Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 00:32:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/04_2023/6of4_20042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/04_2023/6of4_20042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/04_2023/6of4_20042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/04_2023/6of4_20042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/04_2023/6of4_20042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6of4_20042/04_2023/6of4_20042.pdb" } resolution = 3.2 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= 0.018 sd= 0.673 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 54 5.16 5 C 7028 2.51 5 N 1920 2.21 5 O 1996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 6.52, per 1000 atoms: 0.59 Number of scatterers: 10998 At special positions: 0 Unit cell: (146.88, 89.64, 89.64, 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 54 16.00 O 1996 8.00 N 1920 7.00 C 7028 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: 4.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 10 sheets defined 40.4% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.271A pdb=" N LEU A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 67 through 84 removed outlier: 3.500A pdb=" N GLU A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.261A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.935A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.501A pdb=" N ASN B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 292 through 296 removed outlier: 4.522A pdb=" N SER B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.870A pdb=" N CYS B 333 " --> pdb=" O PRO B 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.633A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.239A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.591A pdb=" N LEU B 658 " --> pdb=" O PRO B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 691 removed outlier: 4.045A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 691 " --> pdb=" O LYS B 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 4.271A pdb=" N LEU D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 41 through 64 Processing helix chain 'D' and resid 67 through 84 removed outlier: 3.500A pdb=" N GLU D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 115 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.261A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'E' and resid 196 through 202 removed outlier: 3.935A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 211 Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 242 through 258 removed outlier: 3.502A pdb=" N ASN E 246 " --> pdb=" O HIS E 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 258 " --> pdb=" O THR E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 292 through 296 removed outlier: 4.522A pdb=" N SER E 296 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.870A pdb=" N CYS E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS E 334 " --> pdb=" O PRO E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 334' Processing helix chain 'E' and resid 367 through 387 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.632A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.238A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN E 544 " --> pdb=" O SER E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 660 removed outlier: 3.591A pdb=" N LEU E 658 " --> pdb=" O PRO E 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 691 removed outlier: 4.045A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS E 691 " --> pdb=" O LYS E 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.672A pdb=" N GLU B 646 " --> pdb=" O SER B 639 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 637 " --> pdb=" O HIS B 648 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU B 650 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE B 635 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET B 548 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125 removed outlier: 3.963A pdb=" N ARG B 123 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 130 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 358 removed outlier: 7.026A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 420 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 349 removed outlier: 3.672A pdb=" N GLU E 646 " --> pdb=" O SER E 639 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 637 " --> pdb=" O HIS E 648 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU E 650 " --> pdb=" O ILE E 635 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE E 635 " --> pdb=" O LEU E 650 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.963A pdb=" N ARG E 123 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 130 " --> pdb=" O ARG E 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AB1, first strand: chain 'E' and resid 351 through 358 removed outlier: 7.027A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 420 " --> pdb=" O ILE E 263 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1392 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: 3.06 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3528 1.34 - 1.45: 1629 1.45 - 1.57: 6051 1.57 - 1.69: 0 1.69 - 1.80: 88 Bond restraints: 11296 Sorted by residual: bond pdb=" C ALA E 535 " pdb=" N PRO E 536 " ideal model delta sigma weight residual 1.335 1.309 0.026 1.38e-02 5.25e+03 3.49e+00 bond pdb=" C ALA B 535 " pdb=" N PRO B 536 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.38e-02 5.25e+03 3.38e+00 bond pdb=" CB TRP A 355 " pdb=" CG TRP A 355 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.04e+00 bond pdb=" CB TRP D 355 " pdb=" CG TRP D 355 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.01e+00 bond pdb=" CB TRP D 60 " pdb=" CG TRP D 60 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.74e+00 ... (remaining 11291 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.68: 506 105.68 - 112.79: 6024 112.79 - 119.89: 3619 119.89 - 127.00: 5025 127.00 - 134.11: 238 Bond angle restraints: 15412 Sorted by residual: angle pdb=" N PRO E 455 " pdb=" CA PRO E 455 " pdb=" CB PRO E 455 " ideal model delta sigma weight residual 103.00 110.52 -7.52 1.10e+00 8.26e-01 4.67e+01 angle pdb=" N PRO B 455 " pdb=" CA PRO B 455 " pdb=" CB PRO B 455 " ideal model delta sigma weight residual 103.00 110.48 -7.48 1.10e+00 8.26e-01 4.62e+01 angle pdb=" N ALA B 290 " pdb=" CA ALA B 290 " pdb=" C ALA B 290 " ideal model delta sigma weight residual 110.80 124.04 -13.24 2.13e+00 2.20e-01 3.86e+01 angle pdb=" N ALA E 290 " pdb=" CA ALA E 290 " pdb=" C ALA E 290 " ideal model delta sigma weight residual 110.80 124.02 -13.22 2.13e+00 2.20e-01 3.85e+01 angle pdb=" C HIS A 146 " pdb=" N GLU A 147 " pdb=" CA GLU A 147 " ideal model delta sigma weight residual 122.15 106.53 15.62 2.83e+00 1.25e-01 3.05e+01 ... (remaining 15407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6128 17.44 - 34.87: 436 34.87 - 52.31: 86 52.31 - 69.75: 78 69.75 - 87.18: 14 Dihedral angle restraints: 6742 sinusoidal: 2650 harmonic: 4092 Sorted by residual: dihedral pdb=" CA ARG B 295 " pdb=" C ARG B 295 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual -180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA ARG E 295 " pdb=" C ARG E 295 " pdb=" N SER E 296 " pdb=" CA SER E 296 " ideal model delta harmonic sigma weight residual -180.00 -132.61 -47.39 0 5.00e+00 4.00e-02 8.98e+01 dihedral pdb=" CA ALA D 91 " pdb=" C ALA D 91 " pdb=" N GLY D 92 " pdb=" CA GLY D 92 " ideal model delta harmonic sigma weight residual -180.00 -148.19 -31.81 0 5.00e+00 4.00e-02 4.05e+01 ... (remaining 6739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1012 0.048 - 0.096: 511 0.096 - 0.143: 149 0.143 - 0.191: 48 0.191 - 0.239: 6 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ALA B 290 " pdb=" N ALA B 290 " pdb=" C ALA B 290 " pdb=" CB ALA B 290 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ALA E 290 " pdb=" N ALA E 290 " pdb=" C ALA E 290 " pdb=" CB ALA E 290 " both_signs ideal model delta sigma weight residual False 2.48 2.25 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PRO E 455 " pdb=" N PRO E 455 " pdb=" C PRO E 455 " pdb=" CB PRO E 455 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1723 not shown) Planarity restraints: 1978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 330 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO E 331 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 331 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 331 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 330 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 331 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 509 " 0.042 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO E 510 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 510 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 510 " 0.034 5.00e-02 4.00e+02 ... (remaining 1975 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 187 2.65 - 3.21: 10602 3.21 - 3.78: 15009 3.78 - 4.34: 19213 4.34 - 4.90: 33309 Nonbonded interactions: 78320 Sorted by model distance: nonbonded pdb=" OG SER E 272 " pdb=" O MET E 424 " model vdw 2.091 2.440 nonbonded pdb=" OG SER B 272 " pdb=" O MET B 424 " model vdw 2.091 2.440 nonbonded pdb=" O SER B 444 " pdb=" OG1 THR B 445 " model vdw 2.170 2.440 nonbonded pdb=" O SER E 444 " pdb=" OG1 THR E 445 " model vdw 2.170 2.440 nonbonded pdb=" NH2 ARG E 201 " pdb=" OD1 ASN E 215 " model vdw 2.229 2.520 ... (remaining 78315 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.330 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.010 0.064 11296 Z= 0.692 Angle : 1.187 15.624 15412 Z= 0.643 Chirality : 0.062 0.239 1726 Planarity : 0.009 0.073 1978 Dihedral : 15.119 87.184 4090 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 3.55 % Allowed : 19.61 % Favored : 76.85 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.99 (0.17), residues: 1382 helix: -2.88 (0.15), residues: 456 sheet: -1.37 (0.33), residues: 202 loop : -4.37 (0.18), residues: 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 301 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 5 residues processed: 324 average time/residue: 0.2744 time to fit residues: 120.8330 Evaluate side-chains 188 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1101 time to fit residues: 2.8285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.0030 chunk 81 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 115 GLN B 120 ASN B 144 ASN B 151 GLN B 174 HIS D 62 GLN D 146 HIS E 115 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 11296 Z= 0.210 Angle : 0.815 11.563 15412 Z= 0.407 Chirality : 0.045 0.275 1726 Planarity : 0.007 0.060 1978 Dihedral : 6.210 81.336 1528 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.78 % Favored : 88.78 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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: -1.29 (0.23), residues: 1382 helix: 1.83 (0.21), residues: 478 sheet: -0.46 (0.33), residues: 256 loop : -3.33 (0.22), residues: 648 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 24 residues processed: 240 average time/residue: 0.2074 time to fit residues: 72.6323 Evaluate side-chains 208 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1010 time to fit residues: 6.2866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 0.0470 chunk 43 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 533 GLN E 120 ASN E 327 ASN E 533 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 11296 Z= 0.173 Angle : 0.701 9.162 15412 Z= 0.341 Chirality : 0.042 0.188 1726 Planarity : 0.006 0.052 1978 Dihedral : 5.704 73.147 1528 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.55 % Favored : 90.01 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.05 (0.24), residues: 1382 helix: 3.04 (0.23), residues: 482 sheet: -0.00 (0.33), residues: 258 loop : -2.69 (0.24), residues: 642 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 1.294 Fit side-chains outliers start: 36 outliers final: 13 residues processed: 223 average time/residue: 0.2084 time to fit residues: 70.7002 Evaluate side-chains 198 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1579 time to fit residues: 5.9351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 11296 Z= 0.334 Angle : 0.736 9.523 15412 Z= 0.365 Chirality : 0.045 0.224 1726 Planarity : 0.006 0.051 1978 Dihedral : 5.606 66.913 1528 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.78 % Favored : 88.78 