Starting phenix.real_space_refine on Wed Sep 17 05:00:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v93_43048/09_2025/8v93_43048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v93_43048/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v93_43048/09_2025/8v93_43048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v93_43048/09_2025/8v93_43048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v93_43048/09_2025/8v93_43048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v93_43048/09_2025/8v93_43048.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.20, per 1000 atoms: 0.26 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: 0.21 Conformation dependent library (CDL) restraints added in 186.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 0.61 Time building geometry restraints manager: 0.31 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: 1.020 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.870 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG B 72 TYR 0.031 0.002 TYR B 106 PHE 0.027 0.002 PHE B 107 TRP 0.049 0.003 TRP A 107 HIS 0.011 0.003 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 4799) covalent geometry : angle 0.97897 ( 6531) SS BOND : bond 0.00327 ( 5) SS BOND : angle 1.89067 ( 10) hydrogen bonds : bond 0.18506 ( 139) hydrogen bonds : angle 9.63487 ( 351) *********************** 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 : 0.169 Fit side-chains REVERT: B 34 MET cc_start: 0.1360 (mmt) cc_final: 0.0594 (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: 0.6179 (m-80) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0740 time to fit residues: 10.6171 Evaluate side-chains 76 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.4863 r_free = 0.4863 target = 0.249724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.225420 restraints weight = 5978.815| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 2.61 r_work: 0.4522 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 4804 Z= 0.165 Angle : 0.649 8.305 6541 Z= 0.343 Chirality : 0.045 0.161 724 Planarity : 0.007 0.128 838 Dihedral : 4.832 19.669 660 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 2.34 % Allowed : 10.92 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.33), residues: 602 helix: None (None), residues: 0 sheet: 0.14 (0.34), residues: 239 loop : -1.99 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 61 TYR 0.015 0.002 TYR B 106 PHE 0.017 0.002 PHE A 64 TRP 0.025 0.002 TRP C 35 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4799) covalent geometry : angle 0.64706 ( 6531) SS BOND : bond 0.00787 ( 5) SS BOND : angle 1.35863 ( 10) hydrogen bonds : bond 0.03316 ( 139) hydrogen bonds : angle 7.17144 ( 351) *********************** 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 104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.174 Fit side-chains REVERT: A 32 TYR cc_start: 0.5699 (m-80) cc_final: 0.5417 (m-80) REVERT: D 53 THR cc_start: 0.7987 (m) cc_final: 0.7637 (p) REVERT: D 101 LYS cc_start: 0.6421 (pttm) cc_final: 0.6172 (pttt) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 0.0749 time to fit residues: 9.2956 Evaluate side-chains 83 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.212695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.183839 restraints weight = 5990.197| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.71 r_work: 0.4137 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.7496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 4804 Z= 0.314 Angle : 0.890 9.984 6541 Z= 0.462 Chirality : 0.051 0.160 724 Planarity : 0.007 0.127 838 Dihedral : 5.876 21.377 660 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.81 % Favored : 91.86 % Rotamer: Outliers : 5.26 % Allowed : 9.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.41 (0.33), residues: 240 loop : -1.97 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 72 TYR 0.028 0.003 TYR A 94 PHE 0.020 0.004 PHE L 86 TRP 0.040 0.004 TRP A 107 HIS 0.006 0.002 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00726 ( 4799) covalent geometry : angle 0.88824 ( 6531) SS BOND : bond 0.01049 ( 5) SS BOND : angle 1.55368 ( 10) hydrogen bonds : bond 0.04568 ( 139) hydrogen bonds : angle 8.36897 ( 351) *********************** 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: 27 poor density : 103 time to evaluate : 0.158 Fit side-chains REVERT: A 66 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7078 (m-30) REVERT: C 106 MET cc_start: 0.7211 (mmm) cc_final: 0.6224 (mmt) REVERT: D 53 THR cc_start: 0.8416 (m) cc_final: 0.8143 (p) outliers start: 27 outliers