Starting phenix.real_space_refine on Sat May 10 02:21:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v93_43048/05_2025/8v93_43048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v93_43048/05_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_43048/05_2025/8v93_43048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v93_43048/05_2025/8v93_43048.map" model { file = "/net/cci-nas-00/data/ceres_data/8v93_43048/05_2025/8v93_43048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v93_43048/05_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-5687/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: 3.65, per 1000 atoms: 0.78 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: 1.05 Conformation dependent library (CDL) restraints added in 573.6 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: 0.73 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: 1.23 Time building geometry restraints manager: 1.26 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.470 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- 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 : 0.454 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: 0.1783 time to fit residues: 25.3392 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 : 0.500 ------------------------------------------------------------------------------- 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 = 0.234763 restraints weight = 6039.255| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.56 r_work: 0.4606 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4606 ------------------------------------------------------------------------------- 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 : 0.466 Fit side-chains REVERT: A 82 GLN cc_start: 0.5818 (tt0) cc_final: 0.5570 (tt0) REVERT: B 34 MET cc_start: 0.3759 (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: 0.7871 (m) cc_final: 0.7545 (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: 0.1557 time to fit residues: 19.1796 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 : 0.451 ------------------------------------------------------------------------------- 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: 0.5980 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: 1.9990 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.216764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.188701 restraints weight = 5931.978| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.69 r_work: 0.4204 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 4804 Z= 0.275 Angle : 0.817 10.410 6541 Z= 0.428 Chirality : 0.049 0.149 724 Planarity : 0.007 0.120 838 Dihedral : 5.618 22.148 660 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.48 % Favored : 92.19 % Rotamer: Outliers : 4.29 % Allowed : 10.14 % Favored : 85.58 % 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: -1.90 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.17 (0.33), residues: 244 loop : -2.17 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP A 107 HIS 0.005 0.002 HIS A 35 PHE 0.020 0.003 PHE L 86 TYR 0.024 0.003 TYR D 82 ARG 0.011 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 139) hydrogen bonds : angle 7.97268 ( 351) SS BOND : bond 0.00930 ( 5) SS BOND : angle 1.93170 ( 10) covalent geometry : bond 0.00614 ( 4799) covalent geometry : angle 0.81424 ( 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 130 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7173 (m-30) REVERT: A 98 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.5442 (ttp-170) REVERT: B 106 TYR cc_start: 0.5772 (p90) cc_final: 0.5510 (p90) REVERT: C 106 MET cc_start: 0.6644 (mmm) cc_final: 0.5919 (mmt) REVERT: D 53 THR cc_start: 0.8298 (m) cc_final: 0.8050 (p) outliers start: 22 outliers final: 12 residues processed: 123 average time/residue: 0.1595 time to fit residues: 25.1138 Evaluate side-chains 97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 104 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.214499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186504 restraints weight = 6020.781| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 2.70 r_work: 0.4168 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 4804 Z= 0.172 Angle : 0.662 8.646 6541 Z= 0.346 Chirality : 0.045 0.157 724 Planarity : 0.006 0.121 838 Dihedral : 4.879 20.615 660 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 3.70 % Allowed : 13.45 % Favored : 82.85 % 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 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.19 (0.34), residues: 245 loop : -1.91 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 107 HIS 0.003 0.001 HIS L 34 PHE 0.017 0.002 PHE A 104 TYR 0.024 0.002 TYR A 50 ARG 0.007 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 