Starting phenix.real_space_refine on Fri Nov 15 05:08:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/11_2024/8bpb_16148_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/11_2024/8bpb_16148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/11_2024/8bpb_16148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/11_2024/8bpb_16148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/11_2024/8bpb_16148_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpb_16148/11_2024/8bpb_16148_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 3 6.06 5 S 55 5.16 5 C 5329 2.51 5 N 1447 2.21 5 O 1548 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8384 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 113} Chain breaks: 1 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 7 Unusual residues: {' CA': 2, ' ZN': 1, 'ACT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7743 SG CYS C 289 37.781 59.224 44.747 1.00 57.24 S ATOM 7769 SG CYS C 292 35.184 57.659 42.331 1.00 45.08 S ATOM 7952 SG CYS C 315 38.825 56.578 42.087 1.00 59.56 S ATOM 7627 SG CYS C 274 37.775 47.115 47.263 1.00 38.25 S ATOM 7651 SG CYS C 277 37.170 43.505 48.360 1.00 48.40 S ATOM 7835 SG CYS C 300 40.704 44.735 47.787 1.00 41.17 S Time building chain proxies: 5.26, per 1000 atoms: 0.63 Number of scatterers: 8384 At special positions: 0 Unit cell: (122.094, 92.34, 109.782, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Ca 2 19.99 S 55 16.00 O 1548 8.00 N 1447 7.00 C 5329 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 - 3.00 Amino acid : True - 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: 2.89 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " Number of angles added : 6 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 4 sheets defined 59.0% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.862A pdb=" N PHE A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.795A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 4.222A pdb=" N GLU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 Processing helix chain 'A' and resid 530 through 561 Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 563 through 573 removed outlier: 5.035A pdb=" N LEU A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.095A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.557A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.626A pdb=" N LEU A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 661 through 667 Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.652A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 808 through 829 removed outlier: 5.040A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 852 removed outlier: 4.708A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.530A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 887 " --> pdb=" O ASN A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 915 removed outlier: 5.412A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.725A pdb=" N TYR B 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 46 removed outlier: 3.923A pdb=" N ARG B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.114A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 87 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.702A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.582A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.618A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 278 through 292 removed outlier: 4.069A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.648A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 372 Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 319 through 324 removed outlier: 3.714A pdb=" N VAL C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.616A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.718A pdb=" N ILE A 397 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 4.314A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.618A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 258 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B 299 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 260 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 171 " --> pdb=" O MET B 195 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL B 197 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR B 173 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE B 199 " --> pdb=" O TYR B 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 175 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LYS B 201 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL B 225 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N PHE B 227 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER B 198 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N MET B 229 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N HIS B 200 " --> pdb=" O MET B 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 286 through 288 425 hydrogen bonds defined for protein. 