Starting phenix.real_space_refine on Tue Feb 13 22:49:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_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_23815/02_2024/7mff_23815_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mff_23815/02_2024/7mff_23815_updated.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-dev-5238/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: 4.58, per 1000 atoms: 0.57 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: 3.39 Conformation dependent library (CDL) restraints added in 1.6 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: 1.39 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: 2.04 Time building geometry restraints manager: 3.62 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.020 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.770 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- 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 % Allowed : 0.23 % Favored : 99.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 450 HIS 0.003 0.001 HIS C 164 PHE 0.026 0.001 PHE C 196 TYR 0.019 0.001 TYR D 179 ARG 0.009 0.000 ARG C 80 *********************** 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 : 0.961 Fit side-chains revert: symmetry clash REVERT: C 80 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7893 (mtp-110) REVERT: D 98 LEU cc_start: 0.8275 (mt) cc_final: 0.8059 (mt) REVERT: D 121 MET cc_start: 0.7457 (ttt) cc_final: 0.7115 (ttm) REVERT: D 211 TYR cc_start: 0.6372 (p90) cc_final: 0.6159 (p90) REVERT: A 566 TYR cc_start: 0.8900 (t80) cc_final: 0.8589 (t80) outliers start: 1 outliers final: 1 residues processed: 208 average time/residue: 0.2014 time to fit residues: 56.3089 Evaluate side-chains 171 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 684 ASN 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: 8.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8154 Z= 0.208 Angle : 0.607 11.255 11008 Z= 0.312 Chirality : 0.042 0.146 1218 Planarity : 0.004 0.046 1403 Dihedral : 5.042 40.908 1106 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.87 % Allowed : 10.88 % Favored : 87.25 % 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: 0.55 (0.27), residues: 980 helix: 1.52 (0.21), residues: 563 sheet: -1.36 (0.72), residues: 49 loop : -1.22 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 59 HIS 0.003 0.001 HIS C 164 PHE 0.017 0.002 PHE D 174 TYR 0.020 0.002 TYR D 128 ARG 0.008 0.000 ARG D 91 *********************** 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 197 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 59 TRP cc_start: 0.7553 (t60) cc_final: 0.7301 (t60) REVERT: D 211 TYR cc_start: 0.6342 (p90) cc_final: 0.6106 (p90) REVERT: A 533 GLU cc_start: 0.7804 (pp20) cc_final: 0.7578 (pp20) REVERT: A 566 TYR cc_start: 0.8934 (t80) cc_final: 0.8552 (t80) REVERT: A 582 ILE cc_start: 0.9293 (mm) cc_final: 0.9089 (mm) REVERT: A 638 ASP cc_start: 0.8188 (t0) cc_final: 0.7928 (t0) REVERT: B 597 LEU cc_start: 0.7494 (tp) cc_final: 0.7192 (tp) outliers start: 16 outliers final: 11 residues processed: 190 average time/residue: 0.1904 time to fit residues: 50.0998 Evaluate side-chains 170 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 539 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8154 Z= 0.178 Angle : 0.552 6.905 11008 Z= 0.282 Chirality : 0.040 0.137 1218 Planarity : 0.004 0.047 1403 Dihedral : 4.973 43.770 1106 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.11 % Allowed : 14.27 % Favored : 83.63 % 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: 1.58 (0.21), residues: 572 sheet: -1.28 (0.72), residues: 49 loop : -1.19 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 59 HIS 0.009 0.001 HIS B 539 PHE 0.029 0.002 PHE B 642 TYR 0.015 0.002 TYR D 125 ARG 0.009 0.000 ARG C 80 *********************** 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 192 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 162 PRO cc_start: 0.8667 (Cg_exo) cc_final: 0.8451 (Cg_endo) REVERT: D 211 TYR cc_start: 0.6325 (p90) cc_final: 0.6023 (p90) REVERT: A 566 TYR cc_start: 0.8994 (t80) cc_final: 0.8600 (t80) REVERT: A 709 GLN cc_start: 0.7757 (mp10) cc_final: 0.7425 (mp10) REVERT: B 508 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7935 (t) outliers start: 18 outliers final: 9 residues processed: 183 average time/residue: 0.1939 time to fit residues: 50.0523 Evaluate side-chains 173 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 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 B 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8154 Z= 0.222 Angle : 0.583 6.656 11008 Z= 0.300 Chirality : 0.041 0.159 1218 Planarity : 0.004 0.039 1403 Dihedral : 5.004 44.801 1104 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.69 % Allowed : 16.84 % Favored : 80.47 % 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: 0.68 (0.27), residues: 980 helix: 1.61 (0.21), residues: 572 sheet: -1.25 (0.71), residues: 50 loop : -1.23 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 59 HIS 0.005 0.001 HIS C 164 PHE 0.018 0.002 PHE D 174 TYR 0.023 0.002 TYR B 566 ARG 0.006 0.001 ARG A 506 *********************** 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 196 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 1.004 Fit side-chains REVERT: C 155 ILE cc_start: 0.7608 (tp) cc_final: 0.7281 (mt) REVERT: A 566 TYR cc_start: 0.9058 (t80) cc_final: 0.8698 (t80) REVERT: A 578 LYS cc_start: 0.8443 (pttp) cc_final: 0.8038 (pttm) REVERT: A 654 LEU cc_start: 0.8065 (tt) cc_final: 0.7224 (mt) REVERT: B 508 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7885 (t) outliers start: 23 outliers final: 14 residues processed: 188 average time/residue: 0.1891 time to fit residues: 48.8858 Evaluate side-chains 171 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8154 Z= 0.168 Angle : 0.567 9.131 11008 Z= 0.290 Chirality : 0.040 0.144 1218 Planarity : 0.004 0.039 1403 Dihedral : 4.937 46.112 1104 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.46 % Allowed : 18.71 % Favored : 78.83 % 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: 0.79 (0.27), residues: 980 helix: 1.75 (0.21), residues: 565 sheet: -1.23 (0.71), residues: 50 loop : -1.20 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 59 HIS 0.006 0.001 HIS A 542 PHE 0.015 0.002 PHE C 196 TYR 0.015 0.001 TYR D 125 ARG 0.006 0.000 ARG C 80 *********************** 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 190 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 0.945 Fit side-chains REVERT: C 17 GLU cc_start: 0.7784 (mp0) cc_final: 0.7565 (mp0) REVERT: C 155 ILE cc_start: 0.7671 (tp) cc_final: 0.7375 (mt) REVERT: D 218 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7398 (mmm) REVERT: A 578 LYS cc_start: 0.8507 (pttp) cc_final: 0.7703 (pttp) REVERT: A 664 GLN cc_start: 0.4100 (OUTLIER) cc_final: 0.3538 (pp30) REVERT: A 714 ILE cc_start: 0.8348 (mm) cc_final: 0.8133 (mm) REVERT: B 508 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7821 (t) REVERT: B 550 MET cc_start: 0.8421 (mmm) cc_final: 0.8201 (tpp) REVERT: B 597 LEU cc_start: 0.7956 (tp) cc_final: 0.7700 (tp) REVERT: B 703 GLU cc_start: 0.6531 (pt0) cc_final: 0.5794 (pt0) outliers start: 21 outliers final: 9 residues processed: 182 average time/residue: 0.1893 time to fit residues: 47.4574 Evaluate side-chains 169 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 664 GLN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2520 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= 0.160 Angle : 0.553 9.861 11008 Z= 0.284 Chirality : 0.041 0.147 1218 Planarity : 0.003 0.037 1403 Dihedral : 4.881 46.856 1104 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.81 % Allowed : 18.71 % Favored : 78.48 % 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: 0.82 (0.27), residues: 980 helix: 1.74 (0.21), residues: 568 sheet: -1.16 (0.72), residues: 50 loop : -1.16 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 59 HIS 0.005 0.001 HIS C 164 PHE 0.017 0.002 PHE C 196 TYR 0.016 0.001 TYR D 179 ARG 0.004 0.000 ARG D 167 *********************** 