Starting phenix.real_space_refine on Sat Oct 24 11:28:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36iv_77606/10_2026/36iv_77606.cif Found real_map, /net/cci-nas-00/data/ceres_data/36iv_77606/10_2026/36iv_77606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36iv_77606/10_2026/36iv_77606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36iv_77606/10_2026/36iv_77606.map" model { file = "/net/cci-nas-00/data/ceres_data/36iv_77606/10_2026/36iv_77606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36iv_77606/10_2026/36iv_77606.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1026 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 255 5.49 5 S 18 5.16 5 C 6996 2.51 5 N 2310 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12375 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ALY:plan-2': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2609 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "J" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 2616 Classifications: {'DNA': 127} Link IDs: {'rna3p': 126} Chain: "K" Number of atoms: 1063 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 127, 1059 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 127, 1059 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1085 Time building chain proxies: 2.73, per 1000 atoms: 0.22 Number of scatterers: 12375 At special positions: 0 Unit cell: (95.175, 115.425, 117.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 255 15.00 O 2796 8.00 N 2310 7.00 C 6996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 400.0 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1682 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 70.4% alpha, 2.7% beta 123 base pairs and 217 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.686A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.546A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.526A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.596A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.816A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.737A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.410A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.522A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.763A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.000A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.591A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.386A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.522A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 60 through 69 removed outlier: 3.631A pdb=" N GLN K 64 " --> pdb=" O THR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.636A pdb=" N GLN K 85 " --> pdb=" O TRP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 95 through 101 removed outlier: 3.696A pdb=" N LYS K 99 " --> pdb=" O PRO K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 117 removed outlier: 3.902A pdb=" N GLU K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 138 removed outlier: 4.088A pdb=" N ILE K 126 " --> pdb=" O ALA K 122 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN K 127 " --> pdb=" O GLN K 123 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR K 137 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 162 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.845A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.513A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.369A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.987A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.136A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 446 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 319 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 217 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2340 1.33 - 1.45: 4126 1.45 - 1.57: 6114 1.57 - 1.69: 508 1.69 - 1.81: 32 Bond restraints: 13120 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" C3' DC J 34 " pdb=" C2' DC J 34 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.24e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 17741 1.91 - 3.83: 1003 3.83 - 5.74: 53 5.74 - 7.66: 12 7.66 - 9.57: 3 Bond angle restraints: 18812 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.96 107.23 5.73 1.00e+00 1.00e+00 3.29e+01 angle pdb=" O4' DG I 47 " pdb=" C4' DG I 47 " pdb=" C3' DG I 47 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.16e+01 angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.86e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 119.70 125.23 -5.53 1.20e+00 6.94e-01 2.12e+01 angle pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sigma weight residual 119.70 125.08 -5.38 1.20e+00 6.94e-01 2.01e+01 ... (remaining 18807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 5952 