Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 04:01:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/04_2023/8b8q_15919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/04_2023/8b8q_15919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/04_2023/8b8q_15919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/04_2023/8b8q_15919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/04_2023/8b8q_15919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8q_15919/04_2023/8b8q_15919.pdb" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 Ca 6 9.91 5 S 74 5.16 5 C 7480 2.51 5 N 1834 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5682 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5682 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 8 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.53, per 1000 atoms: 0.57 Number of scatterers: 11370 At special positions: 0 Unit cell: (74.214, 113.274, 128.247, 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) Ca 6 19.99 S 74 16.00 O 1976 8.00 N 1834 7.00 C 7480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.04 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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: 5.02 Conformation dependent library (CDL) restraints added in 1.8 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2624 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 65.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 90 through 109 removed outlier: 3.505A pdb=" N GLY A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.617A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 327 Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.280A pdb=" N GLU A 366 " --> pdb=" O ASN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 409 Processing helix chain 'A' and resid 447 through 484 removed outlier: 3.654A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 538 removed outlier: 3.799A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.855A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 638 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.697A pdb=" N GLU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.922A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 796 through 802 removed outlier: 4.496A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 801 " --> pdb=" O PRO A 797 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 802 " --> pdb=" O TYR A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 796 through 802' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 870 Processing helix chain 'B' and resid 90 through 109 removed outlier: 3.514A pdb=" N GLY B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 234 through 239 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.660A pdb=" N ARG B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 327 Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 362 through 375 removed outlier: 4.264A pdb=" N GLU B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 409 Processing helix chain 'B' and resid 447 through 484 removed outlier: 3.788A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 538 removed outlier: 3.772A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.750A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 662 through 681 removed outlier: 3.785A pdb=" N TYR B 666 " --> pdb=" O LEU B 662 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 709 removed outlier: 4.050A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 797 through 802 removed outlier: 3.911A pdb=" N LEU B 801 " --> pdb=" O PRO B 797 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 802 " --> pdb=" O TYR B 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 797 through 802' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 116 removed outlier: 3.592A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 116 removed outlier: 3.601A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 785 715 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 5.39 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: 3454 1.34 - 1.46: 2819 1.46 - 1.58: 5291 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 11674 Sorted by residual: bond pdb=" C GLU B 272 " pdb=" N TRP B 273 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.21e+00 bond pdb=" CA PRO A 815 " pdb=" C PRO A 815 " ideal model delta sigma weight residual 1.517 1.507 0.010 6.70e-03 2.23e+04 2.18e+00 bond pdb=" C GLY B 582 " pdb=" O GLY B 582 " ideal model delta sigma weight residual 1.243 1.230 0.012 9.30e-03 1.16e+04 1.74e+00 bond pdb=" C ASN B 562 " pdb=" O ASN B 562 " ideal model delta sigma weight residual 1.235 1.251 -0.016 1.26e-02 6.30e+03 1.57e+00 bond pdb=" C ASN A 562 " pdb=" O ASN A 562 " ideal model delta sigma weight residual 1.235 1.250 -0.014 1.26e-02 6.30e+03 1.32e+00 ... (remaining 11669 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.33: 326 106.33 - 113.25: 6144 113.25 - 120.17: 4325 120.17 - 127.09: 4889 127.09 - 134.01: 144 Bond angle restraints: 15828 Sorted by residual: angle pdb=" CA LEU A 662 " pdb=" CB LEU A 662 " pdb=" CG LEU A 662 " ideal model delta sigma weight residual 116.30 126.56 -10.26 3.50e+00 8.16e-02 8.60e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.08 -3.38 1.22e+00 6.72e-01 7.70e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.04 -3.34 1.22e+00 6.72e-01 7.50e+00 angle pdb=" CA LEU B 662 " pdb=" CB LEU B 662 " pdb=" CG LEU B 662 " ideal model delta sigma weight residual 116.30 125.35 -9.05 3.50e+00 8.16e-02 6.69e+00 angle pdb=" N ILE B 786 " pdb=" CA ILE B 786 " pdb=" C ILE B 786 " ideal model delta sigma weight residual 106.21 108.60 -2.39 1.07e+00 8.73e-01 4.99e+00 ... (remaining 15823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 6264 16.25 - 