Starting phenix.real_space_refine on Thu Nov 14 22:43:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/11_2024/8sgj_40457.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/11_2024/8sgj_40457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/11_2024/8sgj_40457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/11_2024/8sgj_40457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/11_2024/8sgj_40457.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgj_40457/11_2024/8sgj_40457.cif" } resolution = 3.1 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= 0.002 sd= 0.063 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 6 9.91 5 S 31 5.16 5 Na 3 4.78 5 C 4948 2.51 5 N 1242 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7667 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5900 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 724} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CA': 6, ' NA': 3} Classifications: {'undetermined': 9, 'water': 1} Link IDs: {None: 9} Time building chain proxies: 5.57, per 1000 atoms: 0.73 Number of scatterers: 7667 At special positions: 0 Unit cell: (97.11, 100.43, 146.08, 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) Ca 6 19.99 S 31 16.00 Na 3 11.00 O 1437 8.00 N 1242 7.00 C 4948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 792 " distance=2.03 Simple disulfide: pdb=" SG CYS L 21 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.4% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 36 through 72 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.517A pdb=" N LEU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.511A pdb=" N HIS A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 155 removed outlier: 3.821A pdb=" N ILE A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.784A pdb=" N TYR A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 4.507A pdb=" N PHE A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.593A pdb=" N VAL A 227 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 656 through 666 Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.597A pdb=" N ILE A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 755 removed outlier: 5.420A pdb=" N PHE A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 764 removed outlier: 3.725A pdb=" N ASN A 764 " --> pdb=" O GLU A 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 764' Processing helix chain 'A' and resid 765 through 795 removed outlier: 3.742A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 788 " --> pdb=" O GLY A 784 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 825 removed outlier: 3.714A pdb=" N ASP A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.583A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 843 " --> pdb=" O ASN A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 861 removed outlier: 3.996A pdb=" N ALA A 850 " --> pdb=" O GLY A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 893 removed outlier: 4.592A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 874 " --> pdb=" O GLY A 870 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 932 removed outlier: 3.780A pdb=" N TYR A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.816A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.582A pdb=" N SER H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.614A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 79 removed outlier: 4.365A pdb=" N TYR A 228 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 195 removed outlier: 4.262A pdb=" N PHE A 865 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 437 through 443 Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 384 removed outlier: 6.894A pdb=" N TYR A 381 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE A 497 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N CYS A 383 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL A 458 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU A 412 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU A 460 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG A 410 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ASN A 462 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP A 408 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 574 Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.842A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.842A pdb=" N THR A 512 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU A 682 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 514 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 534 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL A 597 " --> pdb=" O LYS A 628 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS A 618 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG A 627 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 616 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.546A pdb=" N LEU L 9 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 8 through 11 removed outlier: 6.546A pdb=" N LEU L 9 