253 ARG 0.038 0.002 ARG H 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 198 time to evaluate : 1.889 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 29 MET cc_start: 0.6079 (mmt) cc_final: 0.5845 (mmt) REVERT: B 59 MET cc_start: 0.8492 (pmm) cc_final: 0.8039 (pmm) REVERT: D 1 MET cc_start: 0.7074 (tpp) cc_final: 0.6868 (tpt) REVERT: F 191 MET cc_start: -0.0898 (mtm) cc_final: -0.3023 (ttp) REVERT: H 1 MET cc_start: 0.4687 (tpt) cc_final: 0.2851 (mtt) REVERT: I 364 TYR cc_start: -0.2592 (OUTLIER) cc_final: -0.3183 (t80) REVERT: I 436 PHE cc_start: 0.5852 (OUTLIER) cc_final: 0.5600 (t80) REVERT: I 437 MET cc_start: 0.1210 (OUTLIER) cc_final: 0.0711 (ttt) REVERT: I 501 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5577 (mmpt) REVERT: I 502 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6839 (mm) REVERT: I 507 THR cc_start: 0.7383 (p) cc_final: 0.6909 (t) REVERT: I 508 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6206 (mtt-85) REVERT: J 268 GLU cc_start: 0.8756 (mp0) cc_final: 0.8344 (mm-30) REVERT: J 436 MET cc_start: 0.9233 (tmm) cc_final: 0.8929 (tmm) REVERT: J 447 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.8058 (m-80) outliers start: 87 outliers final: 14 residues processed: 269 average time/residue: 0.4174 time to fit residues: 155.2452 Evaluate side-chains 135 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 364 TYR Chi-restraints excluded: chain I residue 367 ARG Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 373 ILE Chi-restraints excluded: chain I residue 429 ARG Chi-restraints excluded: chain I residue 436 PHE Chi-restraints excluded: chain I residue 437 MET Chi-restraints excluded: chain I residue 448 TYR Chi-restraints excluded: chain I residue 456 ASN Chi-restraints excluded: chain I residue 480 THR Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 501 LYS Chi-restraints excluded: chain I residue 502 LEU Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 517 LEU Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 537 GLU Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN C 22 ASN E 38 GLN E 42 HIS ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN G 78 GLN ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN I 375 HIS I 427 GLN I 561 HIS ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17436 Z= 0.262 Angle : 0.806 10.874 23579 Z= 0.420 Chirality : 0.049 0.728 2650 Planarity : 0.005 0.075 3009 Dihedral : 7.930 82.438 2355 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 32.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.68 % Favored : 92.27 % Rotamer: Outliers : 1.98 % Allowed : 12.71 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.82 (0.17), residues: 2082 helix: -0.32 (0.15), residues: 1071 sheet: -1.30 (0.35), residues: 222 loop : -2.36 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP J 484 HIS 0.035 0.002 HIS H 31 PHE 0.038 0.002 PHE D 110 TYR 0.024 0.002 TYR I 448 ARG 0.014 0.001 ARG J 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 2.156 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: B 44 ARG cc_start: 0.4854 (mmt180) cc_final: 0.4635 (mmt180) REVERT: B 48 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: B 59 MET cc_start: 0.8493 (pmm) cc_final: 0.8168 (pmm) REVERT: D 1 MET cc_start: 0.6898 (tpp) cc_final: 0.6637 (tpt) REVERT: E 1 MET cc_start: 0.7050 (ptt) cc_final: 0.6593 (ttp) REVERT: E 5 TYR cc_start: 0.5649 (t80) cc_final: 0.5421 (t80) REVERT: F 182 ASP cc_start: 0.9060 (t0) cc_final: 0.8671 (m-30) REVERT: F 191 MET cc_start: 0.0122 (mtm) cc_final: -0.0640 (mtt) REVERT: H 3 PHE cc_start: 0.7123 (m-10) cc_final: 0.6900 (m-10) REVERT: H 31 HIS cc_start: 0.6453 (OUTLIER) cc_final: 0.5250 (t-90) REVERT: I 364 TYR cc_start: -0.2649 (OUTLIER) cc_final: -0.2981 (t80) REVERT: I 437 MET cc_start: 0.1258 (OUTLIER) cc_final: 0.0774 (ttt) REVERT: I 560 MET cc_start: 0.5433 (ttp) cc_final: 0.4347 (ttp) REVERT: J 3 MET cc_start: 0.3212 (tpt) cc_final: 0.2823 (tpt) REVERT: J 106 MET cc_start: 0.5793 (ppp) cc_final: 0.5586 (ppp) REVERT: J 238 MET cc_start: 0.8305 (mmm) cc_final: 0.8077 (mmm) REVERT: J 360 MET cc_start: 0.9140 (mtt) cc_final: 0.8718 (mpp) REVERT: J 546 LYS cc_start: 0.7241 (mptt) cc_final: 0.6765 (mmtt) REVERT: J 581 MET cc_start: 0.7601 (ppp) cc_final: 0.7337 (ppp) outliers start: 37 outliers final: 14 residues processed: 167 average time/residue: 0.3141 time to fit residues: 78.6883 Evaluate side-chains 130 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 364 TYR Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 437 MET Chi-restraints excluded: chain I residue 442 ASN Chi-restraints excluded: chain I residue 453 ARG Chi-restraints excluded: chain I residue 473 LEU Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain I residue 561 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 201 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 HIS ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 119 GLN J 125 GLN J 129 ASN ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17436 Z= 0.228 Angle : 0.740 9.938 23579 Z= 0.382 Chirality : 0.045 0.374 2650 Planarity : 0.005 0.070 3009 Dihedral : 6.668 79.573 2314 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 30.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.89 % Favored : 91.07 % Rotamer: Outliers : 2.84 % Allowed : 16.78 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.47 (0.18), residues: 2082 helix: -0.00 (0.15), residues: 1069 sheet: -1.31 (0.35), residues: 223 loop : -2.18 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 557 HIS 0.019 0.002 HIS H 31 PHE 0.030 0.002 PHE D 110 TYR 0.035 0.002 TYR D 34 ARG 0.009 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 122 time to evaluate : 2.062 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 52 MET cc_start: 0.7185 (ppp) cc_final: 0.6764 (ppp) REVERT: B 44 ARG cc_start: 0.4440 (mmt180) cc_final: 0.4170 (mmt180) REVERT: D 1 MET cc_start: 0.7026 (tpp) cc_final: 0.6058 (tpt) REVERT: E 1 MET cc_start: 0.7081 (ptt) cc_final: 0.6624 (ttp) REVERT: E 5 TYR cc_start: 0.5227 (t80) cc_final: 0.4855 (t80) REVERT: E 110 MET cc_start: 0.5074 (mmp) cc_final: 0.4654 (mmp) REVERT: F 182 ASP cc_start: 0.9093 (t0) cc_final: 0.8712 (m-30) REVERT: F 191 MET cc_start: -0.0044 (mtm) cc_final: -0.0711 (mtt) REVERT: H 1 MET cc_start: 0.3369 (tpt) cc_final: 0.2079 (mtt) REVERT: H 31 HIS cc_start: 0.6708 (OUTLIER) cc_final: 0.5523 (t-170) REVERT: I 364 TYR cc_start: -0.2382 (OUTLIER) cc_final: -0.2788 (t80) REVERT: I 437 MET cc_start: 0.1707 (OUTLIER) cc_final: 0.1185 (ttt) REVERT: I 508 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6396 (mmt180) REVERT: I 560 MET cc_start: 0.6019 (ttp) cc_final: 0.5477 (ttp) REVERT: J 1 MET cc_start: 0.0222 (mmt) cc_final: -0.0042 (mmt) REVERT: J 106 MET cc_start: 0.5864 (ppp) cc_final: 0.5606 (ppp) REVERT: J 360 MET cc_start: 0.9151 (mtt) cc_final: 0.8716 (mpp) REVERT: J 455 MET cc_start: 0.8681 (mtt) cc_final: 0.7586 (mtt) REVERT: J 476 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (mm) REVERT: J 544 MET cc_start: 0.7915 (ptt) cc_final: 0.7646 (mtm) outliers start: 53 outliers final: 28 residues processed: 164 average time/residue: 0.3006 time to fit residues: 74.8860 Evaluate side-chains 145 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 364 TYR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 437 MET Chi-restraints excluded: chain I residue 456 ASN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain I residue 542 SER Chi-restraints excluded: chain J residue 119 GLN Chi-restraints excluded: chain J residue 125 GLN Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 476 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 5.9990 chunk 140 optimal weight: 40.0000 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 198 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 