Starting phenix.real_space_refine (version: dev) on Mon Apr 4 18:58:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2022/5z1f_6875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2022/5z1f_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_2022/5z1f_6875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2022/5z1f_6875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2022/5z1f_6875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/04_2022/5z1f_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 Convert atoms to be neutral 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-dev-4553/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: 5.44, per 1000 atoms: 0.64 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: 3.91 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: 0.43 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: 2.52 Time building geometry restraints manager: 4.23 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. 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. 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: 0.300 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: 2.500 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 26.720 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.512 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: 0.1334 time to fit residues: 28.6494 Evaluate side-chains 103 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0475 time to fit residues: 0.9984 ------------------------------------------------------------------------------- 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: 0.7608 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 : 0.584 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: 0.1156 time to fit residues: 20.8525 Evaluate side-chains 106 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0460 time to fit residues: 0.7558 ------------------------------------------------------------------------------- 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: 0.8980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 615 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 8694 Z= 0.206 Angle : 0.725 7.590 11948 Z= 0.375 Chirality : 0.044 0.333 1482 Planarity : 0.006 0.059 1484 Dihedral : 5.573 16.843 1248 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.77 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: -1.71 (0.24), residues: 1182 helix: -0.63 (0.18), residues: 780 sheet: -2.19 (0.83), residues: 46 loop : -1.84 (0.35), residues: 356 *********************** 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 : 0.533 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: 0.1211 time to fit residues: 20.9775 Evaluate side-chains 99 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0411 time to fit residues: 0.7681 ------------------------------------------------------------------------------- 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: 20.0000 chunk 56 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 115 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** 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: 0.7576 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8694 Z= 0.200 Angle : 0.703 7.530 11948 Z= 0.357 Chirality : 0.043 0.335 1482 Planarity : 0.005 0.058 1484 Dihedral : 5.283 30.420 1248 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % 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 : 0.18 % 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: -0.94 (0.25), residues: 1182 helix: 0.11 (0.19), residues: 764 sheet: -2.24 (1.02), residues: 34 loop : -1.84 (0.35), residues: 384 *********************** 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 130 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.1188 time to fit residues: 20.2751 Evaluate side-chains 98 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6945 ------------------------------------------------------------------------------- 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: 0.0770 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 29 optimal weight: 0.4980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4982 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= 0.177 Angle : 0.684 8.569 11948 Z= 0.343 Chirality : 0.042 0.251 1482 Planarity : 0.005 0.059 1484 Dihedral : 4.966 25.959 1248 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -0.52 (0.26), residues: 1182 helix: 0.55 (0.20), residues: 762 sheet: -2.13 (1.03), residues: 34 loop : -1.94 (0.34), residues: 386 *********************** 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 130 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1134 time to fit residues: 19.8713 Evaluate side-chains 99 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6873 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 20.0000 chunk 22 optimal weight: 30.0000 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 116 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.5365 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= 0.185 Angle : 0.685 7.417 11948 Z= 0.345 Chirality : 0.041 0.147 1482 Planarity : 0.005 0.060 1484 Dihedral : 4.903 31.234 1248 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.97 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: -0.29 (0.26), residues: 1182 helix: 0.76 (0.20), residues: 762 sheet: -2.29 (1.01), 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 124 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.504 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1263 time to fit residues: 20.6290 Evaluate side-chains 90 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6989 ------------------------------------------------------------------------------- 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: 0.0470 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 84 optimal weight: 0.0070 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7562 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8694 Z= 0.188 Angle : 0.689 7.436 11948 Z= 0.347 Chirality : 0.041 0.138 1482 Planarity : 0.005 0.058 1484 Dihedral : 4.793 28.703 1248 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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: -0.23 (0.26), residues: 1182 helix: 0.86 (0.20), residues: 762 sheet: -2.47 (1.00), residues: 34 loop : -1.98 (0.34), 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 128 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.526 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1094 time to fit residues: 19.1158 Evaluate side-chains 102 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6558 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.0970 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 8694 Z= 0.227 Angle : 0.703 7.800 11948 Z= 0.362 Chirality : 0.041 0.151 1482 Planarity : 0.007 0.123 1484 Dihedral : 4.671 25.990 1248 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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: -0.09 (0.26), residues: 1182 helix: 1.01 (0.20), residues: 762 sheet: -2.60 (0.96), residues: 34 loop : -2.00 (0.33), residues: 386 *********************** 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 123 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.523 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1115 time to fit residues: 18.8010 Evaluate side-chains 92 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6944 ------------------------------------------------------------------------------- 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: 0.0670 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 0.0060 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 8694 Z= 0.216 Angle : 0.690 7.629 11948 Z= 0.350 Chirality : 0.041 0.144 1482 Planarity : 0.006 0.100 1484 Dihedral : 4.569 24.455 1248 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.11 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: -0.07 (0.26), residues: 1182 helix: 1.00 (0.19), residues: 776 sheet: -2.84 (0.95), residues: 34 loop : -2.01 (0.34), residues: 372 *********************** 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 124 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1087 time to fit residues: 18.3425 Evaluate side-chains 94 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6639 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 9.9990 chunk 119 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 0.4980 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 0.0270 chunk 101 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 8694 Z= 0.216 Angle : 0.696 7.760 11948 Z= 0.351 Chirality : 0.041 0.157 1482 Planarity : 0.006 0.091 1484 Dihedral : 4.578 25.801 1248 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 14.53 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: -0.07 (0.26), residues: 1182 helix: 0.97 (0.19), residues: 782 sheet: -2.71 (0.94), residues: 34 loop : -2.00 (0.35), residues: 366 ********************** 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 124 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1136 time to fit residues: 19.2559 Evaluate side-chains 92 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7312 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 447 HIS A 617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.093767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077070 restraints weight = 17794.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.078829 restraints weight = 12980.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080206 restraints weight = 10036.443| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 8694 Z= 0.212 Angle : 0.683 8.355 11948 Z= 0.344 Chirality : 0.040 0.155 1482 Planarity : 0.006 0.089 1484 Dihedral : 4.522 26.052 1248 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.24 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: 0.08 (0.26), residues: 1182 helix: 1.16 (0.20), residues: 770 sheet: -2.87 (0.93), residues: 34 loop : -1.99 (0.34), residues: 378 =============================================================================== Job complete usr+sys time: 1411.26 seconds wall clock time: 26 minutes 29.56 seconds (1589.56 seconds total)