final: 18 residues processed: 121 average time/residue: 0.0827 time to fit residues: 12.4895 Evaluate side-chains 98 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 66 ASP 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 64 VAL Chi-restraints excluded: chain B residue 86 LEU 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 53 ASN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain L residue 45 ARG 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 8 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.214751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.186811 restraints weight = 5853.902| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.68 r_work: 0.4169 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.7529 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= 0.148 Angle : 0.652 7.992 6541 Z= 0.339 Chirality : 0.045 0.166 724 Planarity : 0.006 0.122 838 Dihedral : 4.799 20.508 660 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.65 % Favored : 95.02 % Rotamer: Outliers : 3.12 % Allowed : 13.45 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.28 (0.34), residues: 249 loop : -1.92 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.021 0.002 TYR A 50 PHE 0.020 0.002 PHE A 104 TRP 0.015 0.002 TRP A 107 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4799) covalent geometry : angle 0.65169 ( 6531) SS BOND : bond 0.00881 ( 5) SS BOND : angle 0.72213 ( 10) hydrogen bonds : bond 0.03324 ( 139) hydrogen bonds : angle 7.20931 ( 351) *********************** 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 111 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.177 Fit side-chains REVERT: A 66 ASP cc_start: 0.7498 (m-30) cc_final: 0.7251 (m-30) REVERT: C 4 MET cc_start: 0.4171 (ptt) cc_final: 0.3631 (ptt) REVERT: C 24 ARG cc_start: 0.5722 (mmm-85) cc_final: 0.5445 (mmm-85) REVERT: C 81 GLU cc_start: 0.7113 (pp20) cc_final: 0.6532 (pp20) REVERT: C 82 ASP cc_start: 0.6528 (m-30) cc_final: 0.6219 (m-30) REVERT: C 106 MET cc_start: 0.7027 (mmm) cc_final: 0.6699 (mmp) REVERT: D 53 THR cc_start: 0.8426 (m) cc_final: 0.8133 (p) REVERT: L 45 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6229 (ptp90) REVERT: L 102 THR cc_start: 0.7610 (m) cc_final: 0.7167 (p) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.0905 time to fit residues: 11.9256 Evaluate side-chains 100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 105 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN D 33 ASN D 135 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.214290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.186706 restraints weight = 5903.593| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.66 r_work: 0.4165 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 4804 Z= 0.137 Angle : 0.617 8.444 6541 Z= 0.320 Chirality : 0.043 0.157 724 Planarity : 0.006 0.120 838 Dihedral : 4.600 19.740 660 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 2.92 % Allowed : 16.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.15 (0.35), residues: 242 loop : -1.84 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.020 0.002 TYR A 50 PHE 0.019 0.002 PHE A 60 TRP 0.013 0.001 TRP A 107 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4799) covalent geometry : angle 0.61737 ( 6531) SS BOND : bond 0.00576 ( 5) SS BOND : angle 0.67802 ( 10) hydrogen bonds : bond 0.03191 ( 139) hydrogen bonds : angle 6.96283 ( 351) *********************** 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 104 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.185 Fit side-chains REVERT: A 66 ASP cc_start: 0.7479 (m-30) cc_final: 0.7226 (m-30) REVERT: C 4 MET cc_start: 0.3885 (ptt) cc_final: 0.3288 (ptt) REVERT: C 24 ARG cc_start: 0.5786 (mmm-85) cc_final: 0.5460 (mmm-85) REVERT: C 81 GLU cc_start: 0.7099 (pp20) cc_final: 0.6484 (pp20) REVERT: C 82 ASP cc_start: 0.6760 (m-30) cc_final: 0.6425 (m-30) REVERT: C 106 MET cc_start: 0.7026 (mmm) cc_final: 0.6038 (mmt) REVERT: D 11 ILE cc_start: 0.6135 (mm) cc_final: 0.5828 (mt) REVERT: D 53 THR cc_start: 0.8443 (m) cc_final: 0.8171 (p) REVERT: L 42 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.4940 (pm20) REVERT: L 65 SER cc_start: 0.6369 (t) cc_final: 0.5492 (p) REVERT: L 102 THR cc_start: 0.7706 (m) cc_final: 0.7354 (p) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.0813 time to fit residues: 10.1045 Evaluate side-chains 97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 C residue 7 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.2980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4544 r_free = 0.4544 target = 0.213286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.186557 restraints weight = 6056.270| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 2.65 r_work: 0.4175 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.7903 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= 0.130 Angle : 0.596 8.358 6541 Z= 0.310 Chirality : 0.043 0.156 724 Planarity : 0.006 0.118 838 Dihedral : 4.400 19.986 660 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 4.09 % Allowed : 16.