Starting phenix.real_space_refine on Sun Apr 27 05:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v93_43048/04_2025/8v93_43048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v93_43048/04_2025/8v93_43048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v93_43048/04_2025/8v93_43048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v93_43048/04_2025/8v93_43048.map" model { file = "/net/cci-nas-00/data/ceres_data/8v93_43048/04_2025/8v93_43048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v93_43048/04_2025/8v93_43048.cif" } resolution = 3.12 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= -0.001 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2968 2.51 5 N 779 2.21 5 O 923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4686 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 907 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "D" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1219 Classifications: {'peptide': 163} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 153} Chain breaks: 1 Chain: "L" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 3.30, per 1000 atoms: 0.70 Number of scatterers: 4686 At special positions: 0 Unit cell: (61.36, 70.8, 116.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 923 8.00 N 779 7.00 C 2968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 44 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 0.97 Conformation dependent library (CDL) restraints added in 523.0 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 16 sheets defined 1.6% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.933A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.876A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 4.858A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.155A pdb=" N GLU A 10 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 93 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N MET A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 19 removed outlier: 3.510A pdb=" N THR A 71 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 82 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.595A pdb=" N LYS B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.281A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.281A pdb=" N GLY B 10 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N CYS B 96 " --> pdb=" O TRP B 110 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TRP B 110 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ARG B 98 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.544A pdb=" N THR C 5 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.905A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 13 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU C 33 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 5 removed outlier: 4.078A pdb=" N LYS D 4 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 43 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS D 44 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS D 101 " --> pdb=" O CYS D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.889A pdb=" N VAL D 22 " --> pdb=" O TYR D 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 18 removed outlier: 6.712A pdb=" N PHE D 144 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE D 130 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TRP D 146 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL D 128 " --> pdb=" O TRP D 146 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 148 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 24 through 29 removed outlier: 5.536A pdb=" N ALA D 25 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 36 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU D 34 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 109 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 36 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.739A pdb=" N PHE L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.723A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 48 through 49 145 hydrogen bonds defined for protein. 