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.11 (0.24), residues: 1382 helix: 2.76 (0.23), residues: 486 sheet: -0.27 (0.32), residues: 264 loop : -2.44 (0.25), residues: 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.437 Fit side-chains outliers start: 28 outliers final: 17 residues processed: 218 average time/residue: 0.1950 time to fit residues: 64.5229 Evaluate side-chains 204 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 187 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1017 time to fit residues: 5.0895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 100 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS B 222 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11296 Z= 0.183 Angle : 0.659 10.471 15412 Z= 0.321 Chirality : 0.042 0.136 1726 Planarity : 0.006 0.047 1978 Dihedral : 5.213 63.760 1528 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.76 % Favored : 91.10 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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 (0.24), residues: 1382 helix: 3.01 (0.23), residues: 488 sheet: -0.17 (0.32), residues: 264 loop : -2.30 (0.25), residues: 630 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 1.292 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 206 average time/residue: 0.1886 time to fit residues: 60.4143 Evaluate side-chains 194 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1111 time to fit residues: 3.4515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 HIS ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11296 Z= 0.223 Angle : 0.655 8.130 15412 Z= 0.320 Chirality : 0.042 0.150 1726 Planarity : 0.006 0.045 1978 Dihedral : 5.080 60.590 1528 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.62 % Favored : 90.23 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.20 (0.24), residues: 1382 helix: 2.97 (0.23), residues: 488 sheet: -0.18 (0.32), residues: 264 loop : -2.19 (0.25), residues: 630 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 196 time to evaluate : 1.261 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 210 average time/residue: 0.1886 time to fit residues: 61.8740 Evaluate side-chains 196 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1103 time to fit residues: 3.5980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11296 Z= 0.186 Angle : 0.651 8.577 15412 Z= 0.313 Chirality : 0.042 0.293 1726 Planarity : 0.005 0.041 1978 Dihedral : 4.828 30.975 1528 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.17 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 (0.24), residues: 1382 helix: 3.11 (0.23), residues: 486 sheet: 0.06 (0.32), residues: 260 loop : -2.25 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 1.329 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 199 average time/residue: 0.1895 time to fit residues: 57.8155 Evaluate side-chains 198 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 187 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1201 time to fit residues: 4.1499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11296 Z= 0.191 Angle : 0.649 8.449 15412 Z= 0.311 Chirality : 0.042 0.262 1726 Planarity : 0.005 0.044 1978 Dihedral : 4.763 30.681 1528 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.19 % Favored : 90.67 % Rotamer Outliers : 1.02 % 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: 0.37 (0.24), residues: 1382 helix: 3.14 (0.23), residues: 486 sheet: 0.11 (0.32), residues: 260 loop : -2.19 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.363 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 200 average time/residue: 0.1921 time to fit residues: 59.9495 Evaluate side-chains 191 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1174 time to fit residues: 3.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 129 optimal weight: 0.0470 chunk 75 optimal weight: 0.0770 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.0000 overall best weight: 0.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 11296 Z= 0.137 Angle : 0.631 8.112 15412 Z= 0.300 Chirality : 0.041 0.258 1726 Planarity : 0.005 0.044 1978 Dihedral : 4.633 30.228 1528 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.45 % Favored : 92.40 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.62 (0.25), residues: 1382 helix: 3.21 (0.24), residues: 488 sheet: 0.40 (0.33), residues: 256 loop : -1.99 (0.26), residues: 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.319 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 184 average time/residue: 0.1858 time to fit residues: 53.0631 Evaluate side-chains 175 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1004 time to fit residues: 1.9618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 11296 Z= 0.162 Angle : 0.637 11.297 15412 Z= 0.301 Chirality : 0.041 0.251 1726 Planarity : 0.005 0.043 1978 Dihedral : 4.553 29.786 1528 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer Outliers : 0.42 % 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: 0.56 (0.25), residues: 1382 helix: 3.08 (0.24), residues: 502 sheet: 0.37 (0.33), residues: 256 loop : -2.07 (0.26), residues: 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 1.389 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 184 average time/residue: 0.1902 time to fit residues: 53.8227 Evaluate side-chains 182 residues out of total 1202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1260 time to fit residues: 2.2717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082008 restraints weight = 19137.506| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.17 r_work: 0.3004 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 85 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11296 Z= 0.225 Angle : 0.656 7.982 15412 Z= 0.316 Chirality : 0.042 0.244 1726 Planarity : 0.005 0.042 1978 Dihedral : 4.590 30.284 1528 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.83 % Favored : 91.03 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1382 helix: 3.06 (0.24), residues: 498 sheet: 0.02 (0.32), residues: 254 loop : -2.07 (0.25), residues: 630 =============================================================================== Job complete usr+sys time: 2279.24 seconds wall clock time: 42 minutes 7.47 seconds (2527.47 seconds total)