GLN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN I 375 HIS ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 129 ASN ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 338 ASN ** J 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17436 Z= 0.207 Angle : 0.697 12.228 23579 Z= 0.361 Chirality : 0.044 0.277 2650 Planarity : 0.004 0.065 3009 Dihedral : 6.383 75.585 2314 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.83 % Favored : 92.12 % Rotamer: Outliers : 3.59 % Allowed : 18.61 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.25 (0.18), residues: 2082 helix: 0.19 (0.15), residues: 1072 sheet: -1.20 (0.35), residues: 222 loop : -2.11 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 600 HIS 0.017 0.002 HIS I 449 PHE 0.025 0.002 PHE J 230 TYR 0.020 0.002 TYR I 435 ARG 0.004 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 123 time to evaluate : 2.215 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: A 52 MET cc_start: 0.7468 (ppp) cc_final: 0.7148 (ppp) REVERT: B 45 LEU cc_start: -0.1170 (OUTLIER) cc_final: -0.1499 (pt) REVERT: D 1 MET cc_start: 0.6960 (tpp) cc_final: 0.6092 (tpt) REVERT: D 114 MET cc_start: 0.8622 (ppp) cc_final: 0.8373 (ppp) REVERT: E 1 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6581 (ttp) REVERT: E 5 TYR cc_start: 0.5191 (t80) cc_final: 0.4948 (t80) REVERT: E 21 PHE cc_start: 0.4389 (m-80) cc_final: 0.3773 (m-80) REVERT: F 182 ASP cc_start: 0.9110 (t0) cc_final: 0.8754 (m-30) REVERT: F 191 MET cc_start: -0.0009 (mtm) cc_final: -0.0535 (mtt) REVERT: H 31 HIS cc_start: 0.6504 (OUTLIER) cc_final: 0.5534 (t-170) REVERT: I 364 TYR cc_start: -0.2023 (OUTLIER) cc_final: -0.2513 (t80) REVERT: I 437 MET cc_start: 0.1268 (ppp) cc_final: 0.0716 (ttt) REVERT: I 508 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6377 (mmt180) REVERT: I 514 MET cc_start: 0.7802 (ttt) cc_final: 0.7466 (tpp) REVERT: I 560 MET cc_start: 0.5237 (ttp) cc_final: 0.4912 (ttp) REVERT: J 198 MET cc_start: 0.8924 (ppp) cc_final: 0.8713 (ppp) REVERT: J 238 MET cc_start: 0.8404 (mmm) cc_final: 0.8198 (mmm) REVERT: J 360 MET cc_start: 0.9124 (mtt) cc_final: 0.8715 (mpp) REVERT: J 455 MET cc_start: 0.8689 (mtt) cc_final: 0.7630 (mtt) REVERT: J 475 MET cc_start: 0.8346 (ppp) cc_final: 0.7987 (ppp) outliers start: 67 outliers final: 32 residues processed: 178 average time/residue: 0.2874 time to fit residues: 79.5998 Evaluate side-chains 151 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 113 HIS Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 364 TYR Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 414 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 81 optimal weight: 0.0030 chunk 169 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 HIS ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17436 Z= 0.189 Angle : 0.702 12.615 23579 Z= 0.356 Chirality : 0.044 0.327 2650 Planarity : 0.004 0.062 3009 Dihedral : 6.141 71.141 2311 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.59 % Favored : 92.36 % Rotamer: Outliers : 2.95 % Allowed : 19.89 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 2082 helix: 0.37 (0.15), residues: 1071 sheet: -1.16 (0.36), residues: 218 loop : -2.08 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 557 HIS 0.013 0.002 HIS H 31 PHE 0.040 0.002 PHE I 553 TYR 0.019 0.002 TYR I 435 ARG 0.012 0.000 ARG I 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 123 time to evaluate : 2.020 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: A 52 MET cc_start: 0.7450 (ppp) cc_final: 0.7166 (ppp) REVERT: B 45 LEU cc_start: -0.0482 (OUTLIER) cc_final: -0.0824 (pt) REVERT: D 1 MET cc_start: 0.6919 (tpp) cc_final: 0.6055 (tpt) REVERT: E 1 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6748 (ttp) REVERT: E 5 TYR cc_start: 0.5088 (t80) cc_final: 0.4796 (t80) REVERT: E 21 PHE cc_start: 0.4323 (m-80) cc_final: 0.3920 (m-80) REVERT: E 110 MET cc_start: 0.4585 (mmp) cc_final: 0.3414 (mmp) REVERT: E 136 TYR cc_start: 0.7166 (m-80) cc_final: 0.6921 (m-80) REVERT: F 182 ASP cc_start: 0.9080 (t0) cc_final: 0.8740 (m-30) REVERT: G 51 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7453 (mmm) REVERT: I 437 MET cc_start: 0.1285 (ppp) cc_final: 0.0723 (ttt) REVERT: I 508 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6104 (mmt180) REVERT: I 514 MET cc_start: 0.7827 (ttt) cc_final: 0.7566 (tpp) REVERT: J 360 MET cc_start: 0.9123 (mtt) cc_final: 0.8717 (mpp) REVERT: J 455 MET cc_start: 0.8804 (mtt) cc_final: 0.7738 (mtt) REVERT: J 475 MET cc_start: 0.8426 (ppp) cc_final: 0.7795 (ppp) outliers start: 55 outliers final: 32 residues processed: 167 average time/residue: 0.2826 time to fit residues: 72.6397 Evaluate side-chains 147 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 456 ASN Chi-restraints excluded: chain I residue 489 MET Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain I residue 536 GLU Chi-restraints excluded: chain I residue 548 GLN Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 164 optimal weight: 0.0000 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17436 Z= 0.196 Angle : 0.700 12.272 23579 Z= 0.354 Chirality : 0.044 0.277 2650 Planarity : 0.004 0.059 3009 Dihedral : 5.957 66.929 2309 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.32 % Rotamer: Outliers : 3.16 % Allowed : 20.43 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % 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: -0.98 (0.18), residues: 2082 helix: 0.47 (0.15), residues: 1073 sheet: -1.22 (0.35), residues: 219 loop : -2.02 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 600 HIS 0.012 0.001 HIS H 31 PHE 0.029 0.002 PHE D 198 TYR 0.018 0.002 TYR I 435 ARG 0.003 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 116 time to evaluate : 2.072 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 52 MET cc_start: 0.7464 (ppp) cc_final: 0.7209 (ppp) REVERT: B 45 LEU cc_start: -0.0125 (OUTLIER) cc_final: -0.0481 (pt) REVERT: D 1 MET cc_start: 0.6976 (tpp) cc_final: 0.6161 (tpt) REVERT: D 204 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8820 (pp20) REVERT: E 1 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6898 (ttp) REVERT: E 5 TYR cc_start: 0.5269 (t80) cc_final: 0.4981 (t80) REVERT: E 21 PHE cc_start: 0.4257 (m-80) cc_final: 0.3893 (m-80) REVERT: E 110 MET cc_start: 0.4542 (mmp) cc_final: 0.4018 (mmp) REVERT: F 182 ASP cc_start: 0.9037 (t0) cc_final: 0.8675 (m-30) REVERT: G 51 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7430 (mmm) REVERT: H 110 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6970 (mm) REVERT: I 437 MET cc_start: 0.1316 (ppp) cc_final: 0.0741 (ttt) REVERT: I 508 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.6067 (mmt180) REVERT: J 1 MET cc_start: 0.4689 (tpp) cc_final: 0.4078 (mtt) REVERT: J 360 MET cc_start: 0.9129 (mtt) cc_final: 0.8697 (mpp) REVERT: J 455 MET cc_start: 0.8747 (mtt) cc_final: 0.7696 (mtt) REVERT: J 475 MET cc_start: 0.8485 (ppp) cc_final: 0.7829 (ppp) outliers start: 59 outliers final: 38 residues processed: 162 average time/residue: 0.2872 time to fit residues: 71.6691 Evaluate side-chains 155 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 112 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 456 ASN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain I residue 536 GLU Chi-restraints excluded: chain I residue 548 GLN Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain J residue 89 MET Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 230 PHE Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 447 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 chunk 144 optimal weight: 0.0980 chunk 112 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17436 Z= 0.173 Angle : 0.697 13.387 23579 Z= 0.349 Chirality : 0.043 0.269 2650 Planarity : 0.004 0.059 3009 Dihedral : 5.690 59.794 2309 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.06 % Favored : 92.89 % Rotamer: Outliers : 2.47 % Allowed : 22.04 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % 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: -0.85 (0.18), residues: 2082 helix: 0.61 (0.16), residues: 1069 sheet: -1.26 (0.35), residues: 218 loop : -1.97 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 557 HIS 0.011 0.001 HIS H 31 PHE 0.027 0.001 PHE D 198 TYR 0.019 0.001 TYR I 435 ARG 0.004 0.000 ARG I 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 127 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.4567 (p90) REVERT: B 45 LEU cc_start: -0.0546 (OUTLIER) cc_final: -0.0857 (pt) REVERT: D 1 MET cc_start: 0.6801 (tpp) cc_final: 0.6103 (tpt) REVERT: E 1 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6703 (ttp) REVERT: E 5 TYR cc_start: 0.5259 (t80) cc_final: 0.4953 (t80) REVERT: E 21 PHE cc_start: 0.4143 (m-80) cc_final: 0.3795 (m-80) REVERT: E 136 TYR cc_start: 0.7236 (m-80) cc_final: 0.6847 (m-80) REVERT: F 182 ASP cc_start: 0.8965 (t0) cc_final: 0.8615 (m-30) REVERT: F 188 ASP cc_start: 0.8241 (m-30) cc_final: 0.7854 (p0) REVERT: G 51 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7470 (mmm) REVERT: H 110 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.6957 (mm) REVERT: I 437 MET cc_start: 0.0948 (ppp) cc_final: 0.0336 (ttt) REVERT: I 560 MET cc_start: 0.4226 (ttp) cc_final: 0.3764 (ttp) REVERT: J 1 MET cc_start: 0.4521 (tpp) cc_final: 0.3994 (mtt) REVERT: J 238 MET cc_start: 0.8398 (mmm) cc_final: 0.7980 (mmm) REVERT: J 360 MET cc_start: 0.9178 (mtt) cc_final: 0.8835 (mpp) REVERT: J 455 MET cc_start: 0.8820 (mtt) cc_final: 0.7749 (mtt) REVERT: J 475 MET cc_start: 0.8501 (ppp) cc_final: 0.8048 (ppp) outliers start: 46 outliers final: 30 residues processed: 165 average time/residue: 0.2924 time to fit residues: 73.9690 Evaluate side-chains 149 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 548 GLN Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 447 PHE Chi-restraints excluded: chain J residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 134 optimal weight: 0.0020 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17436 Z= 0.203 Angle : 0.729 15.460 23579 Z= 0.365 Chirality : 0.044 0.290 2650 Planarity : 0.004 0.058 3009 Dihedral : 5.513 54.181 2305 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.64 % Favored : 92.32 % Rotamer: Outliers : 3.11 % Allowed : 22.04 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % 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: -0.80 (0.18), residues: 2082 helix: 0.64 (0.16), residues: 1070 sheet: -1.38 (0.34), residues: 219 loop : -1.89 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 557 HIS 0.011 0.001 HIS H 31 PHE 0.051 0.002 PHE I 553 TYR 0.018 0.002 TYR I 435 ARG 0.017 0.000 ARG I 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 117 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.7217 (ppp) cc_final: 0.6971 (ppp) REVERT: B 17 TYR cc_start: 0.5363 (OUTLIER) cc_final: 0.4630 (p90) REVERT: B 45 LEU cc_start: -0.0376 (OUTLIER) cc_final: -0.0674 (pt) REVERT: D 1 MET cc_start: 0.7140 (tpp) cc_final: 0.6426 (tpt) REVERT: D 114 MET cc_start: 0.8526 (ppp) cc_final: 0.8278 (mpp) REVERT: D 203 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8556 (tm-30) REVERT: E 1 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6891 (ttp) REVERT: E 5 TYR cc_start: 0.5295 (t80) cc_final: 0.4984 (t80) REVERT: E 21 PHE cc_start: 0.4380 (m-80) cc_final: 0.4024 (m-80) REVERT: E 110 MET cc_start: 0.6405 (mmp) cc_final: 0.4279 (mmp) REVERT: F 182 ASP cc_start: 0.9062 (t0) cc_final: 0.8751 (m-30) REVERT: F 188 ASP cc_start: 0.8208 (m-30) cc_final: 0.7893 (p0) REVERT: G 19 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6647 (mm) REVERT: G 51 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: H 110 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.6920 (mm) REVERT: I 437 MET cc_start: 0.0950 (ppp) cc_final: 0.0361 (ttt) REVERT: I 470 MET cc_start: 0.6521 (mmm) cc_final: 0.6044 (mtt) REVERT: I 508 ARG cc_start: 0.5727 (OUTLIER) cc_final: 0.5363 (mmt180) REVERT: J 238 MET cc_start: 0.8331 (mmm) cc_final: 0.7943 (mmm) REVERT: J 360 MET cc_start: 0.9152 (mtt) cc_final: 0.8814 (mtt) REVERT: J 455 MET cc_start: 0.8753 (mtt) cc_final: 0.7891 (mtt) REVERT: J 475 MET cc_start: 0.8498 (ppp) cc_final: 0.7864 (ppp) outliers start: 58 outliers final: 38 residues processed: 163 average time/residue: 0.2734 time to fit residues: 69.5978 Evaluate side-chains 156 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 110 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain I residue 537 GLU Chi-restraints excluded: chain I residue 594 VAL Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.0970 chunk 172 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 174 optimal weight: 0.1980 chunk 183 optimal weight: 0.7980 chunk 120 optimal weight: 0.1980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 ASN E 42 HIS ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17436 Z= 0.182 Angle : 0.732 16.096 23579 Z= 0.363 Chirality : 0.044 0.251 2650 Planarity : 0.004 0.059 3009 Dihedral : 5.413 47.984 2305 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 2.47 % Allowed : 22.90 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % 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: -0.71 (0.18), residues: 2082 helix: 0.70 (0.16), residues: 1072 sheet: -1.33 (0.34), residues: 219 loop : -1.82 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 557 HIS 0.009 0.001 HIS H 31 PHE 0.026 0.001 PHE D 198 TYR 0.019 0.001 TYR I 551 ARG 0.013 0.000 ARG I 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 TYR cc_start: 0.4997 (OUTLIER) cc_final: 0.4495 (p90) REVERT: B 45 LEU cc_start: -0.0838 (OUTLIER) cc_final: -0.1109 (pt) REVERT: D 1 MET cc_start: 0.7053 (tpp) cc_final: 0.6373 (tpt) REVERT: D 203 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: E 1 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6756 (ttp) REVERT: E 5 TYR cc_start: 0.5262 (t80) cc_final: 0.4969 (t80) REVERT: E 21 PHE cc_start: 0.4325 (m-80) cc_final: 0.3948 (m-80) REVERT: E 110 MET cc_start: 0.5505 (mmp) cc_final: 0.5013 (mmp) REVERT: E 136 TYR cc_start: 0.6936 (m-80) cc_final: 0.6459 (m-80) REVERT: F 129 LEU cc_start: 0.6432 (tp) cc_final: 0.6069 (tp) REVERT: F 177 MET cc_start: 0.7020 (mmm) cc_final: 0.6759 (tmm) REVERT: F 182 ASP cc_start: 0.8963 (t0) cc_final: 0.8623 (m-30) REVERT: F 188 ASP cc_start: 0.8102 (m-30) cc_final: 0.7758 (p0) REVERT: G 19 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6601 (mm) REVERT: G 51 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7432 (ptp) REVERT: H 1 MET cc_start: 0.3253 (tpt) cc_final: 0.1972 (tpp) REVERT: H 21 ASP cc_start: 0.5211 (OUTLIER) cc_final: 0.4914 (p0) REVERT: H 110 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6925 (mm) REVERT: I 437 MET cc_start: 0.0957 (ppp) cc_final: 0.0394 (mtm) REVERT: I 470 MET cc_start: 0.6498 (mmm) cc_final: 0.6033 (mtt) REVERT: I 508 ARG cc_start: 0.5684 (OUTLIER) cc_final: 0.5378 (mmt180) REVERT: J 238 MET cc_start: 0.8324 (mmm) cc_final: 0.7932 (mmm) REVERT: J 360 MET cc_start: 0.9178 (mtt) cc_final: 0.8835 (mpp) REVERT: J 455 MET cc_start: 0.8784 (mtt) cc_final: 0.7794 (mtt) REVERT: J 475 MET cc_start: 0.8539 (ppp) cc_final: 0.7918 (ppp) outliers start: 46 outliers final: 29 residues processed: 158 average time/residue: 0.2747 time to fit residues: 67.5840 Evaluate side-chains 148 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 110 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 534 LEU Chi-restraints excluded: chain J residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.0370 chunk 118 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17436 Z= 0.179 Angle : 0.736 16.076 23579 Z= 0.365 Chirality : 0.044 0.243 2650 Planarity : 0.004 0.061 3009 Dihedral : 5.302 43.162 2305 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 2.14 % Allowed : 23.59 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % 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: -0.68 (0.18), residues: 2082 helix: 0.71 (0.16), residues: 1069 sheet: -1.33 (0.35), residues: 215 loop : -1.79 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 557 HIS 0.007 0.001 HIS I 449 PHE 0.061 0.002 PHE I 553 TYR 0.027 0.002 TYR I 564 ARG 0.012 0.000 ARG I 532 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4164 Ramachandran restraints generated. 