Starting phenix.real_space_refine on Sat Dec 9 12:36:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmj_27541/12_2023/8dmj_27541_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmj_27541/12_2023/8dmj_27541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmj_27541/12_2023/8dmj_27541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmj_27541/12_2023/8dmj_27541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmj_27541/12_2023/8dmj_27541_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmj_27541/12_2023/8dmj_27541_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 7002 2.51 5 N 1821 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 307": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "C GLU 287": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11030 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 1 Chain: "B" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 1 Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2502 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 12, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.95, per 1000 atoms: 0.54 Number of scatterers: 11030 At special positions: 0 Unit cell: (106.11, 110.97, 157.14, 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 67 16.00 O 2140 8.00 N 1821 7.00 C 7002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.46 Conformation dependent library (CDL) restraints added in 2.1 seconds 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 24 sheets defined 25.0% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 72 through 93 removed outlier: 3.507A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 190 through 220 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.745A pdb=" N LYS A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 74 through 93 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 190 through 214 Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.671A pdb=" N ARG B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.720A pdb=" N LYS B 362 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 removed outlier: 3.598A pdb=" N LYS C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 93 Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 190 through 214 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 358 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.615A pdb=" N CYS C 363 " --> pdb=" O THR C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.719A pdb=" N LYS H 64 " --> pdb=" O GLU H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.611A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 333 removed outlier: 5.693A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 295 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 44 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.736A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 225 removed outlier: 5.924A pdb=" N VAL A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 266 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR A 54 " --> pdb=" O LEU C 433 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER C 435 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP A 56 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN C 437 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 58 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 437 removed outlier: 6.503A pdb=" N THR B 54 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY A 434 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 56 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 332 through 333 removed outlier: 5.898A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE B 315 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 326 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AB1, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB2, first strand: chain 'B' and resid 431 through 437 removed outlier: 4.824A pdb=" N ASP C 56 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 435 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL C 58 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN B 437 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LYS C 60 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 332 through 333 removed outlier: 7.742A pdb=" N VAL C 338 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LYS C 45 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS C 340 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS C 47 " --> pdb=" O CYS C 340 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS C 40 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU C 297 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 42 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA C 291 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 11.554A pdb=" N ILE C 48 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 10.653A pdb=" N GLN C 289 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE C 315 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE C 326 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AB6, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.868A pdb=" N GLU D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 107 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 89 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 34 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.868A pdb=" N GLU D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR D 107 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.522A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.079A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.982A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR H 107 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 14 removed outlier: 3.560A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1266 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: 3.98 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3538 1.35 - 1.46: 2608 1.46 - 1.58: 4996 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 11238 Sorted by residual: bond pdb=" N VAL L 29 " pdb=" CA VAL L 29 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.04e-02 9.25e+03 1.20e+01 bond pdb=" N ILE B 288 " pdb=" CA ILE B 288 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.30e-02 5.92e+03 8.55e+00 bond pdb=" N ILE C 288 " pdb=" CA ILE C 288 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.30e-02 5.92e+03 7.93e+00 bond pdb=" N LEU C 285 " pdb=" CA LEU C 285 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.53e+00 bond pdb=" N ILE C 90 " pdb=" CA ILE C 90 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.22e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.64: 229 105.64 - 112.75: 6043 112.75 - 119.86: 3576 119.86 - 126.97: 5291 126.97 - 134.07: 108 Bond angle restraints: 15247 Sorted by residual: angle pdb=" CA GLN B 290 " pdb=" C GLN B 290 " pdb=" O GLN B 290 " ideal model delta sigma weight residual 121.67 117.98 3.69 9.30e-01 1.16e+00 1.57e+01 angle pdb=" N VAL L 29 " pdb=" CA VAL L 29 " pdb=" C VAL L 29 " ideal model delta sigma weight residual 112.43 108.86 3.57 9.20e-01 1.18e+00 1.51e+01 angle pdb=" CA ILE B 288 " pdb=" C ILE B 288 " pdb=" O ILE B 288 " ideal model delta sigma weight residual 121.58 118.06 3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" CA ILE C 288 " pdb=" C ILE C 288 " pdb=" O ILE C 288 " ideal model delta sigma weight residual 121.58 118.06 3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" N THR L 69 " pdb=" CA THR L 69 " pdb=" C THR L 69 " ideal model delta sigma weight residual 114.56 110.30 4.26 1.27e+00 6.20e-01 1.12e+01 ... (remaining 15242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6061 17.68 - 35.36: 527 35.36 - 53.05: 162 53.05 - 70.73: 27 70.73 - 88.41: 7 Dihedral angle restraints: 6784 sinusoidal: 2665 harmonic: 4119 Sorted by residual: dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual -86.00 -150.10 64.10 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 53.92 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS C 71 " pdb=" SG CYS C 71 " pdb=" SG CYS C 192 " pdb=" CB CYS C 192 " ideal model delta sinusoidal sigma weight residual -86.00 -123.78 37.78 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 6781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1262 0.040 - 0.081: 318 0.081 - 0.121: 163 0.121 - 0.161: 22 0.161 - 0.201: 4 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA ILE L 31 " pdb=" N ILE L 31 " pdb=" C ILE L 31 " pdb=" CB ILE L 31 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA ILE B 90 " pdb=" N ILE B 90 " pdb=" C ILE B 90 " pdb=" CB ILE B 90 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 1766 not shown) Planarity restraints: 1934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 36 " 0.021 2.00e-02 2.50e+03 1.94e-02 9.38e+00 pdb=" CG TRP D 36 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP D 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 36 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 36 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 36 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 346 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 347 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 215 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 216 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 216 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 216 " 0.026 5.00e-02 4.00e+02 ... (remaining 1931 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 342 2.71 - 3.26: 10914 3.26 - 3.81: 17797 3.81 - 4.35: 22488 4.35 - 4.90: 38853 Nonbonded interactions: 90394 Sorted by model distance: nonbonded pdb=" OH TYR B 248 " pdb=" O PRO B 283 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR A 248 " pdb=" O PRO A 283 " model vdw 2.173 2.440 nonbonded pdb=" O VAL A 213 " pdb=" OG1 THR A 227 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASN B 84 " pdb=" OH TYR B 274 " model vdw 2.236 2.440 nonbonded pdb=" OH TYR C 248 " pdb=" O PRO C 283 " model vdw 2.255 2.440 ... (remaining 90389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 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: 17.780 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 33.330 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.003 0.038 11238 Z= 0.202 Angle : 0.638 11.559 15247 Z= 0.373 Chirality : 0.046 0.201 1769 Planarity : 0.004 0.048 1934 Dihedral : 14.821 88.412 4091 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.32 % Allowed : 15.20 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1405 helix: 0.25 (0.30), residues: 300 sheet: -0.18 (0.26), residues: 416 loop : -0.38 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 36 HIS 0.004 0.001 HIS E 30 PHE 0.027 0.001 PHE H 29 TYR 0.028 0.001 TYR A 79 ARG 0.006 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 1.306 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 204 average time/residue: 0.2370 time to fit residues: 68.7451 Evaluate side-chains 201 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1247 time to fit residues: 2.5203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 0.0010 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 64 ASN A 217 ASN A 219 GLN A 303 ASN A 325 ASN B 289 GLN B 414 ASN C 194 GLN C 325 ASN C 393 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11238 Z= 0.333 Angle : 0.608 6.421 15247 Z= 0.319 Chirality : 0.048 0.182 1769 Planarity : 0.004 0.048 1934 Dihedral : 5.227 30.681 1529 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.80 % Allowed : 14.24 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.22), residues: 1405 helix: 0.27 (0.28), residues: 315 sheet: -0.46 (0.26), residues: 405 loop : -0.47 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 36 HIS 0.005 0.001 HIS H 99 PHE 0.013 0.002 PHE C 282 TYR 0.026 0.002 TYR E 49 ARG 0.004 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 250 average time/residue: 0.2309 time to fit residues: 82.4355 Evaluate side-chains 237 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.164 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1216 time to fit residues: 6.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 217 ASN B 325 ASN B 424 ASN C 194 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11238 Z= 0.321 Angle : 0.594 8.265 15247 Z= 0.307 Chirality : 0.047 0.183 1769 Planarity : 0.004 0.047 1934 Dihedral : 5.183 32.391 1529 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.88 % Allowed : 15.36 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1405 helix: 0.34 (0.29), residues: 318 sheet: -0.36 (0.26), residues: 399 loop : -0.61 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 36 HIS 0.004 0.001 HIS H 99 PHE 0.013 0.002 PHE L 91 TYR 0.023 0.002 TYR E 49 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 1.269 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 229 average time/residue: 0.2180 time to fit residues: 72.4115 Evaluate side-chains 214 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1327 time to fit residues: 4.9014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 85 optimal weight: 0.1980 chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 112 optimal weight: 0.1980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 386 ASN B 414 ASN B 424 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11238 Z= 0.204 Angle : 0.539 8.249 15247 Z= 0.278 Chirality : 0.046 0.173 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.843 29.519 1529 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.24 % Allowed : 17.60 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1405 helix: 0.59 (0.29), residues: 321 sheet: -0.29 (0.25), residues: 411 loop : -0.60 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 36 HIS 0.003 0.001 HIS E 30 PHE 0.012 0.001 PHE A 282 TYR 0.016 0.001 TYR E 49 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.172 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 212 average time/residue: 0.2140 time to fit residues: 65.9526 Evaluate side-chains 195 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1042 time to fit residues: 4.1876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 303 ASN B 51 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 11238 Z= 0.451 Angle : 0.655 10.823 15247 Z= 0.336 