35.18 - 70.35: 1270 70.35 - 105.53: 23 105.53 - 140.70: 4 140.70 - 175.87: 2 Dihedral angle restraints: 7251 sinusoidal: 4646 harmonic: 2605 Sorted by residual: dihedral pdb=" CA ASN F 64 " pdb=" C ASN F 64 " pdb=" N VAL F 65 " pdb=" CA VAL F 65 " ideal model delta harmonic sigma weight residual 180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.87 -175.87 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1467 0.048 - 0.096: 549 0.096 - 0.143: 95 0.143 - 0.191: 15 0.191 - 0.239: 4 Chirality restraints: 2130 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.57 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA GLU K 151 " pdb=" N GLU K 151 " pdb=" C GLU K 151 " pdb=" CB GLU K 151 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA TRP K 81 " pdb=" N TRP K 81 " pdb=" C TRP K 81 " pdb=" CB TRP K 81 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 2127 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C LYS F 59 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C LEU F 62 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU F 62 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU F 63 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO G 80 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.033 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2938 2.82 - 3.34: 10511 3.34 - 3.86: 24381 3.86 - 4.38: 28300 4.38 - 4.90: 40318 Nonbonded interactions: 106448 Sorted by model distance: nonbonded pdb=" OH TYR K 65 " pdb=" O LYS K 160 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR G 50 " pdb=" OE1 GLN H 92 " model vdw 2.354 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.365 3.040 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.387 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.404 3.040 ... (remaining 106443 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'C' and resid 12 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.006 0.053 13120 Z= 0.524 Angle : 0.898 9.574 18812 Z= 0.732 Chirality : 0.049 0.239 2130 Planarity : 0.006 0.060 1505 Dihedral : 26.847 175.875 5569 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 872 helix: -0.19 (0.18), residues: 599 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 76 TYR 0.016 0.002 TYR K 137 PHE 0.022 0.002 PHE K 157 TRP 0.015 0.003 TRP K 75 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.52 (13120) covalent geometry : angle 0.89841 / 0.73 (18812) hydrogen bonds : bond 0.10322 / 7.14 ( 765) hydrogen bonds : angle 4.78715 / 3.39 ( 1964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8865 (t0) cc_final: 0.8633 (t0) REVERT: C 90 ASP cc_start: 0.8352 (t70) cc_final: 0.8125 (t0) REVERT: F 44 LYS cc_start: 0.8840 (tttt) cc_final: 0.8604 (tttp) REVERT: G 72 ASP cc_start: 0.8590 (m-30) cc_final: 0.8286 (m-30) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.8746 time to fit residues: 122.0490 Evaluate side-chains 81 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 106, 38] chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.077851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.051620 restraints weight = 48984.631| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.17 r_work: 0.2926 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13120 Z= 0.164 Angle : 0.670 8.725 18812 Z= 0.388 Chirality : 0.046 0.273 2130 Planarity : 0.005 0.045 1505 Dihedral : 30.525 173.291 3776 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.67 % Allowed : 10.12 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.27), residues: 872 helix: 1.24 (0.20), residues: 605 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 68 TYR 0.010 0.001 TYR K 139 PHE 0.012 0.002 PHE K 157 TRP 0.025 0.003 TRP K 120 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (13120) covalent geometry : angle 0.67011 / 0.39 (18812) hydrogen bonds : bond 0.04850 / 3.29 ( 765) hydrogen bonds : angle 3.63846 / 2.57 ( 1964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.7948 (mtm) REVERT: C 90 ASP cc_start: 0.8452 (t70) cc_final: 0.8140 (t0) REVERT: D 39 TYR cc_start: 0.8376 (t80) cc_final: 0.7999 (t80) REVERT: G 72 ASP cc_start: 0.8778 (m-30) cc_final: 0.8443 (m-30) REVERT: G 76 THR cc_start: 0.9187 (p) cc_final: 0.8758 (t) outliers start: 5 outliers final: 1 residues processed: 89 average time/residue: 0.7210 time to fit residues: 68.5482 Evaluate side-chains 74 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain K residue 58 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [78, 90, 13, 50, 31, 0, 37, 29, 39, 12, 93] chunk 78 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 overall best weight: 1.