Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 16:59:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/04_2023/7mff_23815_updated.pdb" } resolution = 3.89 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= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 45 5.16 5 C 5084 2.51 5 N 1366 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 96": "OD1" <-> "OD2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2": "OD1" <-> "OD2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 224} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2163 Classifications: {'peptide': 271} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 257} Chain breaks: 1 Chain: "B" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2171 Classifications: {'peptide': 272} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'215': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'215': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.58 Number of scatterers: 8003 At special positions: 0 Unit cell: (102.448, 106.492, 106.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 2 15.00 O 1506 8.00 N 1366 7.00 C 5084 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: 3.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1902 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 4 sheets defined 57.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.741A pdb=" N GLN C 15 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 32 removed outlier: 3.608A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 29 " --> pdb=" O CYS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 67 removed outlier: 3.808A pdb=" N ARG C 55 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 104 removed outlier: 3.576A pdb=" N ARG C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU C 81 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 82 " --> pdb=" O MET C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 132 removed outlier: 3.639A pdb=" N VAL C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 159 removed outlier: 3.985A pdb=" N GLY C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 removed outlier: 3.504A pdb=" N TYR C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.558A pdb=" N PHE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 229 removed outlier: 3.877A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 215 " --> pdb=" O TYR C 211 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 217 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 19 through 32 removed outlier: 3.838A pdb=" N GLN D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 68 removed outlier: 3.577A pdb=" N VAL D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 55 " --> pdb=" O VAL D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 103 removed outlier: 3.511A pdb=" N THR D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 130 removed outlier: 3.520A pdb=" N ASP D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR D 125 " --> pdb=" O MET D 121 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 159 removed outlier: 3.636A pdb=" N GLY D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 148 " --> pdb=" O GLN D 144 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU D 159 " --> pdb=" O ILE D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 removed outlier: 3.834A pdb=" N PHE D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 200 Processing helix chain 'D' and resid 211 through 228 Processing helix chain 'A' and resid 492 through 507 removed outlier: 3.907A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 500 " --> pdb=" O GLN A 496 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.655A pdb=" N TYR A 566 " --> pdb=" O GLN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 635 through 651 Processing helix chain 'A' and resid 663 through 670 removed outlier: 3.783A pdb=" N PHE A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 707 through 719 removed outlier: 3.620A pdb=" N ARG A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 507 removed outlier: 4.064A pdb=" N LYS B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 550 through 569 Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 622 through 625 No H-bonds generated for 'chain 'B' and resid 622 through 625' Processing helix chain 'B' and resid 635 through 651 removed outlier: 3.527A pdb=" N VAL B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 670 removed outlier: 3.862A pdb=" N PHE B 667 " --> pdb=" O ASP B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 696 Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 707 through 720 removed outlier: 3.551A pdb=" N ALA B 712 " --> pdb=" O PRO B 708 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 516 through 520 removed outlier: 6.967A pdb=" N VAL A 528 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR A 519 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 526 