Starting phenix.real_space_refine on Thu Mar 14 22:55:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/03_2024/6nq1_0478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/03_2024/6nq1_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_0478/03_2024/6nq1_0478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/03_2024/6nq1_0478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/03_2024/6nq1_0478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nq1_0478/03_2024/6nq1_0478.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.65, per 1000 atoms: 0.56 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: 3.94 Conformation dependent library (CDL) restraints added in 1.7 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: 0.91 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: 2.63 Time building geometry restraints manager: 4.28 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.000 Extract box with map and model: 3.470 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.200 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 % Allowed : 9.80 % Favored : 90.02 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 655 HIS 0.010 0.002 HIS A 411 PHE 0.018 0.002 PHE B 626 TYR 0.017 0.002 TYR A 74 ARG 0.004 0.001 ARG B 60 *********************** 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 : 1.188 Fit side-chains revert: symmetry clash REVERT: A 379 MET cc_start: 0.7338 (mmt) cc_final: 0.6731 (mtp) REVERT: A 446 LEU cc_start: 0.9209 (tt) cc_final: 0.9005 (tp) REVERT: A 653 ASN cc_start: 0.9141 (t0) cc_final: 0.8554 (t0) REVERT: B 379 MET cc_start: 0.7309 (mmt) cc_final: 0.6707 (mtp) REVERT: B 446 LEU cc_start: 0.9213 (tt) cc_final: 0.9007 (tp) REVERT: B 653 ASN cc_start: 0.9145 (t0) cc_final: 0.8705 (t0) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.2463 time to fit residues: 51.6737 Evaluate side-chains 94 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 1.9990 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: 1.7188 ------------------------------------------------------------------------------- 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 A 653 ASN B 58 GLN B 305 ASN B 375 HIS B 431 HIS B 473 ASN B 653 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10302 Z= 0.219 Angle : 0.684 8.392 14014 Z= 0.350 Chirality : 0.041 0.171 1634 Planarity : 0.005 0.043 1702 Dihedral : 5.203 27.829 1352 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.73 % Allowed : 15.43 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.22), residues: 1222 helix: -0.96 (0.15), residues: 896 sheet: None (None), residues: 0 loop : -2.33 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 685 HIS 0.003 0.001 HIS A 151 PHE 0.019 0.001 PHE A 338 TYR 0.024 0.001 TYR B 479 ARG 0.003 0.000 ARG B 464 *********************** 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 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 45 CYS cc_start: 0.8883 (t) cc_final: 0.8491 (p) REVERT: A 379 MET cc_start: 0.7270 (mmt) cc_final: 0.6871 (mtt) REVERT: B 271 THR cc_start: 0.8640 (p) cc_final: 0.8436 (p) REVERT: B 370 GLN cc_start: 0.7540 (mp10) cc_final: 0.7281 (mp10) REVERT: B 379 MET cc_start: 0.7327 (mmt) cc_final: 0.6947 (mtt) outliers start: 8 outliers final: 3 residues processed: 125 average time/residue: 0.1962 time to fit residues: 36.0648 Evaluate side-chains 94 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 550 LEU 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: 0.9980 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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: 0.8280 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10302 Z= 0.455 Angle : 0.780 9.725 14014 Z= 0.397 Chirality : 0.047 0.195 1634 Planarity : 0.005 0.045 1702 Dihedral : 5.342 28.399 1352 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.72 % Allowed : 17.79 % Favored : 79.49 % 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: -1.01 (0.24), residues: 1222 helix: -0.08 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.11 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 685 HIS 0.006 0.002 HIS B 151 PHE 0.020 0.002 PHE A 136 TYR 0.026 0.002 TYR B 479 ARG 0.005 0.001 ARG B 580 *********************** 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 118 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 45 CYS cc_start: 0.8943 (t) cc_final: 0.8427 (p) REVERT: A 549 MET cc_start: 0.7719 (ptm) cc_final: 0.7437 (ptp) REVERT: B 379 MET cc_start: 0.7022 (mmt) cc_final: 0.6371 (mtp) REVERT: B 549 MET cc_start: 0.7697 (ptm) cc_final: 0.7415 (ptp) outliers start: 30 outliers final: 20 residues processed: 118 average time/residue: 0.2008 time to fit residues: 34.6667 Evaluate side-chains 104 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 550 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10302 Z= 0.186 Angle : 0.633 9.005 14014 Z= 0.314 Chirality : 0.041 0.131 1634 Planarity : 0.004 0.038 1702 Dihedral : 4.932 26.612 1352 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.63 % Allowed : 18.51 % Favored : 79.85 % 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: -0.24 (0.24), residues: 1222 helix: 0.51 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -2.00 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 685 HIS 0.003 0.001 HIS A 226 PHE 0.016 0.001 PHE B 338 TYR 0.024 0.001 TYR B 479 ARG 0.005 0.000 ARG A 557 *********************** 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 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 45 CYS cc_start: 0.8876 (t) cc_final: 0.8399 (p) REVERT: B 45 CYS cc_start: 0.8924 (t) cc_final: 0.8437 (p) outliers start: 18 outliers final: 9 residues processed: 123 average time/residue: 0.1959 time to fit residues: 35.5429 Evaluate side-chains 102 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 486 LEU 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: 0.0870 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 0.0970 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.6360 ------------------------------------------------------------------------------- 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** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3053 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= 0.186 Angle : 0.613 9.046 14014 Z= 0.304 Chirality : 0.040 0.149 1634 Planarity : 0.004 0.039 1702 Dihedral : 4.723 26.396 1352 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.00 % Allowed : 19.87 % Favored : 78.13 % 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: 0.27 (0.25), residues: 1222 helix: 0.91 (0.18), residues: 904 sheet: None (None), residues: 0 loop : -1.88 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 685 HIS 0.002 0.001 HIS A 151 PHE 0.032 0.001 PHE B 582 TYR 0.024 0.001 TYR B 479 ARG 0.005 0.000 ARG B 557 *********************** 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 131 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 45 CYS cc_start: 0.8798 (t) cc_final: 0.8392 (p) REVERT: A 229 LEU cc_start: 0.8618 (tt) cc_final: 0.8270 (mt) REVERT: B 45 CYS cc_start: 0.8893 (t) cc_final: 0.8414 (p) REVERT: B 229 LEU cc_start: 0.8593 (tt) cc_final: 0.8346 (mt) outliers start: 22 outliers final: 18 residues processed: 129 average time/residue: 0.1947 time to fit residues: 37.1118 Evaluate side-chains 112 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10302 Z= 0.287 Angle : 0.664 9.805 14014 Z= 0.331 Chirality : 0.043 0.169 1634 Planarity : 0.004 0.039 1702 Dihedral : 4.789 26.660 1352 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.54 % Allowed : 19.69 % Favored : 76.77 % 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: 0.23 (0.25), residues: 1222 helix: 0.88 (0.17), residues: 914 sheet: None (None), residues: 0 loop : -1.97 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 685 HIS 0.003 0.001 HIS A 151 PHE 0.017 0.002 PHE B 582 TYR 0.021 0.001 TYR B 479 ARG 0.004 0.000 ARG B 557 *********************** 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 138 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 153 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7793 (mp10) REVERT: B 45 CYS cc_start: 0.8857 (t) cc_final: 0.8380 (p) REVERT: B 153 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7795 (mp10) outliers start: 39 outliers final: 28 residues processed: 134 average time/residue: 0.1869 time to fit residues: 37.2141 Evaluate side-chains 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 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: 0.9980 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10302 Z= 0.180 Angle : 0.624 11.065 14014 Z= 0.309 Chirality : 0.041 0.161 1634 Planarity : 0.004 0.040 1702 Dihedral : 4.593 25.407 1352 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.72 % Allowed : 20.51 % Favored : 76.77 % 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: 0.51 (0.25), residues: 1222 helix: 1.12 (0.18), residues: 914 sheet: None (None), residues: 0 loop : -2.04 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 685 HIS 0.001 0.001 HIS B 151 PHE 0.043 0.001 PHE B 582 TYR 0.014 0.001 TYR B 479 ARG 0.003 0.000 ARG A 554 *********************** 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 141 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 153 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7782 (mp10) REVERT: A 545 ARG cc_start: 0.7374 (ptt180) cc_final: 0.6948 (mtp180) REVERT: B 45 CYS cc_start: 0.8844 (t) cc_final: 0.8373 (p) REVERT: B 153 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: B 229 LEU cc_start: 0.8691 (tt) cc_final: 0.8365 (mt) REVERT: B 545 ARG cc_start: 0.7314 (ptt180) cc_final: 0.7028 (mtp180) outliers start: 30 outliers final: 