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.077308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050672 restraints weight = 50444.996| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.18 r_work: 0.2892 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13120 Z= 0.163 Angle : 0.629 8.554 18812 Z= 0.364 Chirality : 0.044 0.253 2130 Planarity : 0.004 0.038 1505 Dihedral : 30.725 174.152 3776 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.80 % Allowed : 9.99 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.28), residues: 872 helix: 1.92 (0.20), residues: 603 sheet: None (None), residues: 0 loop : -0.20 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 30 TYR 0.010 0.001 TYR F 88 PHE 0.011 0.002 PHE C 25 TRP 0.023 0.002 TRP K 120 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (13120) covalent geometry : angle 0.62901 / 0.36 (18812) hydrogen bonds : bond 0.04367 / 2.95 ( 765) hydrogen bonds : angle 3.33698 / 2.36 ( 1964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8399 (mtm) REVERT: C 90 ASP cc_start: 0.8462 (t70) cc_final: 0.8141 (t0) REVERT: D 39 TYR cc_start: 0.8403 (t80) cc_final: 0.8015 (t80) REVERT: D 96 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8572 (ptp-170) REVERT: G 72 ASP cc_start: 0.8770 (m-30) cc_final: 0.8393 (m-30) REVERT: G 76 THR cc_start: 0.9220 (p) cc_final: 0.8770 (t) REVERT: K 159 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8865 (pp30) outliers start: 6 outliers final: 2 residues processed: 89 average time/residue: 0.8010 time to fit residues: 75.8356 Evaluate side-chains 73 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain K residue 58 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [98, 80, 18, 97, 103, 32, 55, 66, 69, 46, 2] chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.076706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049970 restraints weight = 49787.026| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.16 r_work: 0.2870 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13120 Z= 0.179 Angle : 0.634 7.718 18812 Z= 0.363 Chirality : 0.044 0.255 2130 Planarity : 0.004 0.047 1505 Dihedral : 30.769 173.746 3776 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.20 % Allowed : 11.19 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.28), residues: 872 helix: 2.17 (0.21), residues: 605 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 68 TYR 0.010 0.001 TYR K 97 PHE 0.019 0.002 PHE K 83 TRP 0.024 0.003 TRP K 120 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (13120) covalent geometry : angle 0.63441 / 0.36 (18812) hydrogen bonds : bond 0.04448 / 3.01 ( 765) hydrogen bonds : angle 3.30208 / 2.33 ( 1964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8556 (mtm) REVERT: C 90 ASP cc_start: 0.8436 (t70) cc_final: 0.8129 (t70) REVERT: D 31 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8695 (mmmt) REVERT: D 39 TYR cc_start: 0.8436 (t80) cc_final: 0.8132 (t80) REVERT: D 96 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8641 (ptp-170) REVERT: E 120 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7986 (mmt) REVERT: F 52 GLU cc_start: 0.8117 (pm20) cc_final: 0.7899 (pm20) REVERT: G 72 ASP cc_start: 0.8800 (m-30) cc_final: 0.8379 (m-30) REVERT: G 74 LYS cc_start: 0.9475 (mptp) cc_final: 0.9212 (mppt) REVERT: G 76 THR cc_start: 0.9215 (p) cc_final: 0.8795 (t) REVERT: K 149 MET cc_start: 0.8787 (mpt) cc_final: 0.8384 (pmm) outliers start: 9 outliers final: 2 residues processed: 85 average time/residue: 0.7985 time to fit residues: 72.0964 Evaluate side-chains 76 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain K residue 58 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [102, 72, 57, 5, 8, 27, 38, 66, 56, 100, 36] chunk 102 optimal weight: 6.9990 chunk 72 optimal weight: 50.0000 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.076816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.049959 restraints weight = 62899.808| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.39 r_work: 0.2852 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13120 Z= 0.156 Angle : 0.614 7.677 18812 Z= 0.353 Chirality : 0.043 0.254 2130 Planarity : 0.004 0.037 1505 Dihedral : 30.792 173.677 3776 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.67 % Allowed : 11.98 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.28), residues: 872 helix: 2.33 (0.21), residues: 607 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 68 TYR 0.009 0.001 TYR H 37 PHE 0.018 0.001 PHE C 25 TRP 0.027 0.003 TRP K 120 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (13120) covalent geometry : angle 0.61361 / 0.35 (18812) hydrogen bonds : bond 0.04191 / 2.85 ( 765) hydrogen bonds : angle 3.18731 / 2.27 ( 1964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8555 (mtm) REVERT: C 90 ASP cc_start: 0.8448 (t70) cc_final: 0.8177 (t70) REVERT: D 39 TYR cc_start: 0.8494 (t80) cc_final: 