139) hydrogen bonds : angle 7.18000 ( 351) SS BOND : bond 0.00685 ( 5) SS BOND : angle 0.51857 ( 10) covalent geometry : bond 0.00403 ( 4799) covalent geometry : angle 0.66226 ( 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 110 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.500 Fit side-chains REVERT: A 66 ASP cc_start: 0.7482 (m-30) cc_final: 0.7214 (m-30) REVERT: C 106 MET cc_start: 0.6623 (mmm) cc_final: 0.5913 (mmt) REVERT: D 53 THR cc_start: 0.8450 (m) cc_final: 0.8148 (p) REVERT: L 79 GLU cc_start: 0.6399 (pp20) cc_final: 0.6153 (pp20) REVERT: L 102 THR cc_start: 0.7697 (m) cc_final: 0.7311 (p) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 0.1699 time to fit residues: 22.3212 Evaluate side-chains 96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 105 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU 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 74 THR Chi-restraints excluded: chain D residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 49 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 39 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN C 53 ASN D 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.212928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.185179 restraints weight = 5960.329| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.65 r_work: 0.4157 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 4804 Z= 0.154 Angle : 0.636 8.691 6541 Z= 0.330 Chirality : 0.044 0.156 724 Planarity : 0.006 0.119 838 Dihedral : 4.713 19.684 660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.64 % Favored : 93.02 % Rotamer: Outliers : 4.29 % Allowed : 15.20 % Favored : 80.51 % 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: -1.68 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.13 (0.34), residues: 242 loop : -1.90 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 107 HIS 0.003 0.001 HIS L 34 PHE 0.019 0.002 PHE A 60 TYR 0.035 0.002 TYR A 50 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 139) hydrogen bonds : angle 7.20043 ( 351) SS BOND : bond 0.00630 ( 5) SS BOND : angle 0.80078 ( 10) covalent geometry : bond 0.00366 ( 4799) covalent geometry : angle 0.63563 ( 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 106 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.473 Fit side-chains REVERT: A 66 ASP cc_start: 0.7403 (m-30) cc_final: 0.7150 (m-30) REVERT: A 98 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6538 (ttp80) REVERT: B 106 TYR cc_start: 0.5521 (OUTLIER) cc_final: 0.5127 (p90) REVERT: C 106 MET cc_start: 0.6654 (mmm) cc_final: 0.5944 (mmt) REVERT: D 53 THR cc_start: 0.8425 (m) cc_final: 0.8134 (p) REVERT: L 65 SER cc_start: 0.6413 (t) cc_final: 0.5554 (p) REVERT: L 79 GLU cc_start: 0.6608 (pp20) cc_final: 0.6336 (pp20) REVERT: L 102 THR cc_start: 0.7697 (m) cc_final: 0.7343 (p) outliers start: 22 outliers final: 16 residues processed: 97 average time/residue: 0.1757 time to fit residues: 21.6097 Evaluate side-chains 97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 112 LEU 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 105 TYR Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 0.0010 chunk 30 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 0.0470 chunk 56 optimal weight: 0.8980 overall best weight: 0.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN D 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.214463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187062 restraints weight = 5944.879| |-----------------------------------------------------------------------------| r_work (start): 0.4298 rms_B_bonded: 2.66 r_work: 0.4179 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 4804 Z= 0.128 Angle : 0.605 8.226 6541 Z= 0.316 Chirality : 0.043 0.158 724 Planarity : 0.006 0.117 838 Dihedral : 4.512 20.292 660 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.65 % Favored : 94.02 % Rotamer: Outliers : 3.70 % Allowed : 16.18 % Favored : 80.12 % 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: -1.53 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.07 (0.35), residues: 242 loop : -1.