23 residues processed: 139 average time/residue: 0.1733 time to fit residues: 35.8742 Evaluate side-chains 122 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 544 THR 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: 0.9990 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3429 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= 0.208 Angle : 0.641 11.429 14014 Z= 0.317 Chirality : 0.042 0.242 1634 Planarity : 0.004 0.037 1702 Dihedral : 4.547 25.330 1352 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.72 % Allowed : 21.60 % Favored : 75.68 % 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: 0.60 (0.25), residues: 1222 helix: 1.12 (0.17), residues: 920 sheet: None (None), residues: 0 loop : -1.82 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 685 HIS 0.002 0.001 HIS B 151 PHE 0.047 0.001 PHE B 582 TYR 0.013 0.001 TYR B 479 ARG 0.003 0.000 ARG A 554 *********************** 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 131 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: A 545 ARG cc_start: 0.7312 (ptt180) cc_final: 0.6942 (mtp180) REVERT: B 45 CYS cc_start: 0.8822 (t) cc_final: 0.8355 (p) REVERT: B 153 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: B 229 LEU cc_start: 0.8680 (tt) cc_final: 0.8460 (mt) outliers start: 30 outliers final: 28 residues processed: 130 average time/residue: 0.1867 time to fit residues: 35.8581 Evaluate side-chains 123 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 556 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10302 Z= 0.163 Angle : 0.628 12.207 14014 Z= 0.308 Chirality : 0.041 0.192 1634 Planarity : 0.004 0.037 1702 Dihedral : 4.406 23.666 1352 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.45 % Allowed : 22.41 % Favored : 75.14 % 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: 0.87 (0.25), residues: 1222 helix: 1.36 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 685 HIS 0.001 0.000 HIS B 181 PHE 0.046 0.001 PHE B 582 TYR 0.010 0.001 TYR B 479 ARG 0.005 0.000 ARG A 554 *********************** 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 131 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: B 45 CYS cc_start: 0.8795 (t) cc_final: 0.8342 (p) REVERT: B 153 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7623 (mp10) outliers start: 27 outliers final: 22 residues processed: 130 average time/residue: 0.1833 time to fit residues: 35.5283 Evaluate side-chains 120 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10302 Z= 0.280 Angle : 0.673 11.634 14014 Z= 0.334 Chirality : 0.043 0.207 1634 Planarity : 0.005 0.098 1702 Dihedral : 4.558 25.131 1352 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.72 % Allowed : 22.60 % Favored : 74.68 % 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: 0.80 (0.25), residues: 1222 helix: 1.30 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -1.79 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 685 HIS 0.003 0.001 HIS B 151 PHE 0.027 0.002 PHE A 582 TYR 0.011 0.001 TYR A 479 ARG 0.013 0.000 ARG A 554 ********************** 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 125 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7051 (mmt) cc_final: 0.6786 (mpp) REVERT: A 153 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 153 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7639 (mp10) outliers start: 30 outliers final: 27 residues processed: 124 average time/residue: 0.1866 time to fit residues: 34.6683 Evaluate side-chains 119 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 153 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 404 ASP Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 651 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 274 ASN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 370 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.100929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075598 restraints weight = 27710.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075633 restraints weight = 15662.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.075736 restraints weight = 12176.496| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3609 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= 0.239 Angle : 0.648 11.442 14014 Z= 0.322 Chirality : 0.042 0.187 1634 Planarity : 0.005 0.088 1702 Dihedral : 4.557 25.103 1352 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.90 % Allowed : 22.60 % Favored : 74.50 % 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: 0.86 (0.25), residues: 1222 helix: 1.34 (0.18), residues: 912 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 685 HIS 0.002 0.001 HIS B 151 PHE 0.021 0.001 PHE A 582 TYR 0.011 0.001 TYR B 479 ARG 0.012 0.000 ARG B 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.26 seconds wall clock time: 30 minutes 30.03 seconds (1830.03 seconds total)