351 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: 1.12 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 820 1.33 - 1.45: 1467 1.45 - 1.58: 2490 1.58 - 1.71: 1 1.71 - 1.84: 21 Bond restraints: 4799 Sorted by residual: bond pdb=" CA ASP A 101 " pdb=" C ASP A 101 " ideal model delta sigma weight residual 1.524 1.473 0.050 1.26e-02 6.30e+03 1.60e+01 bond pdb=" CA PRO A 102 " pdb=" C PRO A 102 " ideal model delta sigma weight residual 1.517 1.550 -0.033 9.30e-03 1.16e+04 1.25e+01 bond pdb=" C ASP A 101 " pdb=" O ASP A 101 " ideal model delta sigma weight residual 1.238 1.198 0.040 1.28e-02 6.10e+03 9.57e+00 bond pdb=" C ASN B 32 " pdb=" N GLY B 33 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.52e-02 4.33e+03 9.17e+00 bond pdb=" CA ALA B 55 " pdb=" C ALA B 55 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.34e-02 5.57e+03 5.05e+00 ... (remaining 4794 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 6345 2.41 - 4.82: 144 4.82 - 7.22: 26 7.22 - 9.63: 14 9.63 - 12.04: 2 Bond angle restraints: 6531 Sorted by residual: angle pdb=" N PHE B 56 " pdb=" CA PHE B 56 " pdb=" C PHE B 56 " ideal model delta sigma weight residual 112.89 120.19 -7.30 1.24e+00 6.50e-01 3.47e+01 angle pdb=" N ALA B 55 " pdb=" CA ALA B 55 " pdb=" C ALA B 55 " ideal model delta sigma weight residual 110.80 99.58 11.22 2.13e+00 2.20e-01 2.77e+01 angle pdb=" N PRO A 102 " pdb=" CA PRO A 102 " pdb=" C PRO A 102 " ideal model delta sigma weight residual 110.70 116.70 -6.00 1.22e+00 6.72e-01 2.42e+01 angle pdb=" CB MET A 34 " pdb=" CG MET A 34 " pdb=" SD MET A 34 " ideal model delta sigma weight residual 112.70 124.74 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA ARG B 98 " pdb=" CB ARG B 98 " pdb=" CG ARG B 98 " ideal model delta sigma weight residual 114.10 122.01 -7.91 2.00e+00 2.50e-01 1.56e+01 ... (remaining 6526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2550 17.93 - 35.85: 205 35.85 - 53.78: 32 53.78 - 71.70: 5 71.70 - 89.63: 5 Dihedral angle restraints: 2797 sinusoidal: 1042 harmonic: 1755 Sorted by residual: dihedral pdb=" CA THR B 52 " pdb=" C THR B 52 " pdb=" N ASN B 53 " pdb=" CA ASN B 53 " ideal model delta harmonic sigma weight residual -180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 53.25 39.75 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CA TYR B 103 " pdb=" C TYR B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual -180.00 -157.55 -22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 2794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 497 0.047 - 0.094: 155 0.094 - 0.141: 53 0.141 - 0.189: 12 0.189 - 0.236: 7 Chirality restraints: 724 Sorted by residual: chirality pdb=" CG LEU B 86 " pdb=" CB LEU B 86 " pdb=" CD1 LEU B 86 " pdb=" CD2 LEU B 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU B 99 " pdb=" CB LEU B 99 " pdb=" CD1 LEU B 99 " pdb=" CD2 LEU B 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 104 " pdb=" N PRO B 104 " pdb=" C PRO B 104 " pdb=" CB PRO B 104 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 721 not shown) Planarity restraints: 838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 103 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.67e+01 pdb=" N PRO B 104 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 107 " 0.023 2.00e-02 2.50e+03 1.80e-02 8.11e+00 pdb=" CG TRP A 107 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 107 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 107 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 107 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 107 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 107 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 100 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.71e+00 pdb=" C GLY A 100 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY A 100 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A 101 " 0.016 2.00e-02 2.50e+03 ... (remaining 835 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1421 2.83 - 3.34: 3673 3.34 - 3.86: 7801 3.86 - 4.38: 8398 4.38 - 4.90: 15123 Nonbonded interactions: 36416 Sorted by model distance: nonbonded pdb=" OG SER L 40 " pdb=" OE1 GLU L 42 " model vdw 2.308 3.040 nonbonded pdb=" OG SER L 63 " pdb=" OG SER L 74 " model vdw 2.321 3.040 nonbonded pdb=" O GLY B 111 " pdb=" OG SER L 43 " model vdw 2.341 3.040 nonbonded pdb=" OD1 ASP B 102 " pdb=" OH TYR L 50 " model vdw 2.366 3.040 nonbonded pdb=" NH1 ARG L 61 " pdb=" OE2 GLU L 79 " model vdw 2.380 3.120 ... (remaining 36411 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: 0.740 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.570 Find NCS groups from input model: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4541 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 : 0.005 0.094 4804 Z= 0.248 Angle : 0.981 12.038 6541 Z= 0.530 Chirality : 0.056 0.236 724 Planarity : 0.008 0.129 838 Dihedral : 13.541 89.626 1668 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.98 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.91 