Starting phenix.real_space_refine on Mon Mar 11 14:21:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/03_2024/5z1f_6875.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/03_2024/5z1f_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_6875/03_2024/5z1f_6875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/03_2024/5z1f_6875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/03_2024/5z1f_6875.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1f_6875/03_2024/5z1f_6875.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.06, 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: 3.44 Conformation dependent library (CDL) restraints added in 1.8 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: 0.80 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: 2.34 Time building geometry restraints manager: 3.74 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: 0.520 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: 0.020 Extract box with map and model: 2.200 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.700 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.660 ------------------------------------------------------------------------------- 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 % Allowed : 12.73 % Favored : 82.23 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 61 HIS 0.006 0.002 HIS B 84 PHE 0.014 0.002 PHE A 668 TYR 0.019 0.002 TYR A 609 ARG 0.002 0.001 ARG B 178 *********************** 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 : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.9138 (ttt90) cc_final: 0.8859 (ttt-90) REVERT: A 180 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8904 (tp40) REVERT: A 209 LYS cc_start: 0.9324 (tttt) cc_final: 0.8936 (tppt) REVERT: A 315 PHE cc_start: 0.9415 (m-80) cc_final: 0.9046 (m-10) REVERT: A 363 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8750 (tp-100) REVERT: A 579 ILE cc_start: 0.9448 (pp) cc_final: 0.9079 (pt) REVERT: A 580 LEU cc_start: 0.9093 (mt) cc_final: 0.8809 (mt) REVERT: A 651 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.9092 (tp) REVERT: A 662 GLN cc_start: 0.8618 (mt0) cc_final: 0.8141 (mt0) outliers start: 19 outliers final: 4 residues processed: 168 average time/residue: 0.1381 time to fit residues: 29.7855 Evaluate side-chains 109 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 5.9990 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: 8.9990 overall best weight: 2.5922 ------------------------------------------------------------------------------- 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 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: 0.7895 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8694 Z= 0.254 Angle : 0.810 7.780 11948 Z= 0.432 Chirality : 0.046 0.353 1482 Planarity : 0.006 0.057 1484 Dihedral : 6.113 17.900 1248 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.08 % Favored : 94.75 % Rotamer: Outliers : 0.27 % Allowed : 5.04 % Favored : 94.69 % 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: -2.68 (0.23), residues: 1182 helix: -1.43 (0.17), residues: 784 sheet: -2.50 (0.76), residues: 46 loop : -2.10 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 168 HIS 0.009 0.002 HIS B 447 PHE 0.028 0.002 PHE B 664 TYR 0.034 0.002 TYR A 572 ARG 0.006 0.001 ARG A 345 *********************** 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 129 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.6939 (m-40) cc_final: 0.6681 (m-40) REVERT: A 141 ASN cc_start: 0.8493 (t0) cc_final: 0.8253 (m110) REVERT: A 158 TRP cc_start: 0.7933 (t-100) cc_final: 0.7709 (t-100) REVERT: A 178 ARG cc_start: 0.9066 (ttt90) cc_final: 0.8691 (ttt-90) REVERT: A 209 LYS cc_start: 0.9258 (tttt) cc_final: 0.8872 (tptt) REVERT: A 354 ILE cc_start: 0.8517 (pt) cc_final: 0.8266 (pt) REVERT: A 579 ILE cc_start: 0.9380 (pt) cc_final: 0.9132 (pt) REVERT: A 594 LEU cc_start: 0.9398 (pp) cc_final: 0.8790 (mp) REVERT: A 651 ILE cc_start: 0.9410 (mm) cc_final: 0.9139 (tp) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1206 time to fit residues: 20.7133 Evaluate side-chains 101 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 1.9990 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 0.1980 chunk 108 optimal weight: 0.0770 chunk 37 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- 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 615 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3960 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= 0.206 Angle : 0.728 7.723 11948 Z= 0.376 Chirality : 0.042 0.175 1482 Planarity : 0.006 0.060 1484 Dihedral : 5.461 16.718 1248 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.92 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1182 helix: -0.34 (0.19), residues: 768 sheet: -2.33 (0.79), residues: 46 loop : -1.97 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 168 HIS 0.003 0.001 HIS A 173 PHE 0.030 0.002 PHE B 514 TYR 0.034 0.002 TYR B 586 ARG 0.006 0.001 ARG A 450 *********************** 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 127 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.9215 (tttt) cc_final: 0.8756 (tppt) REVERT: A 222 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9021 (mp0) REVERT: A 594 LEU cc_start: 0.9326 (pp) cc_final: 0.8816 (mp) REVERT: A 651 ILE cc_start: 0.9358 (mm) cc_final: 0.9033 (tp) REVERT: A 656 PHE cc_start: 0.8754 (t80) cc_final: 0.8534 (t80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1193 time to fit residues: 20.0803 Evaluate side-chains 95 