Chirality : 0.049 0.184 1769 Planarity : 0.005 0.049 1934 Dihedral : 5.405 35.258 1529 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.16 % Allowed : 17.76 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1405 helix: 0.27 (0.29), residues: 321 sheet: -0.40 (0.25), residues: 411 loop : -0.82 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 92 HIS 0.006 0.001 HIS H 99 PHE 0.016 0.002 PHE C 282 TYR 0.031 0.002 TYR E 49 ARG 0.004 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 1.235 Fit side-chains outliers start: 27 outliers final: 11 residues processed: 227 average time/residue: 0.2129 time to fit residues: 70.9579 Evaluate side-chains 217 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1070 time to fit residues: 3.8314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN B 51 ASN B 320 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11238 Z= 0.336 Angle : 0.610 10.862 15247 Z= 0.310 Chirality : 0.047 0.186 1769 Planarity : 0.004 0.047 1934 Dihedral : 5.207 34.266 1529 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.84 % Allowed : 18.72 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1405 helix: 0.33 (0.29), residues: 321 sheet: -0.43 (0.25), residues: 411 loop : -0.84 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 92 HIS 0.003 0.001 HIS H 99 PHE 0.021 0.002 PHE E 91 TYR 0.025 0.002 TYR E 49 ARG 0.004 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.424 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 213 average time/residue: 0.2272 time to fit residues: 69.5693 Evaluate side-chains 212 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 198 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1031 time to fit residues: 4.3770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 84 optimal weight: 0.1980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN B 51 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11238 Z= 0.211 Angle : 0.556 10.101 15247 Z= 0.282 Chirality : 0.045 0.175 1769 Planarity : 0.004 0.044 1934 Dihedral : 4.873 30.196 1529 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.96 % Allowed : 19.44 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.22), residues: 1405 helix: 0.55 (0.29), residues: 321 sheet: -0.31 (0.25), residues: 411 loop : -0.76 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 92 HIS 0.003 0.001 HIS E 30 PHE 0.024 0.001 PHE E 91 TYR 0.028 0.001 TYR B 30 ARG 0.003 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.342 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 202 average time/residue: 0.2427 time to fit residues: 70.1727 Evaluate side-chains 202 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 194 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1799 time to fit residues: 3.9745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 85 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 122 optimal weight: 0.0870 chunk 129 optimal weight: 0.8980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN B 51 ASN B 224 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11238 Z= 0.237 Angle : 0.565 9.932 15247 Z= 0.287 Chirality : 0.046 0.176 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.870 28.586 1529 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.72 % Allowed : 20.00 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1405 helix: 0.65 (0.29), residues: 321 sheet: -0.30 (0.26), residues: 405 loop : -0.74 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 92 HIS 0.003 0.001 HIS H 99 PHE 0.020 0.001 PHE E 91 TYR 0.019 0.001 TYR E 49 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 202 time to evaluate : 1.235 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 209 average time/residue: 0.2293 time to fit residues: 69.0848 Evaluate side-chains 202 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0957 time to fit residues: 2.1826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0770 chunk 125 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 0.0570 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 0.0970 chunk 132 optimal weight: 0.6980 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN B 51 ASN B 217 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11238 Z= 0.233 Angle : 0.573 10.689 15247 Z= 0.289 Chirality : 0.046 0.205 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.832 27.583 1529 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.88 % Allowed : 19.92 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1405 helix: 0.67 (0.29), residues: 321 sheet: -0.29 (0.26), residues: 405 loop : -0.77 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 92 HIS 0.003 0.001 HIS E 30 PHE 0.024 0.001 PHE E 91 TYR 0.018 0.001 TYR E 49 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 1.305 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 209 average time/residue: 0.2238 time to fit residues: 68.0692 Evaluate side-chains 203 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1044 time to fit residues: 2.8355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 303 ASN B 51 ASN B 217 ASN C 194 GLN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11238 Z= 0.308 Angle : 0.614 13.404 15247 Z= 0.309 Chirality : 0.047 0.205 1769 Planarity : 0.004 0.044 1934 Dihedral : 5.031 29.508 1529 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.24 % Allowed : 20.64 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1405 helix: 0.56 (0.29), residues: 321 sheet: -0.43 (0.26), residues: 409 loop : -0.72 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 92 HIS 0.004 0.001 HIS H 99 PHE 0.027 0.002 PHE E 91 TYR 0.023 0.001 TYR E 49 ARG 0.005 0.000 ARG C 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2810 Ramachandran restraints generated. 1405 Oldfield, 0 Emsley, 1405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 1.250 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 204 average time/residue: 0.2327 time to fit residues: 68.7713 Evaluate side-chains 202 residues out of total 1250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 199 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2231 time to fit residues: 2.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.0970 chunk 97 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 303 ASN C 78 ASN ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.129050 restraints weight = 14814.854| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.88 r_work: 0.3577 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11238 Z= 0.206 Angle : 0.566 11.660 15247 Z= 0.285 Chirality : 0.046 0.197 1769 Planarity : 0.004 0.045 1934 Dihedral : 4.771 26.609 1529 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.24 % Allowed : 20.80 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1405 helix: 0.68 (0.29), residues: 321 sheet: -0.38 (0.26), residues: 409 loop : -0.66 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 92 HIS 0.003 0.001 HIS E 30 PHE 0.024 0.001 PHE E 91 TYR 0.017 0.001 TYR E 49 ARG 0.005 0.000 ARG C 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3012.54 seconds wall clock time: 59 minutes 2.65 seconds (3542.65 seconds total)