Starting phenix.real_space_refine on Wed Mar 12 09:16:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgj_40457/03_2025/8sgj_40457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgj_40457/03_2025/8sgj_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/cci-nas-00/data/ceres_data/8sgj_40457/03_2025/8sgj_40457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgj_40457/03_2025/8sgj_40457.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgj_40457/03_2025/8sgj_40457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgj_40457/03_2025/8sgj_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.86, per 1000 atoms: 0.76 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: 2.22 Conformation dependent library (CDL) restraints added in 1.2 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: 1.05 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: 3.25 Time building geometry restraints manager: 2.32 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: 3.590 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.230 ------------------------------------------------------------------------------- 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 : 0.807 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: 0.2353 time to fit residues: 49.6324 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 : 0.856 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108666 restraints weight = 9835.433| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.92 r_work: 0.3174 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.778 Fit side-chains revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7693 (t70) cc_final: 0.7403 (t0) REVERT: A 711 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 897 GLU cc_start: 0.7698 (mp0) cc_final: 0.7475 (pm20) REVERT: H 13 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7618 (mmm160) REVERT: H 46 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8099 (mt-10) outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.1829 time to fit residues: 30.5305 Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.758 ------------------------------------------------------------------------------- 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 77 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.6104 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098308 restraints weight = 10207.521| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.92 r_work: 0.3030 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 7836 Z= 0.373 Angle : 0.594 9.284 10638 Z= 0.321 Chirality : 0.045 0.157 1215 Planarity : 0.004 0.044 1332 Dihedral : 4.419 23.895 1047 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.09 % Allowed : 9.93 % Favored : 88.98 % 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: 0.77 (0.27), residues: 966 helix: 1.44 (0.27), residues: 343 sheet: 0.37 (0.29), residues: 309 loop : -0.23 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 709 HIS 0.006 0.001 HIS A 501 PHE 0.025 0.002 PHE A 882 TYR 0.016 0.002 TYR A 180 ARG 0.003 0.001 ARG A 441 *********************** 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 124 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8518 (mmm) cc_final: 0.8094 (mmm) REVERT: A 62 ASP cc_start: 0.7923 (t70) cc_final: 0.7639 (t0) REVERT: A 209 ILE cc_start: 0.7576 (mm) cc_final: 0.7345 (mt) REVERT: A 897 GLU cc_start: 0.7759 (mp0) cc_final: 0.7432 (pm20) REVERT: L 55 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8001 (ttp80) REVERT: L 95 ASN cc_start: 0.8532 (p0) cc_final: 0.8305 (p0) REVERT: H 13 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7697 (mmm160) REVERT: H 46 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8083 (mt-10) outliers start: 9 outliers final: 8 residues processed: 120 average time/residue: 0.1928 time to fit residues: 31.7876 Evaluate side-chains 111 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 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 87 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.136981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099905 restraints weight = 10049.365| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.91 r_work: 0.3056 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7836 Z= 0.225 Angle : 0.515 8.867 10638 Z= 0.278 Chirality : 0.042 0.144 1215 Planarity : 0.004 0.041 1332 Dihedral : 4.296 26.527 1047 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.45 % Allowed : 11.38 % Favored : 87.17 % 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: 1.70 (0.27), residues: 343 sheet: 0.38 (0.29), residues: 309 loop : -0.21 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 709 HIS 0.003 0.001 HIS A 501 PHE 0.018 0.002 PHE A 882 TYR 0.012 0.001 TYR A 892 ARG 0.002 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 125 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.999 Fit side-chains REVERT: A 53 MET cc_start: 0.8505 (mmm) cc_final: 0.8099 (mmm) REVERT: A 62 ASP cc_start: 0.7898 (t70) cc_final: 0.7611 (t0) REVERT: A 94 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8350 (mt) REVERT: A 658 GLU cc_start: 0.8447 (tt0) cc_final: 0.7909 (mt-10) REVERT: A 711 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8004 (mm-30) REVERT: A 897 GLU cc_start: 0.7810 (mp0) cc_final: 0.7499 (pm20) REVERT: L 55 ARG cc_start: 0.8569 (ttp80) cc_final: 0.7976 (ttp80) REVERT: L 95 ASN cc_start: 0.8502 (p0) cc_final: 0.8277 (p0) REVERT: H 13 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7738 (mmm160) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 0.2069 time to fit residues: 34.0761 Evaluate side-chains 112 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.133967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096910 restraints weight = 10157.967| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.91 r_work: 0.2992 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7836 