1233 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: 2.23 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2745 1.34 - 1.46: 1962 1.46 - 1.58: 3767 1.58 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8556 Sorted by residual: bond pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N LYS C 32 " pdb=" CA LYS C 32 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.43e+00 bond pdb=" N CYS A 788 " pdb=" CA CYS A 788 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.33e+00 bond pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" N LEU A 787 " pdb=" CA LEU A 787 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.22e-02 6.72e+03 6.18e+00 ... (remaining 8551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11358 2.13 - 4.25: 164 4.25 - 6.38: 19 6.38 - 8.51: 3 8.51 - 10.63: 1 Bond angle restraints: 11545 Sorted by residual: angle pdb=" O PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 121.31 117.41 3.90 4.60e-01 4.73e+00 7.20e+01 angle pdb=" CA PRO C 30 " pdb=" C PRO C 30 " pdb=" N PRO C 31 " ideal model delta sigma weight residual 117.73 121.74 -4.01 9.00e-01 1.23e+00 1.99e+01 angle pdb=" C GLU A 789 " pdb=" CA GLU A 789 " pdb=" CB GLU A 789 " ideal model delta sigma weight residual 116.63 111.50 5.13 1.16e+00 7.43e-01 1.96e+01 angle pdb=" N CYS A 788 " pdb=" CA CYS A 788 " pdb=" C CYS A 788 " ideal model delta sigma weight residual 113.28 108.13 5.15 1.22e+00 6.72e-01 1.78e+01 angle pdb=" CA GLU A 562 " pdb=" CB GLU A 562 " pdb=" CG GLU A 562 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 ... (remaining 11540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 4418 17.81 - 35.63: 528 35.63 - 53.44: 184 53.44 - 71.26: 33 71.26 - 89.07: 12 Dihedral angle restraints: 5175 sinusoidal: 2151 harmonic: 3024 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA GLU A 562 " pdb=" C GLU A 562 " pdb=" N GLN A 563 " pdb=" CA GLN A 563 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA TYR B 304 " pdb=" C TYR B 304 " pdb=" N THR B 305 " pdb=" CA THR B 305 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 787 0.034 - 0.067: 327 0.067 - 0.101: 81 0.101 - 0.135: 36 0.135 - 0.168: 2 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA LEU A 786 " pdb=" N LEU A 786 " pdb=" C LEU A 786 " pdb=" CB LEU A 786 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA GLU A 562 " pdb=" N GLU A 562 " pdb=" C GLU A 562 " pdb=" CB GLU A 562 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL B 171 " pdb=" N VAL B 171 " pdb=" C VAL B 171 " pdb=" CB VAL B 171 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1230 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 269 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO C 270 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 270 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 270 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 39 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C THR B 39 " -0.029 2.00e-02 2.50e+03 pdb=" O THR B 39 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS B 40 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 864 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C GLN A 864 " -0.026 2.00e-02 2.50e+03 pdb=" O GLN A 864 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 865 " 0.009 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 25 2.38 - 3.01: 4713 3.01 - 3.64: 12392 3.64 - 4.27: 19083 4.27 - 4.90: 31978 Nonbonded interactions: 68191 Sorted by model distance: nonbonded pdb=" O ASN B 22 " pdb=" O HOH B 601 " model vdw 1.755 3.040 nonbonded pdb="ZN ZN B 501 " pdb=" O ACT B 504 " model vdw 1.878 2.230 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 1.918 2.230 nonbonded pdb=" OD1 ASP B 177 " pdb="ZN ZN B 501 " model vdw 1.947 2.230 nonbonded pdb=" O HOH A1204 " pdb=" O HOH A1205 " model vdw 1.993 3.040 ... (remaining 68186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.030 Find NCS groups from input model: 0.070 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 0.064 8556 Z= 0.235 Angle : 0.614 10.634 11545 Z= 0.360 Chirality : 0.041 0.168 1233 Planarity : 0.004 0.047 1498 Dihedral : 17.771 89.069 3225 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.96 % Allowed : 24.59 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % 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: 0.64 (0.26), residues: 1016 helix: 1.17 (0.23), residues: 550 sheet: 0.78 (0.62), residues: 76 loop : -0.67 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 909 HIS 0.007 0.001 HIS A 867 PHE 0.012 0.001 PHE A 744 TYR 0.014 0.001 TYR B 304 ARG 0.004 0.000 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.975 Fit side-chains REVERT: A 449 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 668 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3499 (m-10) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 1.3272 time to fit residues: 164.5769 Evaluate side-chains 113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.0040 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN A 756 HIS B 226 ASN C 321 HIS C 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8556 Z= 0.158 Angle : 0.512 6.840 11545 Z= 0.273 Chirality : 0.039 0.150 1233 Planarity : 0.004 0.042 1498 Dihedral : 6.226 55.208 1165 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.95 % Allowed : 22.83 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1016 helix: 1.74 (0.22), residues: 564 sheet: 0.95 (0.63), residues: 76 loop : -0.60 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 749 HIS 0.006 0.001 HIS A 867 PHE 0.009 0.001 PHE A 662 TYR 0.013 0.001 TYR B 304 ARG 0.003 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7635 (t80) cc_final: 0.7338 (t80) REVERT: A 449 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7363 (mm-30) REVERT: A 668 PHE cc_start: 0.4296 (OUTLIER) cc_final: 0.3700 (m-10) REVERT: A 842 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: A 865 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7691 (mt) REVERT: A 867 HIS cc_start: 0.6945 (t70) cc_final: 0.6712 (t70) REVERT: A 937 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7810 (pt0) REVERT: C 302 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6997 (mm-30) outliers start: 36 outliers final: 21 residues processed: 126 average time/residue: 1.3538 time to fit residues: 181.1354 Evaluate side-chains 117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 347 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.0470 chunk 90 optimal weight: 0.0020 overall best weight: 0.