2082 Oldfield, 0 Emsley, 2082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 TYR cc_start: 0.5008 (OUTLIER) cc_final: 0.4394 (p90) REVERT: B 45 LEU cc_start: -0.1093 (OUTLIER) cc_final: -0.1336 (pt) REVERT: D 1 MET cc_start: 0.7292 (tpp) cc_final: 0.6663 (tpt) REVERT: D 144 LEU cc_start: 0.8953 (tp) cc_final: 0.8605 (mp) REVERT: D 203 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: E 1 MET cc_start: 0.7047 (ptt) cc_final: 0.6707 (ttp) REVERT: E 5 TYR cc_start: 0.5338 (t80) cc_final: 0.5057 (t80) REVERT: E 21 PHE cc_start: 0.4303 (m-80) cc_final: 0.3846 (m-80) REVERT: E 110 MET cc_start: 0.5661 (mmp) cc_final: 0.5399 (mmp) REVERT: E 136 TYR cc_start: 0.6811 (m-80) cc_final: 0.6350 (m-80) REVERT: F 129 LEU cc_start: 0.6718 (tp) cc_final: 0.6330 (tp) REVERT: F 177 MET cc_start: 0.6975 (mmm) cc_final: 0.6665 (tmm) REVERT: F 182 ASP cc_start: 0.8975 (t0) cc_final: 0.8653 (m-30) REVERT: G 19 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6619 (mm) REVERT: H 1 MET cc_start: 0.3421 (tpt) cc_final: 0.2331 (tpp) REVERT: H 110 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6896 (mm) REVERT: I 437 MET cc_start: 0.0971 (ppp) cc_final: 0.0368 (mtm) REVERT: I 508 ARG cc_start: 0.5460 (mpp-170) cc_final: 0.5017 (mmt180) REVERT: I 566 PHE cc_start: 0.4257 (OUTLIER) cc_final: 0.3678 (t80) REVERT: J 238 MET cc_start: 0.8350 (mmm) cc_final: 0.7980 (mmm) REVERT: J 360 MET cc_start: 0.9163 (mtt) cc_final: 0.8822 (mtt) REVERT: J 455 MET cc_start: 0.8795 (mtt) cc_final: 0.7845 (mtt) REVERT: J 475 MET cc_start: 0.8532 (ppp) cc_final: 0.7920 (ppp) outliers start: 40 outliers final: 28 residues processed: 153 average time/residue: 0.2830 time to fit residues: 66.9816 Evaluate side-chains 145 residues out of total 1865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 111 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain H residue 30 TYR Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain I residue 435 TYR Chi-restraints excluded: chain I residue 495 CYS Chi-restraints excluded: chain I residue 537 GLU Chi-restraints excluded: chain I residue 566 PHE Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain J residue 534 LEU Chi-restraints excluded: chain J residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 HIS ** J 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 521 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.055117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.040114 restraints weight = 240804.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.039902 restraints weight = 172645.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.040266 restraints weight = 131750.290| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17436 Z= 0.251 Angle : 0.773 14.467 23579 Z= 0.393 Chirality : 0.045 0.261 2650 Planarity : 0.005 0.056 3009 Dihedral : 5.477 42.041 2305 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.83 % Rotamer: Outliers : 2.63 % Allowed : 23.22 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2082 helix: 0.54 (0.16), residues: 1070 sheet: -1.47 (0.34), residues: 214 loop : -1.84 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 557 HIS 0.009 0.002 HIS H 66 PHE 0.031 0.002 PHE I 553 TYR 0.019 0.002 TYR I 448 ARG 0.012 0.001 ARG I 532 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.20 seconds wall clock time: 66 minutes 43.47 seconds (4003.47 seconds total)