Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 21:40:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2023/5z1f_6875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2023/5z1f_6875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2023/5z1f_6875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2023/5z1f_6875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2023/5z1f_6875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2023/5z1f_6875.pdb" } resolution = 4.8 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= 0.002 sd= 0.009 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 24 5.16 5 C 5604 2.51 5 N 1364 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8480 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4240 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 4 Unresolved non-hydrogen bonds: 634 Unresolved non-hydrogen angles: 792 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 384 Chain: "B" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4240 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 145} Link IDs: {'PTRANS': 27, 'TRANS': 573} Chain breaks: 4 Unresolved non-hydrogen bonds: 634 Unresolved non-hydrogen angles: 792 Unresolved non-hydrogen dihedrals: 548 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'GLU:plan': 21, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 384 Time building chain proxies: 5.05, per 1000 atoms: 0.60 Number of scatterers: 8480 At special positions: 0 Unit cell: (127.655, 81.235, 91.785, 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 24 16.00 O 1488 8.00 N 1364 7.00 C 5604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 70.9% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 4 through 24 removed outlier: 3.532A pdb=" N LEU A 22 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 61 through 68 Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.507A pdb=" N VAL A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 97 removed outlier: 3.503A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 Proline residue: A 104 - end of helix Processing helix chain 'A' and resid 151 through 184 Processing helix chain 'A' and resid 188 through 191 removed outlier: 3.632A pdb=" N GLN A 191 " --> pdb=" O LYS A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.949A pdb=" N LYS A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.548A pdb=" N SER A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 377 removed outlier: 4.070A pdb=" N ILE A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 removed outlier: 4.340A pdb=" N ILE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 427 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 444 through 463 removed outlier: 3.759A pdb=" N ARG A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 451 " --> pdb=" O HIS A 447 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 463 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 489 through 523 Proline residue: A 499 - end of helix removed outlier: 3.643A pdb=" N ILE A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 518 " --> pdb=" O PHE A 514 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 522 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.684A pdb=" N HIS A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 576 Proline residue: A 560 - end of helix removed outlier: 4.041A pdb=" N ILE A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE A 575 " --> pdb=" O CYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 599 removed outlier: 3.587A pdb=" N ILE A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 587 " --> pdb=" O GLY A 583 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG A 595 " --> pdb=" O TRP A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 639 removed outlier: 4.274A pdb=" N HIS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 662 Proline residue: A 648 - end of helix Processing helix chain 'A' and resid 664 through 670 removed outlier: 4.005A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 680 Processing helix chain 'A' and resid 686 through 691 removed outlier: 3.887A pdb=" N PHE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 686 through 691' Processing helix chain 'B' and resid 4 through 24 removed outlier: 3.532A pdb=" N LEU B 22 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 61 through 68 Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.507A pdb=" N VAL B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 removed outlier: 3.503A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Proline residue: B 104 - end of helix Processing helix chain 'B' and resid 151 through 184 Processing helix chain 'B' and resid 188 through 191 removed outlier: 3.631A pdb=" N GLN B 191 " --> pdb=" O LYS B 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 233 through 239 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.949A pdb=" N LYS B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 305 Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.548A pdb=" N SER B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 377 removed outlier: 4.070A pdb=" N ILE B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 371 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 removed outlier: 4.341A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 427 Proline residue: B 418 - end of helix Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 444 through 463 removed outlier: 3.759A pdb=" N ARG B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 451 " --> pdb=" O HIS B 447 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 489 through 523 Proline residue: B 499 - end of helix removed outlier: 3.643A pdb=" N ILE B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 516 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 518 " --> pdb=" O PHE B 514 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 522 " --> pdb=" O GLY B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.684A pdb=" N HIS B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 576 Proline residue: B 560 - end of helix removed outlier: 4.041A pdb=" N ILE B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL B 574 " --> pdb=" O PHE B 570 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE B 575 " --> pdb=" O CYS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 599 removed outlier: 3.587A pdb=" N ILE B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 586 " --> pdb=" O PHE B 582 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 587 " --> pdb=" O GLY B 583 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 595 " --> pdb=" O TRP B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 639 removed outlier: 4.274A pdb=" N HIS B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 637 " --> pdb=" O GLY B 633 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 638 " --> pdb=" O TYR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 662 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 664 through 670 removed outlier: 4.005A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 680 Processing helix chain 'B' and resid 686 through 691 removed outlier: 3.887A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 686 through 691' Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 229 removed outlier: 3.992A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 224 through 229 removed outlier: 3.992A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1590 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: 3.95 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: 2588 1.34 - 1.46: 2128 1.46 - 1.58: 3940 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 8694 Sorted by residual: bond pdb=" C ALA A 34 " pdb=" N PRO A 35 " ideal model delta sigma weight residual 1.334 1.594 -0.260 2.34e-02 1.83e+03 1.23e+02 bond pdb=" C ALA B 34 " pdb=" N PRO B 35 " ideal model delta sigma weight residual 1.334 1.593 -0.259 2.34e-02 1.83e+03 1.23e+02 bond pdb=" C PRO B 202 " pdb=" O PRO B 202 " ideal model delta sigma weight residual 1.243 1.231 0.013 8.50e-03 1.38e+04 2.18e+00 bond pdb=" C PRO A 202 " pdb=" O PRO A 202 " ideal model delta sigma weight residual 1.243 1.231 0.012 8.50e-03 1.38e+04 1.96e+00 bond pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 ... (remaining 8689 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.11: 267 107.11 - 113.84: 4991 113.84 - 120.57: 3659 120.57 - 127.30: 2937 127.30 - 134.03: 94 Bond angle restraints: 11948 Sorted by residual: angle pdb=" N GLU B 305 " pdb=" CA GLU B 305 " pdb=" C GLU B 305 " ideal model delta sigma weight residual 107.67 118.15 -10.48 2.09e+00 2.29e-01 2.51e+01 angle pdb=" N GLU A 305 " pdb=" CA GLU A 305 " pdb=" C GLU A 305 " ideal model delta sigma weight residual 107.67 118.13 -10.46 2.09e+00 2.29e-01 2.51e+01 angle pdb=" O PRO A 202 " pdb=" C PRO A 202 " pdb=" N PRO A 203 " ideal model delta sigma weight residual 121.15 123.42 -2.27 4.70e-01 4.53e+00 2.32e+01 angle pdb=" O PRO B 202 " pdb=" C PRO B 202 " pdb=" N PRO B 203 " ideal model delta sigma weight residual 121.15 123.39 -2.24 4.70e-01 4.53e+00 2.26e+01 angle pdb=" N THR A 297 " pdb=" CA THR A 297 " pdb=" C THR A 297 " ideal model delta sigma weight residual 111.07 115.54 -4.47 1.07e+00 8.73e-01 1.75e+01 ... (remaining 11943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4640 17.03 - 34.07: 262 34.07 - 51.10: 88 51.10 - 68.14: 10 68.14 - 85.17: 2 Dihedral angle restraints: 5002 sinusoidal: 1472 harmonic: 3530 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N GLU B 47 " pdb=" CA GLU B 47 " ideal model delta harmonic sigma weight residual -180.00 -150.39 -29.61 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA LEU A 46 " pdb=" C LEU A 46 " pdb=" N GLU A 47 " pdb=" CA GLU A 47 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA THR A 55 " pdb=" C THR A 55 " pdb=" N ARG A 56 " pdb=" CA ARG A 56 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1096 0.051 - 