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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: 0.3980 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 103 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4607 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= 0.197 Angle : 0.707 7.475 11948 Z= 0.360 Chirality : 0.041 0.159 1482 Planarity : 0.005 0.059 1484 Dihedral : 5.255 30.836 1248 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 0.27 % Allowed : 2.92 % Favored : 96.82 % 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: -0.79 (0.26), residues: 1182 helix: 0.24 (0.20), residues: 754 sheet: -2.00 (1.09), residues: 34 loop : -1.78 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 349 HIS 0.004 0.001 HIS A 447 PHE 0.022 0.001 PHE B 459 TYR 0.014 0.002 TYR B 572 ARG 0.008 0.001 ARG A 178 *********************** 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 126 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8435 (t0) cc_final: 0.8006 (m110) REVERT: A 222 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9040 (mp0) REVERT: A 572 TYR cc_start: 0.7579 (m-10) cc_final: 0.7263 (m-10) REVERT: A 594 LEU cc_start: 0.9357 (pp) cc_final: 0.8743 (mp) REVERT: A 651 ILE cc_start: 0.9336 (mm) cc_final: 0.9036 (tp) REVERT: A 656 PHE cc_start: 0.8800 (t80) cc_final: 0.8417 (t80) REVERT: A 668 PHE cc_start: 0.7593 (t80) cc_final: 0.7281 (t80) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1218 time to fit residues: 20.3427 Evaluate side-chains 97 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 0.1980 chunk 65 optimal weight: 0.2980 chunk 1 optimal weight: 0.0970 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.0060 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 0.0470 chunk 0 optimal weight: 30.0000 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 0.0470 chunk 29 optimal weight: 0.2980 overall best weight: 0.0790 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5069 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= 0.184 Angle : 0.688 7.438 11948 Z= 0.340 Chirality : 0.041 0.147 1482 Planarity : 0.005 0.058 1484 Dihedral : 4.901 26.358 1248 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.27 % Allowed : 2.39 % Favored : 97.35 % 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: -0.54 (0.26), residues: 1182 helix: 0.53 (0.20), residues: 764 sheet: -2.39 (1.02), residues: 34 loop : -1.93 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 61 HIS 0.003 0.001 HIS B 173 PHE 0.019 0.001 PHE A 514 TYR 0.012 0.002 TYR B 225 ARG 0.005 0.001 ARG A 178 *********************** 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 129 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8429 (t0) cc_final: 0.8188 (t0) REVERT: A 222 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9083 (mp0) REVERT: A 594 LEU cc_start: 0.9349 (pp) cc_final: 0.8782 (mp) REVERT: A 651 ILE cc_start: 0.9339 (mm) cc_final: 0.9107 (tp) REVERT: A 656 PHE cc_start: 0.8873 (t80) cc_final: 0.8414 (t80) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1121 time to fit residues: 19.5153 Evaluate side-chains 97 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 20.0000 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.0970 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8694 Z= 0.208 Angle : 0.686 7.753 11948 Z= 0.353 Chirality : 0.042 0.152 1482 Planarity : 0.006 0.058 1484 Dihedral : 4.885 29.001 1248 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 (0.26), residues: 1182 helix: 0.76 (0.20), residues: 762 sheet: -2.32 (1.04), residues: 34 loop : -1.90 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 613 HIS 0.003 0.001 HIS B 615 PHE 0.027 0.002 PHE A 668 TYR 0.026 0.002 TYR A 572 ARG 0.007 0.001 ARG A 345 *********************** 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 123 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ASN cc_start: 0.8488 (t0) cc_final: 0.8153 (t0) REVERT: A 180 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 209 LYS cc_start: 0.9286 (tttt) cc_final: 0.8790 (tppt) REVERT: A 222 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9084 (mp0) REVERT: A 594 LEU cc_start: 0.9358 (pp) cc_final: 0.8820 (mp) REVERT: A 651 ILE cc_start: 0.9379 (mm) cc_final: 0.9092 (tp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1233 time to fit residues: 19.9370 Evaluate side-chains 97 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 84 optimal weight: 0.0870 chunk 65 optimal weight: 0.0670 chunk 97 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 0.0020 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.8306 ------------------------------------------------------------------------------- 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 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: 0.7823 moved from start: 0.5751 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= 0.179 Angle : 0.689 8.298 11948 Z= 0.348 Chirality : 0.041 0.145 1482 Planarity : 0.005 0.059 1484 Dihedral : 4.835 29.917 1248 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1182 helix: 0.78 (0.20), residues: 762 sheet: -2.48 (1.03), residues: 34 loop : -1.86 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 168 HIS 0.003 0.001 HIS B 447 PHE 0.030 0.002 PHE B 514 TYR 0.014 0.002 TYR B 572 ARG 0.005 0.001 ARG A 345 *********************** 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 126 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 209 LYS cc_start: 0.9313 (tttt) cc_final: 0.8813 (tppt) REVERT: A 222 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8962 (mp0) REVERT: A 315 PHE cc_start: 0.9103 (m-10) cc_final: 