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS L 34 PHE 0.015 0.002 PHE A 104 TYR 0.029 0.002 TYR B 106 ARG 0.006 0.001 ARG D 60 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 139) hydrogen bonds : angle 6.96052 ( 351) SS BOND : bond 0.00564 ( 5) SS BOND : angle 0.72857 ( 10) covalent geometry : bond 0.00314 ( 4799) covalent geometry : angle 0.60469 ( 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 104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.483 Fit side-chains REVERT: A 66 ASP cc_start: 0.7500 (m-30) cc_final: 0.7252 (m-30) REVERT: B 106 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.5026 (p90) REVERT: C 106 MET cc_start: 0.6590 (mmm) cc_final: 0.5853 (mmt) REVERT: D 53 THR cc_start: 0.8393 (m) cc_final: 0.8146 (p) REVERT: L 79 GLU cc_start: 0.6813 (pp20) cc_final: 0.6479 (pp20) REVERT: L 102 THR cc_start: 0.7678 (m) cc_final: 0.7398 (p) outliers start: 19 outliers final: 12 residues processed: 97 average time/residue: 0.1870 time to fit residues: 22.6174 Evaluate side-chains 90 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 A residue 112 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 86 LEU 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 94 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 0.0020 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** L 34 HIS ** 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 = 0.4509 r_free = 0.4509 target = 0.206873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.179885 restraints weight = 5883.538| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.61 r_work: 0.4107 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.8394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 4804 Z= 0.187 Angle : 0.669 9.227 6541 Z= 0.347 Chirality : 0.045 0.165 724 Planarity : 0.006 0.119 838 Dihedral : 4.846 19.522 660 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 4.48 % Allowed : 16.37 % 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: -1.65 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.38 (0.35), residues: 242 loop : -1.66 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 107 HIS 0.003 0.001 HIS A 35 PHE 0.017 0.002 PHE L 86 TYR 0.031 0.002 TYR A 50 ARG 0.005 0.001 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 139) hydrogen bonds : angle 7.24165 ( 351) SS BOND : bond 0.00798 ( 5) SS BOND : angle 1.18061 ( 10) covalent geometry : bond 0.00442 ( 4799) covalent geometry : angle 0.66791 ( 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 103 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7381 (m-30) REVERT: B 106 TYR cc_start: 0.5774 (OUTLIER) cc_final: 0.5332 (p90) REVERT: D 53 THR cc_start: 0.8469 (m) cc_final: 0.8178 (p) REVERT: L 79 GLU cc_start: 0.7070 (pp20) cc_final: 0.6022 (pp20) REVERT: L 102 THR cc_start: 0.7799 (m) cc_final: 0.7434 (p) outliers start: 23 outliers final: 17 residues processed: 93 average time/residue: 0.1964 time to fit residues: 22.4668 Evaluate side-chains 96 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 86 LEU 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 D residue 94 VAL Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 18 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.209309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183050 restraints weight = 5992.584| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 2.56 r_work: 0.4140 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 4804 Z= 0.146 Angle : 0.636 8.482 6541 Z= 0.330 Chirality : 0.045 0.211 724 Planarity : 0.006 0.119 838 Dihedral : 4.715 20.855 660 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 4.29 % Allowed : 17.15 % Favored : 78.56 % 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: -1.62 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.41 (0.35), residues: 239 loop : -1.58 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 94 HIS 0.003 0.001 HIS A 35 PHE 0.015 0.002 PHE A 104 TYR 0.028 0.002 TYR B 106 ARG 0.005 0.001 ARG D 60 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 139) hydrogen bonds : angle 7.09753 ( 351) SS BOND : bond 0.00622 ( 5) SS BOND : angle 0.88390 ( 10) covalent geometry : bond 0.00356 ( 4799) covalent geometry : angle 0.63561 ( 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 104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: B 106 TYR cc_start: 0.5707 (OUTLIER) cc_final: 0.5405 (p90) REVERT: D 53 THR cc_start: 0.8438 (m) cc_final: 0.8187 (p) REVERT: D 101 LYS cc_start: 0.7485 (pttt) cc_final: 0.7263 (pttm) REVERT: L 79 GLU cc_start: 0.7148 (pp20) cc_final: 0.6197 (pp20) REVERT: L 102 THR cc_start: 0.7789 (m) cc_final: 0.7495 (p) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 0.1863 time to fit residues: 22.1269 Evaluate side-chains 97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 86 LEU 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 33 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 94 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: 2.