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.18 (0.33), residues: 253 loop : -2.22 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 107 HIS 0.011 0.003 HIS L 34 PHE 0.027 0.002 PHE B 107 TYR 0.031 0.002 TYR B 106 ARG 0.007 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.18506 ( 139) hydrogen bonds : angle 9.63487 ( 351) SS BOND : bond 0.00327 ( 5) SS BOND : angle 1.89067 ( 10) covalent geometry : bond 0.00469 ( 4799) covalent geometry : angle 0.97897 ( 6531) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.486 Fit side-chains REVERT: B 34 MET cc_start: 0.1360 (mmt) cc_final: 0.0593 (ttm) REVERT: D 52 ILE cc_start: 0.5643 (tp) cc_final: 0.5019 (mp) REVERT: L 22 PHE cc_start: 0.6428 (m-80) cc_final: 0.6183 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1753 time to fit residues: 24.9803 Evaluate side-chains 78 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.0010 chunk 52 optimal weight: 4.9990 overall best weight: 0.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 45 GLN D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.258342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.234762 restraints weight = 6039.255| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.56 r_work: 0.4605 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 4804 Z= 0.142 Angle : 0.623 8.446 6541 Z= 0.330 Chirality : 0.044 0.147 724 Planarity : 0.007 0.129 838 Dihedral : 4.731 19.541 660 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.15 % Favored : 94.52 % Rotamer: Outliers : 2.53 % Allowed : 11.11 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.54 (0.33), residues: 602 helix: None (None), residues: 0 sheet: 0.10 (0.34), residues: 247 loop : -1.96 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 35 HIS 0.004 0.001 HIS L 34 PHE 0.020 0.002 PHE A 104 TYR 0.020 0.002 TYR B 106 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 139) hydrogen bonds : angle 7.14344 ( 351) SS BOND : bond 0.01081 ( 5) SS BOND : angle 1.32436 ( 10) covalent geometry : bond 0.00347 ( 4799) covalent geometry : angle 0.62164 ( 6531) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.464 Fit side-chains REVERT: A 82 GLN cc_start: 0.5819 (tt0) cc_final: 0.5570 (tt0) REVERT: B 34 MET cc_start: 0.3760 (mmt) cc_final: 0.2815 (ttm) REVERT: D 4 LYS cc_start: 0.5801 (pttm) cc_final: 0.5508 (pptt) REVERT: D 53 THR cc_start: 0.7870 (m) cc_final: 0.7544 (p) REVERT: D 101 LYS cc_start: 0.6215 (pttm) cc_final: 0.5957 (pttp) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 0.1593 time to fit residues: 19.7970 Evaluate side-chains 78 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 70 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.228076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.199831 restraints weight = 5919.383| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.74 r_work: 0.4304 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 4804 Z= 0.186 Angle : 0.672 7.301 6541 Z= 0.352 Chirality : 0.046 0.155 724 Planarity : 0.006 0.121 838 Dihedral : 4.864 19.574 660 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.98 % Favored : 92.69 % Rotamer: Outliers : 3.31 % Allowed : 11.50 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.34), residues: 602 helix: None (None), residues: 0 sheet: 0.04 (0.34), residues: 241 loop : -1.92 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 107 HIS 0.004 0.002 HIS A 35 PHE 0.018 0.003 PHE B 107 TYR 0.016 0.002 TYR A 50 ARG 0.007 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 139) hydrogen bonds : angle 7.23529 ( 351) SS BOND : bond 0.00393 ( 5) SS BOND : angle 1.41105 ( 10) covalent geometry : bond 0.00440 ( 4799) covalent geometry : angle 0.67035 ( 6531) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 21 SER cc_start: 0.6029 (t) cc_final: 0.5723 (t) REVERT: A 66 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7061 (m-30) REVERT: C 106 MET cc_start: 0.5705 (mmm) cc_final: 0.5484 (mmp) REVERT: D 53 THR cc_start: 0.8320 (m) cc_final: 0.7998 (p) REVERT: D 71 PHE cc_start: 0.4303 (m-10) cc_final: 0.4078 (m-10) REVERT: D 95 TYR cc_start: 0.6995 (m-80) cc_final: 0.6794 (m-80) REVERT: D 135 ASN cc_start: 0.8262 (OUTLIER) cc_final: 0.7337 (m-40) REVERT: L 79 GLU cc_start: 0.6200 (pm20) cc_final: 0.5993 (pp20) outliers start: 17 outliers final: 9 residues processed: 111 average time/residue: 0.1651 time to fit residues: 23.2001 Evaluate side-chains 93 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.211814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183548 