Starting phenix.real_space_refine (version: dev) on Fri May 13 04:27:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/05_2022/6nq1_0478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/05_2022/6nq1_0478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/05_2022/6nq1_0478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/05_2022/6nq1_0478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/05_2022/6nq1_0478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/05_2022/6nq1_0478.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 664": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "B ARG 663": "NH1" <-> "NH2" Residue "B ARG 664": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 10046 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5023 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Chain: "B" Number of atoms: 5023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5023 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 21, 'TRANS': 599} Chain breaks: 4 Time building chain proxies: 6.02, per 1000 atoms: 0.60 Number of scatterers: 10046 At special positions: 0 Unit cell: (118.77, 127.33, 107, 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 60 16.00 O 1690 8.00 N 1622 7.00 C 6674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 623 " - pdb=" SG CYS B 623 " distance=2.04 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 180 " 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: 4.18 Conformation dependent library (CDL) restraints added in 1.4 seconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 39 through 58 removed outlier: 3.515A pdb=" N PHE A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.507A pdb=" N TYR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.560A pdb=" N GLN A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.863A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 147 removed outlier: 3.503A pdb=" N VAL A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.985A pdb=" N LEU A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.521A pdb=" N LYS A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.818A pdb=" N SER A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 removed outlier: 3.636A pdb=" N THR A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.910A pdb=" N PHE A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.657A pdb=" N ASN A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 removed outlier: 3.702A pdb=" N THR A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 343 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.823A pdb=" N GLN A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.683A pdb=" N GLU A 402 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 403 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 404 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 433 through 459 removed outlier: 3.679A pdb=" N SER A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 489 removed outlier: 4.105A pdb=" N GLY A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.898A pdb=" N LEU A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 523 removed outlier: 3.841A pdb=" N VAL A 514 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 removed outlier: 3.794A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.854A pdb=" N ALA A 569 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 601 removed outlier: 3.661A pdb=" N ILE A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.538A pdb=" N ALA A 633 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 651 removed outlier: 3.530A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 667 Processing helix chain 'A' and resid 670 through 682 removed outlier: 3.552A pdb=" N PHE A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 removed outlier: 3.588A pdb=" N ASN A 687 " --> pdb=" O VAL A 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 58 removed outlier: 3.515A pdb=" N PHE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 78 removed outlier: 3.507A pdb=" N TYR B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 removed outlier: 3.560A pdb=" N GLN B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.862A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 147 removed outlier: 3.503A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 155 through 178 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 198 removed outlier: 3.985A pdb=" N LEU B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 removed outlier: 3.520A pdb=" N LYS B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 239 removed outlier: 3.818A pdb=" N SER B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.637A pdb=" N THR B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.911A pdb=" N PHE B 292 " --> pdb=" O TYR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 313 removed outlier: 3.658A pdb=" N ASN B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 308 " --> pdb=" O MET B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 343 removed outlier: 3.702A pdb=" N THR B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 removed outlier: 3.823A pdb=" N GLN B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.683A pdb=" N GLU B 402 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 403 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP B 404 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 433 through 459 removed outlier: 3.679A pdb=" N SER B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 489 removed outlier: 4.105A pdb=" N GLY B 470 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE B 471 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.898A pdb=" N LEU B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 523 removed outlier: 3.841A pdb=" N VAL B 514 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 553 removed outlier: 3.794A pdb=" N PHE B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 558 Processing helix chain 'B' and resid 565 through 577 removed outlier: 3.854A pdb=" N ALA B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 601 removed outlier: 3.661A pdb=" N ILE B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 removed outlier: 4.539A pdb=" N ALA