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.466A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1182 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: 2.84 Time building geometry restraints manager: 2.19 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: 2308 1.34 - 1.46: 1441 1.46 - 1.57: 4042 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 7836 Sorted by residual: bond pdb=" CB TRP A 29 " pdb=" CG TRP A 29 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.33e+00 bond pdb=" CA TYR H 60 " pdb=" C TYR H 60 " ideal model delta sigma weight residual 1.521 1.496 0.025 1.23e-02 6.61e+03 4.16e+00 bond pdb=" N TRP A 29 " pdb=" CA TRP A 29 " ideal model delta sigma weight residual 1.455 1.434 0.021 1.30e-02 5.92e+03 2.69e+00 bond pdb=" CA LYS A 697 " pdb=" CB LYS A 697 " ideal model delta sigma weight residual 1.527 1.567 -0.039 2.48e-02 1.63e+03 2.52e+00 bond pdb=" C TYR H 60 " pdb=" O TYR H 60 " ideal model delta sigma weight residual 1.234 1.218 0.016 1.22e-02 6.72e+03 1.68e+00 ... (remaining 7831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 10356 1.85 - 3.71: 234 3.71 - 5.56: 37 5.56 - 7.42: 7 7.42 - 9.27: 4 Bond angle restraints: 10638 Sorted by residual: angle pdb=" N TRP A 29 " pdb=" CA TRP A 29 " pdb=" C TRP A 29 " ideal model delta sigma weight residual 110.20 103.08 7.12 1.58e+00 4.01e-01 2.03e+01 angle pdb=" N GLN H 82 " pdb=" CA GLN H 82 " pdb=" C GLN H 82 " ideal model delta sigma weight residual 109.07 115.29 -6.22 1.61e+00 3.86e-01 1.49e+01 angle pdb=" C GLY L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C TYR H 60 " pdb=" CA TYR H 60 " pdb=" CB TYR H 60 " ideal model delta sigma weight residual 110.45 102.87 7.58 2.15e+00 2.16e-01 1.24e+01 angle pdb=" C ILE A 643 " pdb=" N ALA A 644 " pdb=" CA ALA A 644 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 ... (remaining 10633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4166 17.09 - 34.19: 320 34.19 - 51.28: 55 51.28 - 68.37: 5 68.37 - 85.47: 8 Dihedral angle restraints: 4554 sinusoidal: 1746 harmonic: 2808 Sorted by residual: dihedral pdb=" CA LEU A 637 " pdb=" C LEU A 637 " pdb=" N SER A 638 " pdb=" CA SER A 638 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" C TYR H 60 " pdb=" N TYR H 60 " pdb=" CA TYR H 60 " pdb=" CB TYR H 60 " ideal model delta harmonic sigma weight residual -122.60 -113.98 -8.62 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" CA GLY A 549 " pdb=" C GLY A 549 " pdb=" N GLY A 550 " pdb=" CA GLY A 550 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 860 0.046 - 0.093: 271 0.093 - 0.139: 75 0.139 - 0.186: 6 0.186 - 0.232: 3 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CB THR A 642 " pdb=" CA THR A 642 " pdb=" OG1 THR A 642 " pdb=" CG2 THR A 642 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 717 " pdb=" CA ILE A 717 " pdb=" CG1 ILE A 717 " pdb=" CG2 ILE A 717 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB THR A 877 " pdb=" CA THR A 877 " pdb=" OG1 THR A 877 " pdb=" CG2 THR A 877 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1212 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 28 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C ILE A 28 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 28 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP A 29 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO A 133 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 812 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 813 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 813 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 813 " 0.027 5.00e-02 4.00e+02 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 84 2.58 - 3.16: 5975 3.16 - 3.74: 11638 3.74 - 4.32: 16557 4.32 - 4.90: 28278 Nonbonded interactions: 62532 Sorted by model distance: nonbonded pdb=" OE2 GLU A 451 " pdb="CA CA A1003 " model vdw 1.994 2.510 nonbonded pdb=" OD2 ASP A 421 " pdb="CA CA A1003 " model vdw 2.115 2.510 nonbonded pdb=" OD1 ASP A 421 " pdb="CA CA A1003 " model vdw 2.182 2.510 nonbonded pdb=" OD1 ASP A 408 " pdb=" OG1 THR A 428 " model vdw 2.188 3.040 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.204 3.040 ... (remaining 62527 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=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: 2.920 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: 0.070 Process input model: 22.