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 193 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 0.955 Fit side-chains REVERT: C 155 ILE cc_start: 0.7773 (tp) cc_final: 0.7521 (mt) REVERT: D 218 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: A 578 LYS cc_start: 0.8384 (pttp) cc_final: 0.7545 (pttp) REVERT: A 714 ILE cc_start: 0.8342 (mm) cc_final: 0.8132 (mm) REVERT: B 508 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7836 (t) REVERT: B 703 GLU cc_start: 0.6455 (pt0) cc_final: 0.5858 (pt0) outliers start: 24 outliers final: 12 residues processed: 184 average time/residue: 0.1861 time to fit residues: 47.4388 Evaluate side-chains 169 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 0.0970 chunk 59 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.2794 ------------------------------------------------------------------------------- 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 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: 0.7117 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8154 Z= 0.143 Angle : 0.548 6.877 11008 Z= 0.283 Chirality : 0.040 0.172 1218 Planarity : 0.003 0.036 1403 Dihedral : 4.811 49.476 1104 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.75 % Allowed : 20.47 % Favored : 77.78 % 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: 1.86 (0.22), residues: 564 sheet: -1.23 (0.72), residues: 50 loop : -1.12 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 59 HIS 0.004 0.001 HIS B 568 PHE 0.020 0.002 PHE C 196 TYR 0.022 0.001 TYR A 538 ARG 0.007 0.000 ARG C 80 *********************** 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 191 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 0.940 Fit side-chains REVERT: C 155 ILE cc_start: 0.7773 (tp) cc_final: 0.7505 (mt) REVERT: D 211 TYR cc_start: 0.5570 (p90) cc_final: 0.4828 (p90) REVERT: B 508 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8055 (t) REVERT: B 703 GLU cc_start: 0.6387 (pt0) cc_final: 0.5824 (pt0) outliers start: 15 outliers final: 5 residues processed: 183 average time/residue: 0.1895 time to fit residues: 48.2251 Evaluate side-chains 164 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 ASN ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8154 Z= 0.222 Angle : 0.603 8.140 11008 Z= 0.310 Chirality : 0.042 0.202 1218 Planarity : 0.004 0.040 1403 Dihedral : 4.992 48.867 1104 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.75 % Allowed : 21.40 % Favored : 76.84 % 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: 0.79 (0.27), residues: 980 helix: 1.74 (0.21), residues: 571 sheet: -1.14 (0.74), residues: 50 loop : -1.27 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 619 HIS 0.007 0.001 HIS A 542 PHE 0.022 0.002 PHE B 642 TYR 0.035 0.002 TYR A 538 ARG 0.005 0.000 ARG D 167 *********************** 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 180 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 0.882 Fit side-chains REVERT: C 155 ILE cc_start: 0.7810 (tp) cc_final: 0.7530 (mt) REVERT: C 160 MET cc_start: 0.6296 (mtm) cc_final: 0.6045 (mtm) REVERT: D 211 TYR cc_start: 0.5761 (p90) cc_final: 0.5052 (p90) REVERT: A 578 LYS cc_start: 0.8656 (pttp) cc_final: 0.7648 (pttp) REVERT: A 627 MET cc_start: 0.4088 (tpt) cc_final: 0.3830 (tpt) REVERT: A 714 ILE cc_start: 0.8340 (mm) cc_final: 0.8132 (mm) REVERT: B 508 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7882 (t) REVERT: B 543 ILE cc_start: 0.6524 (mm) cc_final: 0.6311 (mm) REVERT: B 668 MET cc_start: 0.7429 (mtt) cc_final: 0.6870 (tpp) REVERT: B 703 GLU cc_start: 0.6563 (pt0) cc_final: 0.5963 (pt0) outliers start: 15 outliers final: 11 residues processed: 174 average time/residue: 0.1954 time to fit residues: 46.4807 Evaluate side-chains 168 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 623 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 ** 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 ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8154 Z= 0.177 Angle : 0.604 10.077 11008 Z= 0.306 