0.8241 (t80) REVERT: D 96 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8626 (ptp-170) REVERT: G 72 ASP cc_start: 0.8795 (m-30) cc_final: 0.8386 (m-30) REVERT: G 74 LYS cc_start: 0.9468 (mptp) cc_final: 0.9218 (mppt) REVERT: G 76 THR cc_start: 0.9251 (p) cc_final: 0.8846 (t) outliers start: 5 outliers final: 0 residues processed: 82 average time/residue: 0.7517 time to fit residues: 65.7549 Evaluate side-chains 72 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 96 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [13, 65, 66, 23, 86, 18, 81, 71, 3, 62, 8] chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.076664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050180 restraints weight = 48381.859| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.13 r_work: 0.2867 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13120 Z= 0.165 Angle : 0.626 7.815 18812 Z= 0.357 Chirality : 0.043 0.253 2130 Planarity : 0.004 0.036 1505 Dihedral : 30.798 173.685 3776 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.40 % Allowed : 13.45 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.28), residues: 872 helix: 2.38 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.01 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.018 0.001 TYR C 57 PHE 0.020 0.002 PHE K 83 TRP 0.031 0.003 TRP K 120 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (13120) covalent geometry : angle 0.62555 / 0.36 (18812) hydrogen bonds : bond 0.04277 / 2.91 ( 765) hydrogen bonds : angle 3.15796 / 2.25 ( 1964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8634 (mtm) REVERT: C 90 ASP cc_start: 0.8412 (t70) cc_final: 0.8141 (t70) REVERT: D 39 TYR cc_start: 0.8468 (t80) cc_final: 0.8240 (t80) REVERT: D 96 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8608 (ptp-170) REVERT: G 72 ASP cc_start: 0.8800 (m-30) cc_final: 0.8400 (m-30) REVERT: G 74 LYS cc_start: 0.9475 (mptp) cc_final: 0.9202 (mppt) REVERT: G 76 THR cc_start: 0.9218 (p) cc_final: 0.8814 (t) outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.7647 time to fit residues: 62.7045 Evaluate side-chains 71 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain D residue 96 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [6, 1, 27, 67, 100, 34, 81, 43, 101, 36, 52] chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.077300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051084 restraints weight = 48355.707| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.11 r_work: 0.2877 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 13120 Z= 0.133 Angle : 0.612 8.995 18812 Z= 0.352 Chirality : 0.042 0.254 2130 Planarity : 0.004 0.037 1505 Dihedral : 30.719 173.670 3776 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.27 % Allowed : 13.85 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.28), residues: 872 helix: 2.46 (0.20), residues: 610 sheet: None (None), residues: 0 loop : 0.07 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.018 0.001 TYR C 57 PHE 0.012 0.001 PHE C 25 TRP 0.035 0.003 TRP K 120 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.13 (13120) covalent geometry : angle 0.61156 / 0.35 (18812) hydrogen bonds : bond 0.03999 / 2.74 ( 765) hydrogen bonds : angle 3.07268 / 2.19 ( 1964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8379 (t70) cc_final: 0.8133 (t70) REVERT: D 39 TYR cc_start: 0.8424 (t80) cc_final: 0.8134 (t80) REVERT: D 96 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8391 (ptp-170) REVERT: G 72 ASP cc_start: 0.8778 (m-30) cc_final: 0.8395 (m-30) REVERT: G 74 LYS cc_start: 0.9472 (mptp) cc_final: 0.9200 (mppt) REVERT: G 76 THR cc_start: 0.9218 (p) cc_final: 0.8814 (t) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.8174 time to fit residues: 68.7277 Evaluate side-chains 69 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain K residue 85 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [14, 30, 53, 46, 89, 16, 82, 37, 67, 61, 65] chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.077335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050665 restraints weight = 62711.346| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.40 r_work: 0.2856 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13120 Z= 0.136 Angle : 0.618 9.375 18812 Z= 0.354 Chirality : 0.042 0.253 2130 Planarity : 0.004 0.049 1505 Dihedral : 30.680 173.626 3776 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.27 % Allowed : 14.38 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.28), residues: 872 helix: 2.56 (0.20), residues: 607 sheet: None (None), residues: 0 loop : 0.08 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 68 TYR 0.019 0.001 TYR C 57 PHE 0.024 0.002 PHE K 83 TRP 0.036 0.003 TRP K 120 