restraints weight = 6008.023| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 2.71 r_work: 0.4139 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.7454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 4804 Z= 0.210 Angle : 0.725 7.991 6541 Z= 0.378 Chirality : 0.047 0.154 724 Planarity : 0.006 0.122 838 Dihedral : 4.958 20.642 660 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.31 % Favored : 92.36 % Rotamer: Outliers : 5.85 % Allowed : 11.50 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.69 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.25 (0.34), residues: 247 loop : -1.83 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 107 HIS 0.004 0.002 HIS L 92 PHE 0.018 0.002 PHE L 86 TYR 0.032 0.003 TYR A 50 ARG 0.009 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 139) hydrogen bonds : angle 7.35239 ( 351) SS BOND : bond 0.00715 ( 5) SS BOND : angle 0.89394 ( 10) covalent geometry : bond 0.00487 ( 4799) covalent geometry : angle 0.72508 ( 6531) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7542 (m-30) cc_final: 0.7229 (m-30) REVERT: A 98 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6221 (ttt-90) REVERT: B 34 MET cc_start: 0.4463 (tpp) cc_final: 0.4176 (mmp) REVERT: C 81 GLU cc_start: 0.7123 (pp20) cc_final: 0.6542 (pp20) REVERT: C 106 MET cc_start: 0.6899 (mmm) cc_final: 0.6212 (mmt) REVERT: D 11 ILE cc_start: 0.6758 (mm) cc_final: 0.6420 (mt) REVERT: D 53 THR cc_start: 0.8315 (m) cc_final: 0.8013 (p) REVERT: D 95 TYR cc_start: 0.7354 (m-80) cc_final: 0.7094 (m-80) REVERT: D 100 ASP cc_start: 0.7557 (m-30) cc_final: 0.7252 (m-30) REVERT: L 102 THR cc_start: 0.7697 (m) cc_final: 0.7324 (p) outliers start: 30 outliers final: 20 residues processed: 110 average time/residue: 0.1906 time to fit residues: 25.9683 Evaluate side-chains 105 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 82 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 135 ASN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.210675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.183198 restraints weight = 5941.909| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.62 r_work: 0.4148 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.7728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 4804 Z= 0.164 Angle : 0.649 8.468 6541 Z= 0.336 Chirality : 0.045 0.172 724 Planarity : 0.006 0.120 838 Dihedral : 4.730 19.471 660 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.81 % Favored : 93.85 % Rotamer: Outliers : 2.92 % Allowed : 16.18 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.70 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.22 (0.35), residues: 237 loop : -1.84 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 107 HIS 0.002 0.001 HIS C 90 PHE 0.017 0.002 PHE L 86 TYR 0.029 0.002 TYR A 50 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 139) hydrogen bonds : angle 7.23242 ( 351) SS BOND : bond 0.00637 ( 5) SS BOND : angle 1.02477 ( 10) covalent geometry : bond 0.00390 ( 4799) covalent geometry : angle 0.64830 ( 6531) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.621 Fit side-chains REVERT: A 63 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7855 (tptt) REVERT: A 66 ASP cc_start: 0.7425 (m-30) cc_final: 0.7178 (m-30) REVERT: C 61 ARG cc_start: 0.4941 (mtm180) cc_final: 0.4733 (mtm180) REVERT: D 11 ILE cc_start: 0.6752 (mm) cc_final: 0.6419 (mt) REVERT: D 53 THR cc_start: 0.8278 (m) cc_final: 0.7961 (p) REVERT: D 95 TYR cc_start: 0.7295 (m-80) cc_final: 0.7014 (m-80) REVERT: D 100 ASP cc_start: 0.7419 (m-30) cc_final: 0.7161 (m-30) REVERT: L 65 SER cc_start: 0.6433 (t) cc_final: 0.5576 (p) REVERT: L 102 THR cc_start: 0.7732 (m) cc_final: 0.7374 (p) outliers start: 15 outliers final: 12 residues processed: 101 average time/residue: 0.1847 time to fit residues: 23.2181 Evaluate side-chains 96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 82 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.197482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.171372 restraints weight = 6157.405| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.49 r_work: 0.4023 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.9064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 4804 Z= 0.301 Angle : 0.821 11.049 6541 Z= 0.424 Chirality : 0.048 0.171 724 Planarity : 0.007 0.128 838 Dihedral : 5.466 21.014 660 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.80 % Favored : 90.86 % Rotamer: Outliers : 4.68 % Allowed : 16.18 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -2.04 