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 18 optimal weight: 0.0270 chunk 47 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.211129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.185189 restraints weight = 5961.343| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.55 r_work: 0.4167 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.8506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 4804 Z= 0.131 Angle : 0.637 8.521 6541 Z= 0.328 Chirality : 0.044 0.201 724 Planarity : 0.006 0.118 838 Dihedral : 4.564 21.359 660 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 3.90 % Allowed : 17.74 % Favored : 78.36 % 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: -1.49 (0.35), residues: 602 helix: None (None), residues: 0 sheet: -0.33 (0.36), residues: 240 loop : -1.50 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 47 HIS 0.003 0.001 HIS L 34 PHE 0.018 0.002 PHE A 60 TYR 0.029 0.002 TYR B 106 ARG 0.005 0.001 ARG D 60 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 139) hydrogen bonds : angle 6.90981 ( 351) SS BOND : bond 0.00633 ( 5) SS BOND : angle 0.88296 ( 10) covalent geometry : bond 0.00329 ( 4799) covalent geometry : angle 0.63628 ( 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 106 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.7598 (m-30) cc_final: 0.7377 (m-30) REVERT: B 106 TYR cc_start: 0.5680 (OUTLIER) cc_final: 0.5449 (p90) REVERT: L 65 SER cc_start: 0.6573 (t) cc_final: 0.5770 (p) REVERT: L 79 GLU cc_start: 0.7216 (pp20) cc_final: 0.6248 (pp20) REVERT: L 102 THR cc_start: 0.7731 (m) cc_final: 0.7498 (p) outliers start: 20 outliers final: 16 residues processed: 100 average time/residue: 0.2081 time to fit residues: 25.6816 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 : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER 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 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 86 LEU 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 94 THR Chi-restraints excluded: chain D residue 94 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: 5.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 D 135 ASN D 147 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.201798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175456 restraints weight = 5994.202| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.50 r_work: 0.4075 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.9201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 4804 Z= 0.224 Angle : 0.747 9.403 6541 Z= 0.383 Chirality : 0.047 0.248 724 Planarity : 0.007 0.122 838 Dihedral : 5.076 22.121 660 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.47 % Favored : 91.36 % Rotamer: Outliers : 3.90 % Allowed : 17.54 % Favored : 78.56 % 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: -1.63 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.42 (0.36), residues: 230 loop : -1.57 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 94 HIS 0.003 0.001 HIS A 35 PHE 0.021 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 0.03683 ( 139) hydrogen bonds : angle 7.51491 ( 351) SS BOND : bond 0.00827 ( 5) SS BOND : angle 1.95666 ( 10) covalent geometry : bond 0.00527 ( 4799) covalent geometry : angle 0.74361 ( 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 100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: B 106 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.5785 (p90) REVERT: C 30 TYR cc_start: 0.7682 (m-80) cc_final: 0.7432 (m-80) REVERT: L 79 GLU cc_start: 0.7391 (pp20) cc_final: 0.6615 (pp20) REVERT: L 102 THR cc_start: 0.7733 (m) cc_final: 0.7314 (p) outliers start: 20 outliers final: 16 residues processed: 92 average time/residue: 0.1894 time to fit residues: 21.5071 Evaluate side-chains 92 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 86 LEU 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 94 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 94 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 28 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.205530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.179826 restraints weight = 5959.602| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 2.49 r_work: 0.4115 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.9168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 4804 Z= 0.162 Angle : 0.691 8.847 6541 Z= 0.354 Chirality : 0.045 0.219 724 Planarity : 0.006 0.120 838 Dihedral : 4.815 22.647 660 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 3.12 % Allowed : 19.10 % Favored : 77.78 % 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: -1.55 (0.35), residues: 602 helix: None (None), residues: 0 sheet: -0.52 (0.35), residues: 236 loop : -1.40 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 94 HIS 0.004 0.002 HIS L 34 PHE 0.015 0.002 PHE A 104 TYR 0.027 0.002 TYR B 106 ARG 0.005 0.001 ARG D 60 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 139) hydrogen bonds : angle 7.28884 ( 351) SS BOND : bond 0.00629 ( 5) SS BOND : angle 1.23259 ( 10) covalent geometry : bond 0.00398 ( 4799) covalent geometry : angle 0.68979 ( 6531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.08 seconds wall clock time: 45 minutes 33.92 seconds (2733.92 seconds total)