0.103: 298 0.103 - 0.154: 70 0.154 - 0.205: 14 0.205 - 0.257: 4 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA GLU B 305 " pdb=" N GLU B 305 " pdb=" C GLU B 305 " pdb=" CB GLU B 305 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU A 305 " pdb=" N GLU A 305 " pdb=" C GLU A 305 " pdb=" CB GLU A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS B 300 " pdb=" N LYS B 300 " pdb=" C LYS B 300 " pdb=" CB LYS B 300 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1479 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 108 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 107 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO A 108 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 202 " -0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO A 203 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.046 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1312 2.75 - 3.29: 9749 3.29 - 3.83: 14301 3.83 - 4.36: 16456 4.36 - 4.90: 25235 Nonbonded interactions: 67053 Sorted by model distance: nonbonded pdb=" O ASN B 492 " pdb=" OG1 THR B 496 " model vdw 2.213 2.440 nonbonded pdb=" O ASN A 492 " pdb=" OG1 THR A 496 " model vdw 2.213 2.440 nonbonded pdb=" O GLU A 232 " pdb=" CD GLU A 232 " model vdw 2.214 3.270 nonbonded pdb=" O GLU B 232 " pdb=" CD GLU B 232 " model vdw 2.214 3.270 nonbonded pdb=" O LEU A 635 " pdb=" OH TYR A 642 " model vdw 2.223 2.440 ... (remaining 67048 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 Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 0.650 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: 2.430 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 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: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.006 0.260 8694 Z= 0.418 Angle : 0.868 10.477 11948 Z= 0.490 Chirality : 0.052 0.257 1482 Planarity : 0.008 0.089 1484 Dihedral : 13.130 85.173 2706 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 1.02 % Allowed : 9.81 % Favored : 89.17 % Rotamer Outliers : 5.04 % 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: -4.90 (0.19), residues: 1182 helix: -3.32 (0.13), residues: 750 sheet: -2.20 (0.75), residues: 46 loop : -2.77 (0.28), residues: 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 168 average time/residue: 0.1443 time to fit residues: 31.1109 Evaluate side-chains 103 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0515 time to fit residues: 1.0306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 351 ASN A 363 GLN A 615 HIS ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8694 Z= 0.237 Angle : 0.789 7.896 11948 Z= 0.420 Chirality : 0.045 0.316 1482 Planarity : 0.006 0.057 1484 Dihedral : 6.132 18.016 1248 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.25 % Favored : 94.42 % Rotamer Outliers : 0.80 % 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: -2.85 (0.23), residues: 1182 helix: -1.56 (0.17), residues: 782 sheet: -2.36 (0.76), residues: 46 loop : -2.19 (0.33), residues: 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 134 average time/residue: 0.1189 time to fit residues: 21.2723 Evaluate side-chains 106 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0418 time to fit residues: 0.6930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 108 optimal weight: 0.0670 chunk 37 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 615 HIS ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8694 Z= 0.219 Angle : 0.725 7.638 11948 Z= 0.378 Chirality : 0.044 0.349 1482 Planarity : 0.005 0.060 1484 Dihedral : 5.463 16.772 1248 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.26 % Favored : 93.40 % Rotamer Outliers : 0.53 % 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: -1.61 (0.25), residues: 1182 helix: -0.46 (0.18), residues: 772 sheet: -2.22 (0.82), residues: 46 loop : -2.02 (0.34), residues: 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.1285 time to fit residues: 22.1439 Evaluate side-chains 98 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.7604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 57 optimal weight: 0.0170 chunk 103 optimal weight: 6.9990 chunk 31 optimal weight: 0.0570 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8694 Z= 0.191 Angle : 0.703 7.588 11948 Z= 0.357 Chirality : 0.043 0.334 1482 Planarity : 0.005 0.060 1484 Dihedral : 5.256 29.717 1248 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % 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: -0.94 (0.26), residues: 1182 helix: 0.12 (0.19), residues: 768 sheet: -2.32 (1.00), residues: 34 loop : -1.86 (0.35), residues: 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1270 time to fit residues: 20.9676 Evaluate side-chains 93 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 615 HIS ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8694 Z= 0.187 Angle : 0.693 7.443 11948 Z= 0.349 Chirality : 0.043 0.270 1482 Planarity : 0.005 0.059 1484 Dihedral : 5.005 29.041 1248 