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 464 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 473 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG A 462 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.600A pdb=" N SER A 535 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 516 through 520 removed outlier: 6.584A pdb=" N VAL B 528 " --> pdb=" O MET B 517 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR B 519 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 526 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 527 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 464 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B 473 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ARG B 462 " --> pdb=" O LYS B 473 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 582 through 585 404 hydrogen bonds defined for protein. 1200 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: 1.93 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2613 1.34 - 1.46: 1779 1.46 - 1.58: 3675 1.58 - 1.70: 9 1.70 - 1.81: 78 Bond restraints: 8154 Sorted by residual: bond pdb=" C2 215 A 801 " pdb=" C7 215 A 801 " ideal model delta sigma weight residual 1.389 1.477 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C2 215 B 801 " pdb=" C7 215 B 801 " ideal model delta sigma weight residual 1.389 1.476 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C3 215 A 801 " pdb=" C8 215 A 801 " ideal model delta sigma weight residual 1.391 1.477 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C3 215 B 801 " pdb=" C8 215 B 801 " ideal model delta sigma weight residual 1.391 1.477 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C28 215 A 801 " pdb=" C32 215 A 801 " ideal model delta sigma weight residual 1.553 1.470 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 8149 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.88: 158 105.88 - 112.90: 4384 112.90 - 119.93: 2755 119.93 - 126.96: 3624 126.96 - 133.98: 87 Bond angle restraints: 11008 Sorted by residual: angle pdb=" CA PRO D 162 " pdb=" N PRO D 162 " pdb=" CD PRO D 162 " ideal model delta sigma weight residual 112.00 104.95 7.05 1.40e+00 5.10e-01 2.53e+01 angle pdb=" C HIS B 585 " pdb=" N GLU B 586 " pdb=" CA GLU B 586 " ideal model delta sigma weight residual 122.07 126.12 -4.05 1.43e+00 4.89e-01 8.01e+00 angle pdb=" CA GLU B 586 " pdb=" CB GLU B 586 " pdb=" CG GLU B 586 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.26e+00 angle pdb=" C3 215 A 801 " pdb=" C2 215 A 801 " pdb=" C7 215 A 801 " ideal model delta sigma weight residual 126.01 133.90 -7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C3 215 B 801 " pdb=" C2 215 B 801 " pdb=" C7 215 B 801 " ideal model delta sigma weight residual 126.01 133.75 -7.74 3.00e+00 1.11e-01 6.66e+00 ... (remaining 11003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4390 17.99 - 35.98: 461 35.98 - 53.97: 89 53.97 - 71.96: 18 71.96 - 89.95: 6 Dihedral angle restraints: 4964 sinusoidal: 2029 harmonic: 2935 Sorted by residual: dihedral pdb=" CA SER B 616 " pdb=" C SER B 616 " pdb=" N ILE B 617 " pdb=" CA ILE B 617 " ideal model delta harmonic sigma weight residual -180.00 -159.51 -20.49 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA GLU B 730 " pdb=" C GLU B 730 " pdb=" N PRO B 731 " pdb=" CA PRO B 731 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP B 449 " pdb=" CB ASP B 449 " pdb=" CG ASP B 449 " pdb=" OD1 ASP B 449 " ideal model delta sinusoidal sigma weight residual -30.00 -86.33 56.33 1 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 763 0.030 - 0.060: 332 0.060 - 0.090: 74 0.090 - 0.120: 45 0.120 - 0.150: 4 Chirality restraints: 1218 Sorted by residual: chirality pdb=" CA PRO D 162 " pdb=" N PRO D 162 " pdb=" C PRO D 162 " pdb=" CB PRO D 162 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A 582 " pdb=" N ILE A 582 " pdb=" C ILE A 582 " pdb=" CB ILE A 582 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 513 " pdb=" N ILE B 513 " pdb=" C ILE B 513 " pdb=" CB ILE B 513 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1215 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 215 A 801 " 0.029 2.00e-02 2.50e+03 3.83e-02 3.29e+01 pdb=" C11 215 A 801 " 0.038 2.00e-02 2.50e+03 pdb=" C28 215 A 801 " -0.000 2.00e-02 2.50e+03 pdb=" C29 215 A 801 " 0.007 2.00e-02 2.50e+03 pdb=" C3 215 A 801 " -0.065 2.00e-02 2.50e+03 pdb=" C30 215 A 801 " 0.032 2.00e-02 2.50e+03 pdb=" C32 215 A 801 " -0.072 2.00e-02 2.50e+03 pdb=" C8 215 A 801 " 0.017 2.00e-02 2.50e+03 pdb=" C9 215 A 801 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN D 161 " -0.054 5.00e-02 4.00e+02 7.80e-02 9.72e+00 pdb=" N PRO D 162 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 162 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 162 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 675 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 676 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 