Z= 0.318 Angle : 0.550 10.313 10638 Z= 0.296 Chirality : 0.043 0.150 1215 Planarity : 0.004 0.042 1332 Dihedral : 4.337 27.372 1047 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.69 % Allowed : 12.71 % Favored : 85.59 % 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: 0.85 (0.27), residues: 966 helix: 1.56 (0.27), residues: 348 sheet: 0.34 (0.31), residues: 293 loop : -0.18 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 709 HIS 0.005 0.001 HIS A 501 PHE 0.016 0.002 PHE A 587 TYR 0.014 0.002 TYR A 180 ARG 0.003 0.000 ARG A 441 *********************** 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 129 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8525 (mmm) cc_final: 0.8103 (mmm) REVERT: A 62 ASP cc_start: 0.7930 (t70) cc_final: 0.7628 (t0) REVERT: A 94 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 658 GLU cc_start: 0.8470 (tt0) cc_final: 0.7905 (mt-10) REVERT: A 711 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 764 ASN cc_start: 0.7110 (t0) cc_final: 0.6568 (t0) REVERT: L 55 ARG cc_start: 0.8602 (ttp80) cc_final: 0.8034 (ttp80) REVERT: L 95 ASN cc_start: 0.8487 (p0) cc_final: 0.8275 (p0) outliers start: 14 outliers final: 12 residues processed: 123 average time/residue: 0.2004 time to fit residues: 33.8899 Evaluate side-chains 118 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.136298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099463 restraints weight = 9982.693| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.89 r_work: 0.3028 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2812 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= 0.181 Angle : 0.497 9.447 10638 Z= 0.264 Chirality : 0.041 0.143 1215 Planarity : 0.003 0.038 1332 Dihedral : 4.211 25.774 1047 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.82 % Allowed : 13.68 % Favored : 84.50 % 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: 1.02 (0.27), residues: 966 helix: 1.92 (0.27), residues: 343 sheet: 0.29 (0.30), residues: 304 loop : -0.19 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.015 0.001 PHE A 925 TYR 0.010 0.001 TYR A 180 ARG 0.005 0.000 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 121 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.873 Fit side-chains REVERT: A 53 MET cc_start: 0.8436 (mmm) cc_final: 0.8025 (mmm) REVERT: A 62 ASP cc_start: 0.7886 (t70) cc_final: 0.7593 (t0) REVERT: A 94 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8363 (mt) REVERT: A 658 GLU cc_start: 0.8383 (tt0) cc_final: 0.7863 (mt-10) REVERT: A 711 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 764 ASN cc_start: 0.7164 (t0) cc_final: 0.6618 (t0) REVERT: L 55 ARG cc_start: 0.8542 (ttp80) cc_final: 0.7989 (ttp80) REVERT: H 10 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7123 (mt-10) outliers start: 15 outliers final: 13 residues processed: 115 average time/residue: 0.2047 time to fit residues: 32.3373 Evaluate side-chains 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 629 VAL 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 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 97 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.133152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096127 restraints weight = 10212.098| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.91 r_work: 0.2981 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7836 Z= 0.337 Angle : 0.554 10.880 10638 Z= 0.295 Chirality : 0.044 0.164 1215 Planarity : 0.004 0.042 1332 Dihedral : 4.298 24.134 1047 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.18 % Allowed : 14.04 % Favored : 83.78 % 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: 0.85 (0.27), residues: 966 helix: 1.68 (0.27), residues: 346 sheet: 0.21 (0.30), residues: 298 loop : -0.18 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 709 HIS 0.004 0.001 HIS A 501 PHE 0.016 0.002 PHE A 587 TYR 0.016 0.002 TYR A 180 ARG 0.004 0.000 ARG H 13 *********************** 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 123 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.7982 (t70) cc_final: 0.7673 (t0) REVERT: A 94 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 658 GLU cc_start: 0.8427 (tt0) cc_final: 0.7894 (mt-10) REVERT: A 764 ASN cc_start: 0.7333 (t0) cc_final: 0.6811 (t0) REVERT: L 55 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8065 (ttp80) REVERT: H 10 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7308 (mt-10) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.1951 time to fit residues: 31.1658 Evaluate side-chains 115 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 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 L residue 31 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.136191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098972 restraints weight = 10127.056| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.93 r_work: 0.3035 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7836 Z= 0.181 Angle : 0.500 11.058 10638 Z= 0.264 Chirality : 0.041 0.154 1215 Planarity : 0.003 0.036 1332 Dihedral : 4.165 23.392 1047 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 14.65 % Favored : 83.29 % 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: 1.03 (0.27), residues: 966 helix: 1.96 (0.27), residues: 344 sheet: 0.21 (0.30), residues: 304 loop : -0.12 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.018 0.001 PHE A 925 TYR 0.010 0.001 TYR A 180 ARG 0.004 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 117 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.251 Fit side-chains REVERT: A 53 MET cc_start: 0.8506 (mmm) cc_final: 0.8152 (mmm) REVERT: A 62 ASP cc_start: 0.7957 (t70) cc_final: 0.7652 (t0) REVERT: A 94 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 162 LYS cc_start: 0.7546 (mtpp) cc_final: 0.7286 (tptm) REVERT: A 658 GLU cc_start: 0.8381 (tt0) cc_final: 