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % 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: -0.48 (0.26), residues: 1182 helix: 0.62 (0.20), residues: 754 sheet: -2.13 (1.05), residues: 34 loop : -1.96 (0.34), residues: 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1170 time to fit residues: 19.9163 Evaluate side-chains 91 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 9.9990 chunk 104 optimal weight: 0.0370 chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 30.0000 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 HIS ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8694 Z= 0.181 Angle : 0.679 7.469 11948 Z= 0.347 Chirality : 0.040 0.148 1482 Planarity : 0.005 0.059 1484 Dihedral : 4.868 30.853 1248 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.26 (0.26), residues: 1182 helix: 0.79 (0.20), residues: 762 sheet: -2.27 (1.00), residues: 34 loop : -1.90 (0.34), residues: 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.548 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1369 time to fit residues: 22.6061 Evaluate side-chains 88 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0010 chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 0.3980 chunk 84 optimal weight: 0.0000 chunk 65 optimal weight: 0.0170 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 0.0010 chunk 115 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8694 Z= 0.187 Angle : 0.683 7.572 11948 Z= 0.344 Chirality : 0.041 0.142 1482 Planarity : 0.005 0.058 1484 Dihedral : 4.812 28.692 1248 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -0.25 (0.26), residues: 1182 helix: 0.88 (0.20), residues: 762 sheet: -2.46 (0.99), residues: 34 loop : -2.08 (0.33), residues: 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1095 time to fit residues: 18.7109 Evaluate side-chains 94 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 10 optimal weight: 0.0050 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8694 Z= 0.184 Angle : 0.689 7.842 11948 Z= 0.343 Chirality : 0.041 0.156 1482 Planarity : 0.005 0.057 1484 Dihedral : 4.601 26.096 1248 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -0.19 (0.26), residues: 1182 helix: 0.92 (0.20), residues: 768 sheet: -2.65 (0.95), residues: 34 loop : -2.05 (0.34), residues: 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1172 time to fit residues: 20.0647 Evaluate side-chains 92 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.510 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0270 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 84 optimal weight: 0.0010 chunk 33 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 70 optimal weight: 0.0060 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 overall best weight: 0.0296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8694 Z= 0.185 Angle : 0.686 9.152 11948 Z= 0.340 Chirality : 0.041 0.173 1482 Planarity : 0.005 0.052 1484 Dihedral : 4.519 23.179 1248 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % 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: -0.04 (0.26), residues: 1182 helix: 1.08 (0.20), residues: 766 sheet: -2.40 (1.01), residues: 34 loop : -2.13 (0.33), residues: 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1086 time to fit residues: 18.9124 Evaluate side-chains 92 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 75 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 0.0030 overall best weight: 0.3308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8694 Z= 0.181 Angle : 0.689 11.009 11948 Z= 0.338 Chirality : 0.041 0.202 1482 Planarity : 0.005 0.052 1484 Dihedral : 4.437 23.445 1248 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % 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: 0.06 (0.27), residues: 1182 helix: 1.14 (0.20), residues: 780 sheet: -2.45 (0.97), residues: 34 loop : -2.13 (0.34), residues: 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1112 time to fit residues: 18.7685 Evaluate side-chains 93 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.524 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 83 optimal weight: 7.9990 chunk 5 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.076778 restraints weight = 17833.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078603 restraints weight = 12926.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080010 restraints weight = 9954.444| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8694 Z= 0.183 Angle : 0.661 7.403 11948 Z= 0.330 Chirality : 0.041 0.188 1482 Planarity : 0.005 0.051 1484 Dihedral : 4.380 20.911 1248 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: 0.30 (0.27), residues: 1182 helix: 1.32 (0.20), residues: 776 sheet: -2.59 (0.99), residues: 34 loop : -1.97 (0.35), residues: 372 =============================================================================== Job complete usr+sys time: 1446.29 seconds wall clock time: 27 minutes 17.72 seconds (1637.72 seconds total)