676 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 676 " -0.023 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 440 2.73 - 3.28: 8492 3.28 - 3.82: 12977 3.82 - 4.36: 15432 4.36 - 4.90: 25950 Nonbonded interactions: 63291 Sorted by model distance: nonbonded pdb=" O TYR B 647 " pdb=" OG1 THR B 651 " model vdw 2.193 2.440 nonbonded pdb=" OH TYR B 647 " pdb=" O ASP B 677 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR C 128 " pdb=" O3P SEP A 729 " model vdw 2.213 2.440 nonbonded pdb=" O GLU C 186 " pdb=" OG SER C 190 " model vdw 2.230 2.440 nonbonded pdb=" OD1 ASP B 576 " pdb=" NZ LYS B 578 " model vdw 2.235 2.520 ... (remaining 63286 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' and (resid 449 through 732 or resid 801)) } ncs_group { reference = (chain 'C' and (resid 2 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 through 70 or (resid 73 and (name N or name \ CA or name C or name O or name CB )) or resid 74 or (resid 75 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name CE )) or resi \ d 76 through 79 or (resid 80 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 81 through 135 or (resid 136 and (name N or name CA or \ name C or name O or name CB )) or resid 137 through 138 or (resid 139 and (name \ N or name CA or name C or name O or name CB )) or resid 140 through 156 or (res \ id 157 and (name N or name CA or name C or name O or name CB or name CG )) or (r \ esid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 t \ hrough 207 or (resid 208 and (name N or name CA or name C or name O or name CB ) \ ) or resid 209 through 211 or (resid 212 and (name N or name CA or name C or nam \ e O or name CB )) or resid 213 through 230)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 7 or (resid 8 through 10 and (name N or name CA o \ r name C or name O or name CB )) or resid 11 through 76 or (resid 77 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 78 through 230 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 1.310 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 23.690 Find NCS groups from input model: 0.430 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 : 0.004 0.100 8154 Z= 0.269 Angle : 0.579 7.885 11008 Z= 0.288 Chirality : 0.038 0.150 1218 Planarity : 0.004 0.078 1403 Dihedral : 15.242 89.955 3062 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.27), residues: 980 helix: 0.77 (0.22), residues: 553 sheet: -1.59 (0.72), residues: 50 loop : -1.01 (0.32), residues: 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.073 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.2083 time to fit residues: 58.1872 Evaluate side-chains 173 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0752 time to fit residues: 1.4999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 219 GLN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8154 Z= 0.216 Angle : 0.618 11.728 11008 Z= 0.316 Chirality : 0.042 0.157 1218 Planarity : 0.004 0.047 1403 Dihedral : 5.033 41.177 1104 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.50 (0.27), residues: 980 helix: 1.45 (0.21), residues: 564 sheet: -1.34 (0.73), residues: 49 loop : -1.21 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 192 average time/residue: 0.1969 time to fit residues: 51.6402 Evaluate side-chains 170 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0745 time to fit residues: 2.7054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 0.0010 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN B 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8154 Z= 0.162 Angle : 0.551 7.026 11008 Z= 0.282 Chirality : 0.040 0.138 1218 Planarity : 0.004 0.046 1403 Dihedral : 4.899 44.101 1104 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.67 (0.27), residues: 980 helix: 1.60 (0.21), residues: 571 sheet: -1.29 (0.72), residues: 49 loop : -1.20 (0.33), residues: 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 185 average time/residue: 0.1988 time to fit residues: 50.1633 Evaluate side-chains 160 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 0.975 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0797 time to fit residues: 1.9686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 0.0030 chunk 78 optimal weight: 10.0000 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8154 Z= 0.175 Angle : 0.551 5.706 11008 Z= 0.285 Chirality : 0.040 0.153 1218 Planarity : 0.003 0.039 1403 Dihedral : 4.921 44.974 1104 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.78 (0.27), residues: 980 helix: 1.70 (0.21), residues: 572 sheet: -1.29 (0.70), residues: 50 loop : -1.17 (0.33), residues: 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.036 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 179 average time/residue: 0.1941 time to fit residues: 47.8904 Evaluate side-chains 162 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 157 