0.7859 (mt-10) REVERT: A 711 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 764 ASN cc_start: 0.7247 (t0) cc_final: 0.6739 (t0) REVERT: L 55 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8063 (ttp80) REVERT: H 10 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7252 (mt-10) REVERT: H 13 ARG cc_start: 0.7790 (mmm160) cc_final: 0.6995 (mmm160) REVERT: H 43 GLN cc_start: 0.8455 (mp10) cc_final: 0.8249 (mp10) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.2604 time to fit residues: 40.2931 Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 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 698 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain H residue 63 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 59 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.136486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099453 restraints weight = 10162.523| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.93 r_work: 0.3052 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7836 Z= 0.171 Angle : 0.494 11.684 10638 Z= 0.260 Chirality : 0.041 0.143 1215 Planarity : 0.003 0.036 1332 Dihedral : 4.068 22.315 1047 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.69 % Allowed : 15.13 % Favored : 83.17 % 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 (0.28), residues: 966 helix: 2.06 (0.27), residues: 344 sheet: 0.25 (0.30), residues: 303 loop : -0.06 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.013 0.001 PHE A 587 TYR 0.009 0.001 TYR A 180 ARG 0.004 0.000 ARG H 84 *********************** 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 119 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.861 Fit side-chains REVERT: A 53 MET cc_start: 0.8517 (mmm) cc_final: 0.8148 (mmm) REVERT: A 62 ASP cc_start: 0.7932 (t70) cc_final: 0.7647 (t0) REVERT: A 94 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 162 LYS cc_start: 0.7494 (mtpp) cc_final: 0.6745 (tptt) REVERT: A 658 GLU cc_start: 0.8381 (tt0) cc_final: 0.7864 (mt-10) REVERT: A 711 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 764 ASN cc_start: 0.7163 (t0) cc_final: 0.6664 (t0) REVERT: L 55 ARG cc_start: 0.8595 (ttp80) cc_final: 0.8065 (ttp80) REVERT: H 10 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7275 (mt-10) REVERT: H 13 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7253 (mmp-170) REVERT: H 84 ARG cc_start: 0.8205 (ptp-110) cc_final: 0.7911 (ptp-170) outliers start: 14 outliers final: 12 residues processed: 114 average time/residue: 0.1941 time to fit residues: 30.7294 Evaluate side-chains 113 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL 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 717 ILE Chi-restraints excluded: chain A residue 863 GLU Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL 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 66 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.134213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097027 restraints weight = 10177.269| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.92 r_work: 0.3019 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7836 Z= 0.280 Angle : 0.539 12.002 10638 Z= 0.283 Chirality : 0.042 0.153 1215 Planarity : 0.004 0.048 1332 Dihedral : 4.161 21.894 1047 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.69 % Allowed : 15.74 % 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: 1.05 (0.27), residues: 966 helix: 1.92 (0.27), residues: 346 sheet: 0.20 (0.30), residues: 304 loop : -0.03 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 709 HIS 0.004 0.001 HIS A 501 PHE 0.019 0.002 PHE A 925 TYR 0.015 0.002 TYR A 180 ARG 0.004 0.000 ARG A 167 ********************** 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: 14 poor density : 98 time to evaluate : 0.927 Fit side-chains REVERT: A 53 MET cc_start: 0.8573 (mmm) cc_final: 0.8193 (mmm) REVERT: A 62 ASP cc_start: 0.8039 (t70) cc_final: 0.7727 (t0) REVERT: A 94 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 160 THR cc_start: 0.8693 (m) cc_final: 0.8482 (m) REVERT: A 658 GLU cc_start: 0.8418 (tt0) cc_final: 0.7906 (mt-10) REVERT: A 711 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8139 (mm-30) REVERT: A 764 ASN cc_start: 0.7285 (t0) cc_final: 0.6853 (t0) REVERT: L 55 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8089 (ttp80) REVERT: H 10 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7317 (mt-10) REVERT: H 13 ARG cc_start: 0.7841 (mmm160) cc_final: 0.6993 (mmm160) outliers start: 14 outliers final: 13 residues processed: 108 average time/residue: 0.2321 time to fit residues: 34.4522 Evaluate side-chains 109 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL 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 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 11 THR Chi-restraints excluded: chain L residue 17 VAL 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 95 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.135826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098717 restraints weight = 10103.847| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.92 r_work: 0.3042 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7836 Z= 0.186 Angle : 0.512 11.904 10638 Z= 0.269 Chirality : 0.041 0.145 1215 Planarity : 0.003 0.038 1332 Dihedral : 4.099 21.494 1047 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.03 % Rotamer: Outliers : 1.94 % Allowed : 15.74 % Favored : 82.32 % 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: 1.15 (0.28), residues: 966 helix: 2.05 (0.27), residues: 344 sheet: 0.24 (0.30), residues: 304 loop : -0.00 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 709 HIS 0.003 0.001 HIS A 243 PHE 0.013 0.001 PHE A 926 TYR 0.010 0.001 TYR A 180 ARG 0.003 0.000 ARG H 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4565.59 seconds wall clock time: 81 minutes 49.65 seconds (4909.65 seconds total)