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.065 7836 Z= 0.263 Angle : 0.699 9.269 10638 Z= 0.385 Chirality : 0.048 0.232 1215 Planarity : 0.006 0.063 1332 Dihedral : 12.734 85.467 2747 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -0.02 (0.26), residues: 966 helix: -0.03 (0.25), residues: 342 sheet: 0.49 (0.29), residues: 311 loop : -0.24 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 95 HIS 0.003 0.001 HIS A 243 PHE 0.028 0.002 PHE A 925 TYR 0.029 0.002 TYR A 46 ARG 0.009 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8276 (mmm) cc_final: 0.8032 (mmm) REVERT: A 62 ASP cc_start: 0.7920 (t70) cc_final: 0.7643 (t0) REVERT: A 162 LYS cc_start: 0.7887 (tttp) cc_final: 0.7024 (tttp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2370 time to fit residues: 49.8799 Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 0.0770 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 57 optimal weight: 0.0030 chunk 88 optimal weight: 4.9990 overall best weight: 0.2948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 HIS A 764 ASN A 834 ASN ** A 886 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN H 6 GLN H 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7836 Z= 0.149 Angle : 0.524 8.331 10638 Z= 0.285 Chirality : 0.042 0.144 1215 Planarity : 0.004 0.047 1332 Dihedral : 4.347 18.279 1047 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.97 % Allowed : 7.75 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 966 helix: 1.32 (0.27), residues: 344 sheet: 0.48 (0.29), residues: 304 loop : -0.15 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.003 0.001 HIS A 165 PHE 0.019 0.001 PHE A 925 TYR 0.017 0.001 TYR A 184 ARG 0.003 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.1922 time to fit residues: 31.8590 Evaluate side-chains 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 509 GLU Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7836 Z= 0.272 Angle : 0.552 9.192 10638 Z= 0.298 Chirality : 0.043 0.149 1215 Planarity : 0.004 0.042 1332 Dihedral : 4.330 24.657 1047 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.21 % Allowed : 10.17 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 966 helix: 1.64 (0.27), residues: 344 sheet: 0.45 (0.29), residues: 309 loop : -0.24 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 709 HIS 0.005 0.001 HIS A 501 PHE 0.020 0.002 PHE A 882 TYR 0.014 0.002 TYR A 180 ARG 0.004 0.001 ARG A 895 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8490 (mmm) cc_final: 0.8140 (mmm) REVERT: A 209 ILE cc_start: 0.8639 (mm) cc_final: 0.8262 (mt) REVERT: L 55 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8035 (ttp80) outliers start: 10 outliers final: 9 residues processed: 118 average time/residue: 0.2013 time to fit residues: 32.4594 Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain H residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8181 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7836 Z= 0.213 Angle : 0.510 8.048 10638 Z= 0.276 Chirality : 0.042 0.142 1215 Planarity : 0.004 0.039 1332 Dihedral : 4.235 26.376 1047 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.69 % Allowed : 10.77 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.05 (0.27), residues: 966 helix: 1.82 (0.27), residues: 344 sheet: 0.47 (0.29), residues: 309 loop : -0.23 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 PHE 0.016 0.001 PHE A 882 TYR 0.012 0.001 TYR A 180 ARG 0.003 0.000 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8492 (mmm) cc_final: 0.8152 (mmm) REVERT: L 55 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8044 (ttp80) outliers start: 14 outliers final: 10 residues processed: 115 average time/residue: 0.1947 time to fit residues: 30.8533 Evaluate side-chains 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain H residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8191 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7836 Z= 0.214 Angle : 0.505 10.553 10638 Z= 0.270 Chirality : 0.042 0.155 1215 Planarity : 0.003 0.036 1332 Dihedral : 4.195 27.507 1047 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.69 % Allowed : 11.62 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.13 (0.27), residues: 966 helix: 1.92 (0.27), residues: 344 sheet: 0.48 (0.30), residues: 309 loop : -0.18 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 709 HIS 0.003 0.001 HIS A 501 PHE 0.014 0.001 PHE A 587 TYR 0.011 0.001 TYR A 180 ARG 0.002 0.000 ARG H 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8474 (mmm) cc_final: 0.8135 (mmm) REVERT: A 94 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8709 (mt) REVERT: L 55 ARG cc_start: 0.8354 (ttp80) cc_final: 0.8061 (ttp80) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.2174 time to fit residues: 34.5298 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain H residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7836 Z= 0.394 Angle : 0.584 8.846 10638 Z= 0.316 Chirality : 0.045 0.158 1215 Planarity : 0.004 0.041 1332 Dihedral : 4.413 25.642 1047 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.94 % Allowed : 12.59 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.81 (0.27), residues: 966 helix: 1.50 (0.27), residues: 349 sheet: 0.33 (0.31), residues: 293 loop : -0.18 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 709 HIS 0.006 0.001 HIS A 501 PHE 0.017 0.002 PHE A 587 TYR 0.017 0.002 TYR A 180 ARG 0.003 0.001 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.879 Fit side-chains REVERT: A 94 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8738 (mt) REVERT: A 764 ASN cc_start: 0.7571 (t0) cc_final: 0.7165 (t0) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.1971 time to fit residues: 31.6379 Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8233 