B 633 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.529A pdb=" N VAL B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 670 through 682 removed outlier: 3.552A pdb=" N PHE B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 698 removed outlier: 3.588A pdb=" N ASN B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1809 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: 2.67 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3010 1.34 - 1.46: 2540 1.46 - 1.58: 4652 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 10302 Sorted by residual: bond pdb=" CB PHE B 582 " pdb=" CG PHE B 582 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.53e+00 bond pdb=" CB TRP A 655 " pdb=" CG TRP A 655 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.43e+00 bond pdb=" CB PHE A 582 " pdb=" CG PHE A 582 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.40e+00 bond pdb=" CB TRP B 655 " pdb=" CG TRP B 655 " ideal model delta sigma weight residual 1.498 1.434 0.064 3.10e-02 1.04e+03 4.20e+00 bond pdb=" CB MET A 650 " pdb=" CG MET A 650 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.29e+00 ... (remaining 10297 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.21: 215 106.21 - 113.21: 5685 113.21 - 120.21: 4146 120.21 - 127.21: 3838 127.21 - 134.22: 130 Bond angle restraints: 14014 Sorted by residual: angle pdb=" C HIS A 431 " pdb=" N TYR A 432 " pdb=" CA TYR A 432 " ideal model delta sigma weight residual 121.54 129.83 -8.29 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C HIS B 431 " pdb=" N TYR B 432 " pdb=" CA TYR B 432 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 angle pdb=" N ILE A 279 " pdb=" CA ILE A 279 " pdb=" C ILE A 279 " ideal model delta sigma weight residual 108.88 116.61 -7.73 2.16e+00 2.14e-01 1.28e+01 angle pdb=" N ILE B 279 " pdb=" CA ILE B 279 " pdb=" C ILE B 279 " ideal model delta sigma weight residual 108.88 116.61 -7.73 2.16e+00 2.14e-01 1.28e+01 angle pdb=" CA ILE B 279 " pdb=" C ILE B 279 " pdb=" N PRO B 280 " ideal model delta sigma weight residual 118.88 123.59 -4.71 1.54e+00 4.22e-01 9.37e+00 ... (remaining 14009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5382 17.87 - 35.74: 539 35.74 - 53.61: 75 53.61 - 71.48: 18 71.48 - 89.36: 9 Dihedral angle restraints: 6023 sinusoidal: 2355 harmonic: 3668 Sorted by residual: dihedral pdb=" CB CYS A 623 " pdb=" SG CYS A 623 " pdb=" SG CYS B 623 " pdb=" CB CYS B 623 " ideal model delta sinusoidal sigma weight residual -86.00 3.36 -89.36 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 122 " pdb=" SG CYS B 122 " pdb=" SG CYS B 180 " pdb=" CB CYS B 180 " ideal model delta sinusoidal sigma weight residual 93.00 174.84 -81.84 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " pdb=" SG CYS A 180 " pdb=" CB CYS A 180 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 ... (remaining 6020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1172 0.054 - 0.108: 380 0.108 - 0.162: 58 0.162 - 0.216: 20 0.216 - 0.270: 4 Chirality restraints: 1634 Sorted by residual: chirality pdb=" CB VAL A 652 " pdb=" CA VAL A 652 " pdb=" CG1 VAL A 652 " pdb=" CG2 VAL A 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 652 " pdb=" CA VAL B 652 " pdb=" CG1 VAL B 652 " pdb=" CG2 VAL B 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL B 179 " pdb=" CA VAL B 179 " pdb=" CG1 VAL B 179 " pdb=" CG2 VAL B 179 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1631 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 101 " -0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO B 102 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 101 " 0.051 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO A 102 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 655 " 0.021 2.00e-02 2.50e+03 1.70e-02 7.24e+00 pdb=" CG TRP B 655 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 655 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 655 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 655 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 655 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 655 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 655 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 655 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 655 " 0.001 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3266 2.82 - 3.34: 9233 3.34 - 3.86: 15727 3.86 - 4.38: 18242 4.38 - 4.90: 30536 Nonbonded interactions: 77004 Sorted by model distance: nonbonded pdb=" OG1 THR A 334 " pdb=" OE1 GLN A 397 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR B 334 " pdb=" OE1 GLN B 397 " model vdw 2.299 2.440 nonbonded pdb=" O ASN B 445 " pdb=" OG SER B 448 " model vdw 2.319 2.440 nonbonded pdb=" O ASN A 445 " pdb=" OG SER A 448 " model vdw 2.319 2.440 nonbonded pdb=" O VAL B 174 " pdb=" OG SER B 177 " model vdw 2.340 2.440 ... (remaining 76999 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6674 2.51 5 N 1622 2.21 5 O 1690 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.890 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: 3.930 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.100 Process input model: 29.220 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 0.083 10302 Z= 0.521 Angle : 0.973 9.223 14014 Z= 0.500 Chirality : 0.056 0.270 1634 Planarity : 0.006 0.077 1702 Dihedral : 14.326 82.260 3634 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.17), residues: 1222 helix: -3.85 (0.09), residues: 886 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.302 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.2469 time to fit residues: 52.0582 Evaluate side-chains 90 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 305 ASN A 375 HIS A 431 HIS A 473 ASN B 58 GLN B 305 ASN B 375 HIS B 431 HIS B 473 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 10302 Z= 0.225 Angle : 0.686 8.143 14014 Z= 0.351 Chirality : 0.041 0.165 1634 Planarity : 0.005 0.042 1702 Dihedral : 5.224 28.029 1352 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.23), residues: 1222 helix: -0.92 (0.16), residues: 896 sheet: None (None), residues: 0 loop : -2.27 (0.37), residues: 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.178 