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.60 (0.35), residues: 230 loop : -1.93 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP L 94 HIS 0.004 0.002 HIS C 90 PHE 0.020 0.003 PHE L 86 TYR 0.053 0.003 TYR A 50 ARG 0.006 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 139) hydrogen bonds : angle 8.03625 ( 351) SS BOND : bond 0.01148 ( 5) SS BOND : angle 1.67878 ( 10) covalent geometry : bond 0.00689 ( 4799) covalent geometry : angle 0.81896 ( 6531) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.518 Fit side-chains REVERT: A 66 ASP cc_start: 0.7460 (m-30) cc_final: 0.7220 (m-30) REVERT: C 81 GLU cc_start: 0.7371 (pp20) cc_final: 0.6894 (pp20) REVERT: D 11 ILE cc_start: 0.7024 (mm) cc_final: 0.6591 (mt) REVERT: D 97 SER cc_start: 0.7071 (p) cc_final: 0.6822 (t) REVERT: D 100 ASP cc_start: 0.7445 (m-30) cc_final: 0.7149 (m-30) REVERT: L 102 THR cc_start: 0.7779 (m) cc_final: 0.7578 (t) outliers start: 24 outliers final: 17 residues processed: 106 average time/residue: 0.1839 time to fit residues: 24.4285 Evaluate side-chains 98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.202442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.176891 restraints weight = 6008.700| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.47 r_work: 0.4088 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.8961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 4804 Z= 0.182 Angle : 0.695 9.304 6541 Z= 0.361 Chirality : 0.046 0.215 724 Planarity : 0.006 0.127 838 Dihedral : 4.953 21.212 660 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.48 % Favored : 93.19 % Rotamer: Outliers : 4.09 % Allowed : 17.15 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.88 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.75 (0.35), residues: 236 loop : -1.63 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 94 HIS 0.004 0.002 HIS L 34 PHE 0.016 0.002 PHE D 71 TYR 0.037 0.003 TYR B 106 ARG 0.006 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 139) hydrogen bonds : angle 7.61900 ( 351) SS BOND : bond 0.00698 ( 5) SS BOND : angle 1.31824 ( 10) covalent geometry : bond 0.00434 ( 4799) covalent geometry : angle 0.69344 ( 6531) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.483 Fit side-chains REVERT: A 66 ASP cc_start: 0.7511 (m-30) cc_final: 0.7282 (m-30) REVERT: B 106 TYR cc_start: 0.6186 (OUTLIER) cc_final: 0.5754 (p90) REVERT: C 81 GLU cc_start: 0.7337 (pp20) cc_final: 0.6713 (pp20) REVERT: D 11 ILE cc_start: 0.6911 (mm) cc_final: 0.6386 (mt) REVERT: L 79 GLU cc_start: 0.6594 (pm20) cc_final: 0.6298 (pp20) REVERT: L 102 THR cc_start: 0.7735 (m) cc_final: 0.7358 (p) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 0.1919 time to fit residues: 24.4608 Evaluate side-chains 100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 0.7980 chunk 23 optimal weight: 0.0170 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.178494 restraints weight = 5988.040| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.59 r_work: 0.4101 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.9005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 4804 Z= 0.167 Angle : 0.672 8.886 6541 Z= 0.349 Chirality : 0.045 0.199 724 Planarity : 0.006 0.126 838 Dihedral : 4.819 20.979 660 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.81 % Favored : 92.86 % Rotamer: Outliers : 3.90 % Allowed : 16.96 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.79 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.71 (0.35), residues: 236 loop : -1.55 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 94 HIS 0.005 0.002 HIS L 92 PHE 0.020 0.002 PHE A 60 TYR 0.037 0.002 TYR B 106 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 139) hydrogen bonds : angle 7.42468 ( 351) SS BOND : bond 0.00601 ( 5) SS BOND : angle 1.15686 ( 10) covalent geometry : bond 0.00405 ( 4799) covalent geometry : angle 0.67143 ( 6531) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.570 Fit side-chains REVERT: A 66 ASP cc_start: 0.7575 (m-30) cc_final: 0.7351 (m-30) REVERT: B 106 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5884 (p90) REVERT: C 81 GLU cc_start: 0.7434 (pp20) cc_final: 0.6631 (pp20) REVERT: D 11 ILE cc_start: 0.6857 (mm) cc_final: 0.6320 (mt) REVERT: L 79 GLU cc_start: 0.6709 (pm20) cc_final: 0.6363 (pp20) REVERT: L 102 THR cc_start: 0.7737 (m) cc_final: 0.7360 (p) outliers start: 20 outliers final: 16 residues processed: 98 average time/residue: 0.1923 time to fit residues: 23.5066 Evaluate side-chains 99 