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7836 Z= 0.202 Angle : 0.517 10.708 10638 Z= 0.276 Chirality : 0.042 0.143 1215 Planarity : 0.003 0.039 1332 Dihedral : 4.279 25.353 1047 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.82 % Allowed : 14.65 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 966 helix: 1.84 (0.27), residues: 344 sheet: 0.16 (0.30), residues: 294 loop : -0.22 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 29 HIS 0.003 0.001 HIS A 243 PHE 0.013 0.001 PHE A 587 TYR 0.011 0.001 TYR A 180 ARG 0.003 0.000 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8587 (mmm) cc_final: 0.8256 (mmm) REVERT: A 94 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8731 (mt) REVERT: A 764 ASN cc_start: 0.7549 (t0) cc_final: 0.7155 (t0) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1949 time to fit residues: 30.2814 Evaluate side-chains 111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7836 Z= 0.181 Angle : 0.504 11.356 10638 Z= 0.267 Chirality : 0.041 0.145 1215 Planarity : 0.004 0.061 1332 Dihedral : 4.171 24.093 1047 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.06 % Allowed : 14.89 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.10 (0.27), residues: 966 helix: 2.00 (0.27), residues: 344 sheet: 0.25 (0.30), residues: 304 loop : -0.06 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 29 HIS 0.003 0.001 HIS A 243 PHE 0.013 0.001 PHE A 587 TYR 0.010 0.001 TYR A 180 ARG 0.010 0.000 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8560 (mmm) cc_final: 0.8230 (mmm) REVERT: A 94 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 764 ASN cc_start: 0.7512 (t0) cc_final: 0.7157 (t0) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.1932 time to fit residues: 30.2307 Evaluate side-chains 114 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.0030 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7836 Z= 0.148 Angle : 0.498 10.472 10638 Z= 0.263 Chirality : 0.041 0.144 1215 Planarity : 0.003 0.036 1332 Dihedral : 4.068 23.329 1047 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.57 % Allowed : 15.86 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.25 (0.28), residues: 966 helix: 2.16 (0.27), residues: 344 sheet: 0.34 (0.31), residues: 297 loop : -0.04 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.012 0.001 PHE A 769 TYR 0.009 0.001 TYR A 180 ARG 0.004 0.000 ARG A 894 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.880 Fit side-chains REVERT: A 53 MET cc_start: 0.8532 (mmm) cc_final: 0.8211 (mmm) REVERT: A 94 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8725 (mt) REVERT: A 764 ASN cc_start: 0.7397 (t0) cc_final: 0.7044 (t0) REVERT: H 13 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7616 (mmp-170) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.1914 time to fit residues: 28.9972 Evaluate side-chains 110 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8213 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7836 Z= 0.196 Angle : 0.511 12.032 10638 Z= 0.269 Chirality : 0.042 0.160 1215 Planarity : 0.003 0.038 1332 Dihedral : 4.033 15.122 1047 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.45 % Allowed : 16.46 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.28), residues: 966 helix: 2.15 (0.28), residues: 344 sheet: 0.29 (0.30), residues: 303 loop : -0.01 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.020 0.001 PHE A 882 TYR 0.011 0.001 TYR A 19 ARG 0.001 0.000 ARG L 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.855 Fit side-chains REVERT: A 53 MET cc_start: 0.8564 (mmm) cc_final: 0.8229 (mmm) REVERT: A 94 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8747 (mt) REVERT: A 764 ASN cc_start: 0.7423 (t0) cc_final: 0.7105 (t0) REVERT: H 13 ARG cc_start: 0.8004 (mmm160) cc_final: 0.7643 (mmp-170) REVERT: H 84 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7995 (ptp-170) outliers start: 12 outliers final: 11 residues processed: 107 average time/residue: 0.1980 time to fit residues: 29.8642 Evaluate side-chains 108 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 698 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.136247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099539 restraints weight = 10004.858| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.88 r_work: 0.3050 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7836 Z= 0.194 Angle : 0.506 11.737 10638 Z= 0.266 Chirality : 0.042 0.156 1215 Planarity : 0.003 0.038 1332 Dihedral : 4.030 15.100 1047 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.07 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 16.10 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.21 (0.28), residues: 966 helix: 2.10 (0.27), residues: 344 sheet: 0.28 (0.30), residues: 303 loop : 0.03 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.028 0.001 PHE A 925 TYR 0.011 0.001 TYR A 180 ARG 0.005 0.000 ARG A 894 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.34 seconds wall clock time: 36 minutes 50.33 seconds (2210.33 seconds total)