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0755 time to fit residues: 2.0810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8154 Z= 0.147 Angle : 0.538 7.974 11008 Z= 0.277 Chirality : 0.040 0.142 1218 Planarity : 0.003 0.037 1403 Dihedral : 4.831 46.801 1104 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.93 (0.27), residues: 980 helix: 1.84 (0.21), residues: 568 sheet: -1.25 (0.70), residues: 50 loop : -1.12 (0.33), residues: 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.035 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 180 average time/residue: 0.1822 time to fit residues: 46.3909 Evaluate side-chains 158 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0770 time to fit residues: 1.6187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN D 146 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8154 Z= 0.162 Angle : 0.561 13.358 11008 Z= 0.285 Chirality : 0.040 0.142 1218 Planarity : 0.003 0.042 1403 Dihedral : 4.823 46.419 1104 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.93 (0.27), residues: 980 helix: 1.86 (0.21), residues: 567 sheet: -1.22 (0.71), residues: 50 loop : -1.15 (0.33), residues: 363 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.056 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 179 average time/residue: 0.1956 time to fit residues: 48.2920 Evaluate side-chains 160 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0828 time to fit residues: 1.9500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN B 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 8154 Z= 0.161 Angle : 0.574 13.696 11008 Z= 0.289 Chirality : 0.041 0.161 1218 Planarity : 0.003 0.043 1403 Dihedral : 4.816 46.981 1104 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.92 (0.27), residues: 980 helix: 1.85 (0.21), residues: 563 sheet: -1.20 (0.72), residues: 50 loop : -1.12 (0.32), residues: 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 169 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 174 average time/residue: 0.1886 time to fit residues: 46.1215 Evaluate side-chains 162 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0769 time to fit residues: 1.4333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 8154 Z= 0.164 Angle : 0.592 13.898 11008 Z= 0.295 Chirality : 0.041 0.181 1218 Planarity : 0.004 0.042 1403 Dihedral : 4.822 47.137 1104 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 980 helix: 1.84 (0.22), residues: 564 sheet: -1.18 (0.72), residues: 50 loop : -1.07 (0.33), residues: 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 167 average time/residue: 0.1788 time to fit residues: 42.1788 Evaluate side-chains 164 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0883 time to fit residues: 1.7468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 chunk 83 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8154 Z= 0.161 Angle : 0.598 14.921 11008 Z= 0.296 Chirality : 0.041 0.166 1218 Planarity : 0.004 0.042 1403 Dihedral : 4.838 49.095 1104 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.97 (0.27), residues: 980 helix: 1.87 (0.22), residues: 562 sheet: -1.07 (0.73), residues: 50 loop : -1.07 (0.33), residues: 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.049 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 178 average time/residue: 0.1878 time to fit residues: 46.6855 Evaluate side-chains 170 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 8154 Z= 0.161 Angle : 0.594 14.731 11008 Z= 0.297 Chirality : 0.041 0.159 1218 Planarity : 0.003 0.041 1403 Dihedral : 4.855 50.570 1104 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.96 (0.27), residues: 980 helix: 1.85 (0.21), residues: 568 sheet: -1.08 (0.74), residues: 50 loop : -1.11 (0.33), residues: 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1960 Ramachandran restraints generated. 980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 179 average time/residue: 0.1985 time to fit residues: 49.2877 Evaluate side-chains 170 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0750 time to fit residues: 1.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 GLN ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141897 restraints weight = 13127.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142500 restraints weight = 9711.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142574 restraints weight = 8159.316| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8154 Z= 0.177 Angle : 0.626 15.000 11008 Z= 0.310 Chirality : 0.041 0.154 1218 Planarity : 0.004 0.041 1403 Dihedral : 4.918 52.419 1104 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 980 helix: 1.73 (0.21), residues: 570 sheet: -1.11 (0.74), residues: 50 loop : -1.09 (0.33), residues: 360 =============================================================================== Job complete usr+sys time: 1720.28 seconds wall clock time: 32 minutes 6.05 seconds (1926.05 seconds total)