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8556 Z= 0.125 Angle : 0.468 6.858 11545 Z= 0.247 Chirality : 0.038 0.142 1233 Planarity : 0.003 0.036 1498 Dihedral : 5.404 54.631 1155 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.51 % Allowed : 23.82 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1016 helix: 2.07 (0.23), residues: 558 sheet: 1.06 (0.63), residues: 76 loop : -0.49 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 909 HIS 0.004 0.001 HIS C 348 PHE 0.008 0.001 PHE A 365 TYR 0.011 0.001 TYR B 304 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.127 Fit side-chains REVERT: A 668 PHE cc_start: 0.4262 (OUTLIER) cc_final: 0.3655 (m-10) REVERT: A 865 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7724 (mt) REVERT: C 302 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7018 (mm-30) outliers start: 32 outliers final: 11 residues processed: 129 average time/residue: 1.3891 time to fit residues: 190.1454 Evaluate side-chains 106 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.1980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 GLN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8556 Z= 0.143 Angle : 0.476 7.486 11545 Z= 0.250 Chirality : 0.038 0.135 1233 Planarity : 0.003 0.035 1498 Dihedral : 5.107 56.017 1148 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.95 % Allowed : 23.60 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.27), residues: 1016 helix: 2.12 (0.22), residues: 559 sheet: 1.08 (0.63), residues: 76 loop : -0.52 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 749 HIS 0.013 0.001 HIS C 318 PHE 0.008 0.001 PHE B 335 TYR 0.011 0.001 TYR B 304 ARG 0.002 0.000 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7543 (t80) cc_final: 0.7198 (t80) REVERT: A 450 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: A 865 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7805 (mt) REVERT: A 880 LEU cc_start: 0.7768 (tp) cc_final: 0.7047 (mt) REVERT: A 910 LYS cc_start: 0.7069 (mtpp) cc_final: 0.6539 (mmmt) REVERT: A 937 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: B 195 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8712 (ttp) REVERT: C 302 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6993 (mm-30) outliers start: 36 outliers final: 15 residues processed: 125 average time/residue: 1.4604 time to fit residues: 194.7206 Evaluate side-chains 114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 347 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.0070 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 ASN A 582 ASN B 34 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8556 Z= 0.148 Angle : 0.473 8.500 11545 Z= 0.249 Chirality : 0.038 0.125 1233 Planarity : 0.003 0.036 1498 Dihedral : 4.921 56.932 1144 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.73 % Allowed : 23.38 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.27), residues: 1016 helix: 2.16 (0.22), residues: 558 sheet: 1.08 (0.63), residues: 76 loop : -0.50 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 749 HIS 0.006 0.001 HIS C 318 PHE 0.008 0.001 PHE B 335 TYR 0.011 0.001 TYR B 304 ARG 0.003 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7562 (t80) cc_final: 0.7234 (t80) REVERT: A 450 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: A 865 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7920 (mt) REVERT: A 880 LEU cc_start: 0.7715 (tp) cc_final: 0.7022 (mt) REVERT: A 910 LYS cc_start: 0.7084 (mtpp) cc_final: 0.6571 (mmmt) REVERT: A 937 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: B 195 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8729 (ttp) REVERT: C 302 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6991 (mm-30) REVERT: C 319 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5761 (tt) outliers start: 34 outliers final: 18 residues processed: 124 average time/residue: 1.3012 time to fit residues: 171.9189 Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8556 Z= 0.173 Angle : 0.493 8.283 11545 Z= 0.259 Chirality : 0.039 0.124 1233 Planarity : 0.003 0.036 1498 Dihedral : 4.998 56.950 1144 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.06 % Allowed : 23.71 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.27), residues: 1016 helix: 2.15 (0.22), residues: 554 sheet: 1.11 (0.63), residues: 76 loop : -0.52 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.006 0.001 HIS A 867 PHE 0.010 0.001 PHE A 744 TYR 0.012 0.001 TYR B 304 ARG 0.003 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7096 (mmmt) cc_final: 0.6881 (mmmm) REVERT: A 450 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6907 (mm-30) REVERT: A 865 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7953 (mt) REVERT: A 880 LEU cc_start: 0.7739 (tp) cc_final: 0.6999 (mt) REVERT: A 910 LYS cc_start: 0.7082 (mtpp) cc_final: 0.6597 (mmmt) REVERT: A 937 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: B 195 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8793 (ttp) REVERT: B 284 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8468 (mptm) REVERT: C 302 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6978 (mm-30) outliers start: 37 outliers final: 22 residues processed: 124 average time/residue: 1.3350 time to fit residues: 176.7378 Evaluate side-chains 122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.0670 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8556 Z= 0.162 Angle : 0.480 8.427 11545 Z= 0.253 Chirality : 0.038 0.125 1233 Planarity : 0.003 0.037 1498 Dihedral : 4.989 58.525 1144 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.06 % Allowed : 23.49 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.27), residues: 1016 helix: 2.18 (0.22), residues: 553 sheet: 1.10 (0.63), residues: 76 loop : -0.55 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 749 HIS 0.006 0.001 HIS