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.206193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.179761 restraints weight = 5977.861| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.59 r_work: 0.4113 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.9024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 4804 Z= 0.157 Angle : 0.664 8.302 6541 Z= 0.345 Chirality : 0.045 0.217 724 Planarity : 0.006 0.124 838 Dihedral : 4.845 21.086 660 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer: Outliers : 3.51 % Allowed : 17.35 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.70 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.62 (0.35), residues: 236 loop : -1.51 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 94 HIS 0.004 0.002 HIS L 34 PHE 0.014 0.002 PHE A 104 TYR 0.037 0.002 TYR B 106 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 139) hydrogen bonds : angle 7.25961 ( 351) SS BOND : bond 0.00614 ( 5) SS BOND : angle 1.15658 ( 10) covalent geometry : bond 0.00384 ( 4799) covalent geometry : angle 0.66281 ( 6531) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.473 Fit side-chains REVERT: A 63 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7798 (tptt) REVERT: B 19 LYS cc_start: 0.7057 (ptmm) cc_final: 0.6842 (tppt) REVERT: B 106 TYR cc_start: 0.6247 (OUTLIER) cc_final: 0.5695 (p90) REVERT: C 81 GLU cc_start: 0.7390 (pp20) cc_final: 0.6529 (pp20) REVERT: D 11 ILE cc_start: 0.6797 (mm) cc_final: 0.6264 (mt) REVERT: L 79 GLU cc_start: 0.6707 (pm20) cc_final: 0.6397 (pp20) REVERT: L 102 THR cc_start: 0.7865 (m) cc_final: 0.7513 (p) outliers start: 18 outliers final: 14 residues processed: 96 average time/residue: 0.1870 time to fit residues: 22.2987 Evaluate side-chains 99 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.200705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.175213 restraints weight = 6143.557| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.51 r_work: 0.4062 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.9370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 4804 Z= 0.208 Angle : 0.706 8.225 6541 Z= 0.369 Chirality : 0.046 0.233 724 Planarity : 0.007 0.125 838 Dihedral : 5.111 24.184 660 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 3.12 % Allowed : 17.74 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.82 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.73 (0.35), residues: 241 loop : -1.58 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 47 HIS 0.004 0.001 HIS L 92 PHE 0.018 0.002 PHE L 86 TYR 0.036 0.003 TYR B 106 ARG 0.006 0.001 ARG A 98 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 139) hydrogen bonds : angle 7.46136 ( 351) SS BOND : bond 0.00795 ( 5) SS BOND : angle 1.64639 ( 10) covalent geometry : bond 0.00496 ( 4799) covalent geometry : angle 0.70397 ( 6531) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: B 106 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5686 (p90) REVERT: C 81 GLU cc_start: 0.7513 (pp20) cc_final: 0.6845 (pp20) REVERT: D 11 ILE cc_start: 0.6867 (mm) cc_final: 0.6353 (mt) REVERT: L 79 GLU cc_start: 0.7042 (pm20) cc_final: 0.6675 (pp20) REVERT: L 102 THR cc_start: 0.7744 (m) cc_final: 0.7350 (p) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.1861 time to fit residues: 20.3597 Evaluate side-chains 92 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.202679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.177579 restraints weight = 6112.366| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.49 r_work: 0.4101 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.9319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 4804 Z= 0.154 Angle : 0.668 8.435 6541 Z= 0.346 Chirality : 0.045 0.209 724 Planarity : 0.006 0.122 838 Dihedral : 4.908 24.071 660 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 2.92 % Allowed : 18.13 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % 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: -1.76 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.69 (0.35), residues: 242 loop : -1.54 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 47 HIS 0.005 0.002 HIS L 34 PHE 0.015 0.002 PHE L 86 TYR 0.037 0.002 TYR B 106 ARG 0.005 0.001 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 139) hydrogen bonds : angle 7.27460 ( 351) SS BOND : bond 0.00563 ( 5) SS BOND : angle 1.06799 ( 10) covalent geometry : bond 0.00380 ( 4799) covalent geometry : angle 0.66699 ( 6531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2652.37 seconds wall clock time: 46 minutes 18.34 seconds (2778.34 seconds total)