0.8594 (m-10) REVERT: A 450 ARG cc_start: 0.8116 (ptt180) cc_final: 0.7808 (ptt-90) REVERT: A 594 LEU cc_start: 0.9324 (pp) cc_final: 0.8849 (mp) REVERT: A 651 ILE cc_start: 0.9388 (mm) cc_final: 0.9068 (tp) REVERT: A 668 PHE cc_start: 0.8072 (t80) cc_final: 0.7864 (t80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1156 time to fit residues: 19.6225 Evaluate side-chains 99 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 0.0070 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 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: 0.7865 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8694 Z= 0.205 Angle : 0.710 7.988 11948 Z= 0.360 Chirality : 0.041 0.156 1482 Planarity : 0.005 0.059 1484 Dihedral : 4.715 28.989 1248 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -0.14 (0.26), residues: 1182 helix: 0.91 (0.20), residues: 772 sheet: -2.35 (1.04), residues: 34 loop : -1.99 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 168 HIS 0.002 0.000 HIS A 615 PHE 0.032 0.002 PHE A 465 TYR 0.021 0.001 TYR B 171 ARG 0.004 0.001 ARG A 661 *********************** 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 126 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 ARG cc_start: 0.8931 (ttt180) cc_final: 0.8704 (ttm170) REVERT: A 180 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8334 (tm-30) REVERT: A 209 LYS cc_start: 0.9346 (tttt) cc_final: 0.8842 (tppt) REVERT: A 222 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8956 (mp0) REVERT: A 450 ARG cc_start: 0.8121 (ptt180) cc_final: 0.7817 (ptt-90) REVERT: A 619 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.8046 (mmt180) REVERT: A 651 ILE cc_start: 0.9380 (mm) cc_final: 0.9050 (tp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1269 time to fit residues: 21.2424 Evaluate side-chains 98 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 0.0980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 0.0870 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.6327 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= 0.184 Angle : 0.694 7.997 11948 Z= 0.349 Chirality : 0.041 0.149 1482 Planarity : 0.005 0.058 1484 Dihedral : 4.625 28.876 1248 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 1182 helix: 0.90 (0.19), residues: 772 sheet: -2.37 (1.04), residues: 34 loop : -1.99 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 613 HIS 0.002 0.001 HIS A 617 PHE 0.029 0.002 PHE A 315 TYR 0.012 0.001 TYR B 171 ARG 0.005 0.001 ARG A 345 *********************** 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 : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 209 LYS cc_start: 0.9340 (tttt) cc_final: 0.8916 (tppt) REVERT: A 450 ARG cc_start: 0.8043 (ptt180) cc_final: 0.7715 (ptt-90) REVERT: A 594 LEU cc_start: 0.9349 (pp) cc_final: 0.8764 (mp) REVERT: A 619 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8137 (mmt180) REVERT: A 651 ILE cc_start: 0.9396 (mm) cc_final: 0.9063 (tp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1177 time to fit residues: 19.6921 Evaluate side-chains 101 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 3.9990 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 overall best weight: 1.7502 ------------------------------------------------------------------------------- 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 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: 0.7859 moved from start: 0.6562 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= 0.213 Angle : 0.730 12.006 11948 Z= 0.366 Chirality : 0.043 0.168 1482 Planarity : 0.005 0.056 1484 Dihedral : 4.639 28.301 1248 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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 (0.26), residues: 1182 helix: 0.96 (0.20), residues: 768 sheet: -2.22 (1.04), residues: 34 loop : -1.90 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 613 HIS 0.002 0.001 HIS B 615 PHE 0.028 0.002 PHE A 627 TYR 0.012 0.001 TYR A 171 ARG 0.007 0.001 ARG A 178 ********************** 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 126 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 209 LYS cc_start: 0.9348 (tttt) cc_final: 0.8897 (tppt) REVERT: A 578 LEU cc_start: 0.9076 (tt) cc_final: 0.8743 (tt) REVERT: A 594 LEU cc_start: 0.9384 (pp) cc_final: 0.8779 (mp) REVERT: A 631 MET cc_start: 0.6663 (mtm) cc_final: 0.6363 (mtm) REVERT: A 651 ILE cc_start: 0.9397 (mm) cc_final: 0.9027 (tp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1163 time to fit residues: 19.9340 Evaluate side-chains 98 residues out of total 522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 0.0770 chunk 68 optimal weight: 0.8980 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073997 restraints weight = 17606.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075745 restraints weight = 12657.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.077061 restraints weight = 9689.423| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6842 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= 0.213 Angle : 0.699 8.705 11948 Z= 0.357 Chirality : 0.042 0.203 1482 Planarity : 0.005 0.054 1484 Dihedral : 4.639 27.609 1248 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.10 (0.27), residues: 1182 helix: 1.12 (0.20), residues: 768 sheet: -1.73 (1.27), residues: 20 loop : -1.99 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 613 HIS 0.008 0.001 HIS A 447 PHE 0.029 0.002 PHE A 582 TYR 0.010 0.001 TYR B 171 ARG 0.008 0.002 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.29 seconds wall clock time: 28 minutes 36.73 seconds (1716.73 seconds total)