32.50: 445 32.50 - 48.75: 117 48.75 - 65.00: 36 65.00 - 81.25: 2 Dihedral angle restraints: 6864 sinusoidal: 2788 harmonic: 4076 Sorted by residual: dihedral pdb=" CA THR B 787 " pdb=" C THR B 787 " pdb=" N ASP B 788 " pdb=" CA ASP B 788 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LYS B 590 " pdb=" C LYS B 590 " pdb=" N TYR B 591 " pdb=" CA TYR B 591 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN B 362 " pdb=" C ASN B 362 " pdb=" N ILE B 363 " pdb=" CA ILE B 363 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 935 0.025 - 0.050: 471 0.050 - 0.075: 200 0.075 - 0.101: 92 0.101 - 0.126: 36 Chirality restraints: 1734 Sorted by residual: chirality pdb=" CA ILE A 762 " pdb=" N ILE A 762 " pdb=" C ILE A 762 " pdb=" CB ILE A 762 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE B 74 " pdb=" N ILE B 74 " pdb=" C ILE B 74 " pdb=" CB ILE B 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1731 not shown) Planarity restraints: 1958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 612 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C ILE A 612 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE A 612 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 613 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 612 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ILE B 612 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE B 612 " -0.014 2.00e-02 2.50e+03 pdb=" N MET B 613 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 613 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C MET A 613 " -0.033 2.00e-02 2.50e+03 pdb=" O MET A 613 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 614 " 0.011 2.00e-02 2.50e+03 ... (remaining 1955 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 254 2.68 - 3.24: 11651 3.24 - 3.79: 18977 3.79 - 4.35: 23980 4.35 - 4.90: 40101 Nonbonded interactions: 94963 Sorted by model distance: nonbonded pdb=" OG SER B 782 " pdb=" O ASP B 811 " model vdw 2.126 2.440 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.152 2.440 nonbonded pdb=" OE1 GLU A 667 " pdb="CA CA A1002 " model vdw 2.189 2.510 nonbonded pdb=" OG SER A 782 " pdb=" O ASP A 811 " model vdw 2.196 2.440 nonbonded pdb=" OE2 GLU B 670 " pdb="CA CA B1001 " model vdw 2.229 2.510 ... (remaining 94958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints 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 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: 9.140 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: 31.570 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.200 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 0.043 11674 Z= 0.247 Angle : 0.542 10.263 15828 Z= 0.302 Chirality : 0.039 0.126 1734 Planarity : 0.004 0.043 1958 Dihedral : 12.629 81.250 4222 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 7.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1346 helix: 1.68 (0.17), residues: 812 sheet: 1.14 (0.71), residues: 54 loop : -1.33 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 215 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 24 residues processed: 296 average time/residue: 1.2238 time to fit residues: 392.9688 Evaluate side-chains 152 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 1.327 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 7 average time/residue: 0.2178 time to fit residues: 4.0661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0670 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN B 108 HIS B 401 GLN B 544 GLN ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11674 Z= 0.208 Angle : 0.588 9.353 15828 Z= 0.311 Chirality : 0.040 0.135 1734 Planarity : 0.004 0.040 1958 Dihedral : 4.383 20.983 1518 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 5.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1346 helix: 1.72 (0.17), residues: 814 sheet: 0.54 (0.65), residues: 54 loop : -1.27 (0.29), residues: 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 143 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 30 residues processed: 190 average time/residue: 0.8884 time to fit residues: 190.8479 Evaluate side-chains 144 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.343 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 26 residues processed: 5 average time/residue: 0.2310 time to fit residues: 3.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 562 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11674 Z= 0.222 Angle : 0.575 8.992 15828 Z= 0.306 Chirality : 0.041 0.161 1734 Planarity : 0.004 0.040 1958 Dihedral : 4.346 20.376 1518 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 6.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.23), residues: 1346 helix: 1.68 (0.17), residues: 814 sheet: -0.20 (0.60), residues: 64 loop : -1.29 (0.29), residues: 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 137 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 36 residues processed: 203 average time/residue: 0.8700 time to fit residues: 198.2061 Evaluate side-chains 152 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.258 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 31 residues processed: 6 average time/residue: 0.2022 time to fit residues: 3.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 111 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11674 Z= 0.282 Angle : 0.599 9.343 15828 Z= 0.322 Chirality : 0.042 0.192 1734 Planarity : 0.004 0.041 1958 Dihedral : 4.443 29.066 1518 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 5.