Chirality : 0.041 0.179 1218 Planarity : 0.004 0.040 1403 Dihedral : 4.943 49.730 1104 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.64 % Allowed : 21.64 % Favored : 76.73 % 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: 0.89 (0.27), residues: 980 helix: 1.82 (0.21), residues: 570 sheet: -1.09 (0.74), residues: 50 loop : -1.21 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 619 HIS 0.006 0.001 HIS A 542 PHE 0.018 0.002 PHE B 642 TYR 0.018 0.001 TYR D 179 ARG 0.007 0.000 ARG C 80 *********************** 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 178 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.944 Fit side-chains REVERT: C 155 ILE cc_start: 0.7794 (tp) cc_final: 0.7512 (mt) REVERT: C 160 MET cc_start: 0.6302 (mtm) cc_final: 0.6066 (mtm) REVERT: D 211 TYR cc_start: 0.5584 (p90) cc_final: 0.4911 (p90) REVERT: B 508 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7827 (t) REVERT: B 668 MET cc_start: 0.7244 (mtt) cc_final: 0.6813 (tpp) REVERT: B 703 GLU cc_start: 0.6406 (pt0) cc_final: 0.5819 (pt0) outliers start: 14 outliers final: 8 residues processed: 172 average time/residue: 0.1901 time to fit residues: 44.9341 Evaluate side-chains 166 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU 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: 5.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.0370 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8062 ------------------------------------------------------------------------------- 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 ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2939 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= 0.171 Angle : 0.648 18.094 11008 Z= 0.316 Chirality : 0.042 0.168 1218 Planarity : 0.004 0.039 1403 Dihedral : 4.938 51.670 1104 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.64 % Allowed : 22.22 % Favored : 76.14 % 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: 0.91 (0.27), residues: 980 helix: 1.83 (0.21), residues: 569 sheet: -1.03 (0.75), residues: 50 loop : -1.18 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 619 HIS 0.008 0.001 HIS A 542 PHE 0.023 0.002 PHE C 196 TYR 0.017 0.001 TYR D 179 ARG 0.005 0.000 ARG D 167 ********************** 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 178 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 0.890 Fit side-chains REVERT: C 155 ILE cc_start: 0.7874 (tp) cc_final: 0.7581 (mt) REVERT: D 211 TYR cc_start: 0.5485 (p90) cc_final: 0.4844 (p90) REVERT: A 627 MET cc_start: 0.3947 (tpt) cc_final: 0.3741 (tpt) REVERT: B 508 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8037 (t) REVERT: B 668 MET cc_start: 0.7171 (mtt) cc_final: 0.6832 (tpp) REVERT: B 703 GLU cc_start: 0.6357 (pt0) cc_final: 0.5785 (pt0) outliers start: 14 outliers final: 8 residues processed: 171 average time/residue: 0.1770 time to fit residues: 41.8888 Evaluate side-chains 163 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 577 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.164921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140134 restraints weight = 13115.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141710 restraints weight = 10807.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.143118 restraints weight = 8466.153| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8154 Z= 0.166 Angle : 0.636 16.432 11008 Z= 0.315 Chirality : 0.041 0.151 1218 Planarity : 0.004 0.040 1403 Dihedral : 4.954 53.524 1104 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.05 % Allowed : 22.34 % Favored : 76.61 % 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: 0.87 (0.27), residues: 980 helix: 1.80 (0.21), residues: 570 sheet: -1.00 (0.74), residues: 50 loop : -1.22 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 619 HIS 0.007 0.001 HIS A 574 PHE 0.028 0.002 PHE C 196 TYR 0.017 0.001 TYR D 179 ARG 0.009 0.000 ARG C 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.55 seconds wall clock time: 33 minutes 51.33 seconds (2031.33 seconds total)