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (13120) covalent geometry : angle 0.61844 / 0.35 (18812) hydrogen bonds : bond 0.04026 / 2.77 ( 765) hydrogen bonds : angle 3.05930 / 2.18 ( 1964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8371 (t70) cc_final: 0.8106 (t70) REVERT: D 39 TYR cc_start: 0.8483 (t80) cc_final: 0.8210 (t80) REVERT: D 96 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8442 (ptp-170) REVERT: G 72 ASP cc_start: 0.8823 (m-30) cc_final: 0.8432 (m-30) REVERT: G 74 LYS cc_start: 0.9468 (mptp) cc_final: 0.9199 (mppt) REVERT: G 76 THR cc_start: 0.9230 (p) cc_final: 0.8818 (t) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.7878 time to fit residues: 62.0743 Evaluate side-chains 69 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 96 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [34, 50, 89, 3, 77, 36, 78, 44, 79, 33, 54] chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.076040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049465 restraints weight = 49662.711| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.15 r_work: 0.2846 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13120 Z= 0.208 Angle : 0.672 9.259 18812 Z= 0.376 Chirality : 0.043 0.254 2130 Planarity : 0.004 0.034 1505 Dihedral : 30.808 173.205 3776 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.27 % Allowed : 14.78 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.28), residues: 872 helix: 2.47 (0.21), residues: 607 sheet: None (None), residues: 0 loop : 0.01 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 68 TYR 0.022 0.001 TYR C 57 PHE 0.023 0.002 PHE C 25 TRP 0.037 0.004 TRP K 120 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (13120) covalent geometry : angle 0.67200 / 0.38 (18812) hydrogen bonds : bond 0.04778 / 3.25 ( 765) hydrogen bonds : angle 3.17847 / 2.27 ( 1964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8389 (t70) cc_final: 0.8135 (t70) REVERT: G 72 ASP cc_start: 0.8806 (m-30) cc_final: 0.8420 (m-30) REVERT: G 74 LYS cc_start: 0.9490 (mptp) cc_final: 0.9235 (mppt) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.7970 time to fit residues: 59.4573 Evaluate side-chains 63 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [103, 101, 54, 4, 17, 107, 51, 30, 8, 60, 81] chunk 103 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.077003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050835 restraints weight = 43777.023| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.02 r_work: 0.2882 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 13120 Z= 0.134 Angle : 0.643 10.368 18812 Z= 0.364 Chirality : 0.042 0.255 2130 Planarity : 0.004 0.077 1505 Dihedral : 30.742 173.222 3776 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 15.31 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.28), residues: 872 helix: 2.56 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 68 TYR 0.019 0.001 TYR C 57 PHE 0.024 0.002 PHE K 83 TRP 0.038 0.004 TRP K 120 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (13120) covalent geometry : angle 0.64271 / 0.36 (18812) hydrogen bonds : bond 0.04066 / 2.77 ( 765) hydrogen bonds : angle 3.09399 / 2.21 ( 1964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.9011 (t0) cc_final: 0.8784 (t0) REVERT: C 90 ASP cc_start: 0.8349 (t70) cc_final: 0.8066 (t70) REVERT: G 72 ASP cc_start: 0.8805 (m-30) cc_final: 0.8437 (m-30) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.7466 time to fit residues: 56.7571 Evaluate side-chains 68 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: [19, 13, 76, 52, 0, 29, 23, 72, 30, 104, 25] chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 50.0000 chunk 30 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.077177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051088 restraints weight = 43329.566| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.02 r_work: 0.2900 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 13120 Z= 0.137 Angle : 0.626 9.554 18812 Z= 0.358 Chirality : 0.041 0.254 2130 Planarity : 0.004 0.034 1505 Dihedral : 30.660 173.347 3776 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.13 % Allowed : 15.58 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.28), residues: 872 helix: 2.59 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 0.11 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 76 TYR 0.020 0.001 TYR C 57 PHE 0.012 0.001 PHE C 25 TRP 0.036 0.003 TRP K 120 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (13120) covalent geometry : angle 0.62642 / 0.36 (18812) hydrogen bonds : bond 0.04106 / 2.82 ( 765) hydrogen bonds : angle 3.07251 / 2.19 ( 1964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4075.10 seconds wall clock time: 69 minutes 57.51 seconds (4197.51 seconds total)