C 318 PHE 0.009 0.001 PHE A 662 TYR 0.012 0.001 TYR B 304 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7188 (mmmt) cc_final: 0.6963 (mmmm) REVERT: A 327 PHE cc_start: 0.7443 (t80) cc_final: 0.7175 (t80) REVERT: A 450 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: A 865 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7948 (mt) REVERT: A 880 LEU cc_start: 0.7698 (tp) cc_final: 0.6975 (mt) REVERT: A 910 LYS cc_start: 0.7071 (mtpp) cc_final: 0.6573 (mmmt) REVERT: A 937 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: B 195 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (ttp) REVERT: B 284 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8464 (mptm) REVERT: C 302 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6979 (mm-30) outliers start: 37 outliers final: 21 residues processed: 119 average time/residue: 1.3419 time to fit residues: 169.7689 Evaluate side-chains 118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.0570 chunk 85 optimal weight: 0.0770 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8556 Z= 0.148 Angle : 0.483 9.126 11545 Z= 0.254 Chirality : 0.038 0.126 1233 Planarity : 0.003 0.036 1498 Dihedral : 4.931 57.995 1144 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.73 % Allowed : 23.60 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1016 helix: 2.20 (0.22), residues: 556 sheet: 1.09 (0.63), residues: 76 loop : -0.55 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 749 HIS 0.004 0.001 HIS C 318 PHE 0.008 0.001 PHE A 662 TYR 0.011 0.001 TYR B 304 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7102 (mmmt) cc_final: 0.6896 (mmmm) REVERT: A 327 PHE cc_start: 0.7381 (t80) cc_final: 0.7084 (t80) REVERT: A 450 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: A 865 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7954 (mt) REVERT: A 880 LEU cc_start: 0.7690 (tp) cc_final: 0.6958 (mt) REVERT: A 910 LYS cc_start: 0.6996 (mtpp) cc_final: 0.6520 (mmmt) REVERT: A 937 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: C 302 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6973 (mm-30) outliers start: 34 outliers final: 20 residues processed: 120 average time/residue: 1.4621 time to fit residues: 186.3442 Evaluate side-chains 115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 931 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8556 Z= 0.200 Angle : 0.514 9.492 11545 Z= 0.270 Chirality : 0.039 0.120 1233 Planarity : 0.003 0.037 1498 Dihedral : 5.067 58.292 1144 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.51 % Allowed : 24.15 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1016 helix: 2.12 (0.22), residues: 555 sheet: 1.05 (0.63), residues: 76 loop : -0.56 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 749 HIS 0.007 0.001 HIS A 867 PHE 0.011 0.001 PHE A 744 TYR 0.013 0.001 TYR B 304 ARG 0.002 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7412 (t80) cc_final: 0.7082 (t80) REVERT: A 450 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: A 865 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7968 (mt) REVERT: A 880 LEU cc_start: 0.7737 (tp) cc_final: 0.7067 (mt) REVERT: A 910 LYS cc_start: 0.7030 (mtpp) cc_final: 0.6593 (mmmt) REVERT: A 937 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: C 302 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6955 (mm-30) outliers start: 32 outliers final: 22 residues processed: 120 average time/residue: 1.3984 time to fit residues: 178.0561 Evaluate side-chains 120 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 92 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8556 Z= 0.167 Angle : 0.507 9.993 11545 Z= 0.265 Chirality : 0.039 0.122 1233 Planarity : 0.003 0.036 1498 Dihedral : 5.018 57.760 1144 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.07 % Allowed : 24.70 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 1016 helix: 2.09 (0.22), residues: 562 sheet: 1.00 (0.63), residues: 76 loop : -0.64 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.005 0.001 HIS A 867 PHE 0.009 0.001 PHE A 334 TYR 0.013 0.001 TYR B 304 ARG 0.008 0.000 ARG C 279 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7393 (t80) cc_final: 0.7085 (t80) REVERT: A 450 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6906 (mm-30) REVERT: A 880 LEU cc_start: 0.7707 (tp) cc_final: 0.7052 (mt) REVERT: A 910 LYS cc_start: 0.7096 (mtpp) cc_final: 0.6618 (mmmt) REVERT: A 937 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7681 (pt0) REVERT: C 302 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6975 (mm-30) outliers start: 28 outliers final: 20 residues processed: 118 average time/residue: 1.4787 time to fit residues: 184.6808 Evaluate side-chains 119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 845 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 937 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.0570 chunk 57 optimal weight: 0.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132960 restraints weight = 9987.764| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.69 r_work: 0.3333 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8556 Z= 0.157 Angle : 0.500 9.769 11545 Z= 0.263 Chirality : 0.038 0.122 1233 Planarity : 0.003 0.037 1498 Dihedral : 4.960 58.072 1144 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.07 % Allowed : 25.03 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1016 helix: 2.13 (0.22), residues: 561 sheet: 1.05 (0.63), residues: 76 loop : -0.62 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 909 HIS 0.004 0.001 HIS A 867 PHE 0.008 0.001 PHE A 744 TYR 0.013 0.001 TYR B 304 ARG 0.008 0.000 ARG C 279 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3621.26 seconds wall clock time: 65 minutes 35.41 seconds (3935.41 seconds total)