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 124 average time/residue: 0.1984 time to fit residues: 36.5016 Evaluate side-chains 97 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0915 time to fit residues: 2.5415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 0.0370 chunk 121 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 111 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 2.6664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 10302 Z= 0.253 Angle : 0.651 10.019 14014 Z= 0.327 Chirality : 0.042 0.159 1634 Planarity : 0.004 0.041 1702 Dihedral : 4.969 27.373 1352 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1222 helix: 0.17 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.16 (0.37), residues: 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.188 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 121 average time/residue: 0.2019 time to fit residues: 35.7894 Evaluate side-chains 102 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0906 time to fit residues: 3.1951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 10302 Z= 0.229 Angle : 0.637 8.650 14014 Z= 0.318 Chirality : 0.042 0.164 1634 Planarity : 0.004 0.039 1702 Dihedral : 4.844 26.885 1352 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1222 helix: 0.61 (0.17), residues: 900 sheet: None (None), residues: 0 loop : -2.05 (0.37), residues: 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.334 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 118 average time/residue: 0.2002 time to fit residues: 34.7985 Evaluate side-chains 96 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0955 time to fit residues: 2.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 82 optimal weight: 0.0970 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10302 Z= 0.153 Angle : 0.607 9.154 14014 Z= 0.301 Chirality : 0.040 0.168 1634 Planarity : 0.004 0.037 1702 Dihedral : 4.591 25.841 1352 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1222 helix: 1.02 (0.18), residues: 900 sheet: None (None), residues: 0 loop : -1.95 (0.38), residues: 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.279 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 121 average time/residue: 0.1928 time to fit residues: 34.6838 Evaluate side-chains 96 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1265 time to fit residues: 1.8711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 70 optimal weight: 0.0050 chunk 29 optimal weight: 0.0870 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.6976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 10302 Z= 0.152 Angle : 0.602 9.944 14014 Z= 0.296 Chirality : 0.040 0.171 1634 Planarity : 0.004 0.036 1702 Dihedral : 4.440 24.736 1352 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1222 helix: 1.28 (0.18), residues: 894 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.409 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 128 average time/residue: 0.1851 time to fit residues: 35.9102 Evaluate side-chains 102 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0953 time to fit residues: 2.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10302 Z= 0.208 Angle : 0.630 10.428 14014 Z= 0.314 Chirality : 0.042 0.226 1634 Planarity : 0.004 0.037 1702 Dihedral : 4.437 24.350 1352 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1222 helix: 1.26 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.88 (0.38), residues: 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 108 average time/residue: 0.1937 time to fit residues: 31.8109 Evaluate side-chains 102 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0975 time to fit residues: 3.5116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 10302 Z= 0.331 Angle : 0.684 10.490 14014 Z= 0.346 Chirality : 0.045 0.217 1634 Planarity : 0.004 0.039 1702 Dihedral : 4.714 26.350 1352 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1222 helix: 1.13 (0.17), residues: 908 sheet: None (None), residues: 0 loop : -1.93 (0.37), residues: 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.326 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.2031 time to fit residues: 27.7088 Evaluate side-chains 86 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0971 time to fit residues: 2.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 10302 Z= 0.317 Angle : 0.688 11.585 14014 Z= 0.345 Chirality : 0.045 0.212 1634 Planarity : 0.004 0.039 1702 Dihedral : 4.754 26.329 1352 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1222 helix: 1.07 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -2.05 (0.37), residues: 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.252 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 90 average time/residue: 0.2107 time to fit residues: 28.7423 Evaluate side-chains 84 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0967 time to fit residues: 2.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10302 Z= 0.177 Angle : 0.647 12.939 14014 Z= 0.317 Chirality : 0.042 0.221 1634 Planarity : 0.004 0.036 1702 Dihedral : 4.504 24.487 1352 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1222 helix: 1.39 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.80 (0.38), residues: 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.317 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1943 time to fit residues: 27.1211 Evaluate side-chains 84 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.076316 restraints weight = 27966.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075939 restraints weight = 16169.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076028 restraints weight = 13063.697| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10302 Z= 0.214 Angle : 0.648 12.607 14014 Z= 0.319 Chirality : 0.042 0.215 1634 Planarity : 0.005 0.089 1702 Dihedral : 4.505 24.875 1352 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1222 helix: 1.39 (0.18), residues: 906 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 316 =============================================================================== Job complete usr+sys time: 1567.45 seconds wall clock time: 29 minutes 34.37 seconds (1774.37 seconds total)