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1346 helix: 1.58 (0.17), residues: 816 sheet: 0.58 (0.67), residues: 44 loop : -1.38 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 128 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 39 residues processed: 188 average time/residue: 0.8632 time to fit residues: 182.4764 Evaluate side-chains 154 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.333 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 37 residues processed: 3 average time/residue: 0.1846 time to fit residues: 2.6894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 119 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 11674 Z= 0.391 Angle : 0.655 9.513 15828 Z= 0.353 Chirality : 0.044 0.155 1734 Planarity : 0.005 0.044 1958 Dihedral : 4.603 25.684 1518 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 5.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1346 helix: 1.38 (0.17), residues: 814 sheet: 0.30 (0.65), residues: 44 loop : -1.59 (0.28), residues: 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 128 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 40 residues processed: 186 average time/residue: 0.8793 time to fit residues: 184.1692 Evaluate side-chains 156 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 116 time to evaluate : 1.368 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 40 outliers final: 35 residues processed: 6 average time/residue: 0.2281 time to fit residues: 3.8411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 110 optimal weight: 0.0060 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 559 GLN B 657 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11674 Z= 0.187 Angle : 0.590 9.517 15828 Z= 0.314 Chirality : 0.041 0.165 1734 Planarity : 0.004 0.041 1958 Dihedral : 4.493 23.521 1518 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 5.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1346 helix: 1.56 (0.17), residues: 816 sheet: 0.54 (0.66), residues: 44 loop : -1.39 (0.28), residues: 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 130 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 37 residues processed: 183 average time/residue: 0.9263 time to fit residues: 190.6566 Evaluate side-chains 155 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.2136 time to fit residues: 3.5959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 133 optimal weight: 0.0010 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 11674 Z= 0.281 Angle : 0.631 12.072 15828 Z= 0.336 Chirality : 0.042 0.157 1734 Planarity : 0.005 0.042 1958 Dihedral : 4.463 24.163 1518 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1346 helix: 1.48 (0.17), residues: 816 sheet: 0.46 (0.65), residues: 44 loop : -1.51 (0.27), residues: 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 130 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 37 residues processed: 176 average time/residue: 0.8919 time to fit residues: 175.7328 Evaluate side-chains 158 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 4 average time/residue: 0.4547 time to fit residues: 5.3153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11674 Z= 0.221 Angle : 0.640 14.851 15828 Z= 0.335 Chirality : 0.041 0.156 1734 Planarity : 0.004 0.041 1958 Dihedral : 4.460 27.148 1518 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1346 helix: 1.63 (0.18), residues: 804 sheet: 0.52 (0.66), residues: 44 loop : -1.45 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 35 residues processed: 172 average time/residue: 0.8545 time to fit residues: 165.2140 Evaluate side-chains 156 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 121 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 4 average time/residue: 0.2201 time to fit residues: 3.1620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 81 optimal weight: 0.0970 chunk 131 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 11674 Z= 0.237 Angle : 0.660 15.152 15828 Z= 0.346 Chirality : 0.042 0.157 1734 Planarity : 0.005 0.041 1958 Dihedral : 4.428 27.481 1518 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1346 helix: 1.58 (0.18), residues: 818 sheet: 0.47 (0.67), residues: 44 loop : -1.38 (0.28), residues: 484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 125 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 34 residues processed: 163 average time/residue: 0.8672 time to fit residues: 159.6179 Evaluate side-chains 155 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 31 residues processed: 3 average time/residue: 0.5120 time to fit residues: 3.7356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.0970 chunk 62 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 11674 Z= 0.208 Angle : 0.684 17.303 15828 Z= 0.361 Chirality : 0.042 0.184 1734 Planarity : 0.005 0.041 1958 Dihedral : 4.467 28.112 1518 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1346 helix: 1.58 (0.18), residues: 818 sheet: 0.60 (0.67), residues: 44 loop : -1.34 (0.28), residues: 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 32 residues processed: 164 average time/residue: 0.8878 time to fit residues: 163.9673 Evaluate side-chains 148 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 1.1409 time to fit residues: 3.0834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.143761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107161 restraints weight = 20718.864| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.81 r_work: 0.3403 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 11674 Z= 0.233 Angle : 0.704 15.727 15828 Z= 0.372 Chirality : 0.043 0.181 1734 Planarity : 0.005 0.047 1958 Dihedral : 4.511 27.699 1518 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1346 helix: 1.52 (0.18), residues: 820 sheet: 0.52 (0.67), residues: 44 loop : -1.38 (0.28), residues: 482 =============================================================================== Job complete usr+sys time: 4173.26 seconds wall clock time: 75 minutes 43.81 seconds (4543.81 seconds total)