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.37 (0.34), residues: 255 loop : -1.59 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 60 TYR 0.026 0.002 TYR A 50 PHE 0.017 0.002 PHE A 104 TRP 0.012 0.002 TRP A 107 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4799) covalent geometry : angle 0.59612 ( 6531) SS BOND : bond 0.00613 ( 5) SS BOND : angle 0.65971 ( 10) hydrogen bonds : bond 0.03040 ( 139) hydrogen bonds : angle 6.75642 ( 351) *********************** 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 110 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.118 Fit side-chains REVERT: C 24 ARG cc_start: 0.5736 (mmm-85) cc_final: 0.5321 (mmm-85) REVERT: C 81 GLU cc_start: 0.7312 (pp20) cc_final: 0.6478 (pp20) REVERT: C 82 ASP cc_start: 0.6160 (m-30) cc_final: 0.5829 (m-30) REVERT: C 106 MET cc_start: 0.7190 (mmm) cc_final: 0.6216 (mmt) REVERT: D 11 ILE cc_start: 0.6063 (mm) cc_final: 0.5839 (mt) REVERT: D 53 THR cc_start: 0.8243 (m) cc_final: 0.8004 (p) REVERT: L 42 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5375 (pm20) REVERT: L 45 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6181 (ptp90) REVERT: L 102 THR cc_start: 0.7743 (m) cc_final: 0.7451 (p) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.0853 time to fit residues: 10.7196 Evaluate side-chains 97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 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 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 45 ARG 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 30 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.0170 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 D 135 ASN D 147 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.211663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.184716 restraints weight = 5978.044| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.61 r_work: 0.4153 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.8181 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= 0.150 Angle : 0.625 8.099 6541 Z= 0.323 Chirality : 0.044 0.153 724 Planarity : 0.006 0.117 838 Dihedral : 4.574 18.721 660 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.64 % Favored : 93.19 % Rotamer: Outliers : 4.09 % Allowed : 16.37 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.35), residues: 602 helix: None (None), residues: 0 sheet: -0.34 (0.34), residues: 249 loop : -1.49 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 72 TYR 0.027 0.002 TYR A 50 PHE 0.016 0.002 PHE A 104 TRP 0.012 0.002 TRP A 107 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4799) covalent geometry : angle 0.62418 ( 6531) SS BOND : bond 0.00428 ( 5) SS BOND : angle 0.95181 ( 10) hydrogen bonds : bond 0.03129 ( 139) hydrogen bonds : angle 6.80705 ( 351) *********************** 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 111 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.176 Fit side-chains REVERT: C 24 ARG cc_start: 0.5687 (mmm-85) cc_final: 0.5388 (mmm-85) REVERT: C 81 GLU cc_start: 0.7231 (pp20) cc_final: 0.6305 (pp20) REVERT: C 82 ASP cc_start: 0.6421 (m-30) cc_final: 0.6120 (m-30) REVERT: C 106 MET cc_start: 0.7338 (mmm) cc_final: 0.6437 (mmt) REVERT: D 11 ILE cc_start: 0.6104 (mm) cc_final: 0.5853 (mt) REVERT: D 53 THR cc_start: 0.8417 (m) cc_final: 0.8105 (p) REVERT: L 42 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5080 (pm20) REVERT: L 65 SER cc_start: 0.6477 (t) cc_final: 0.5687 (p) REVERT: L 102 THR cc_start: 0.7767 (m) cc_final: 0.7402 (p) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.0796 time to fit residues: 10.4628 Evaluate side-chains 101 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 33 optimal weight: 0.0060 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.211979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.185341 restraints weight = 6085.238| |-----------------------------------------------------------------------------| r_work (start): 0.4277 rms_B_bonded: 2.64 r_work: 0.4159 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.8306 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= 0.134 Angle : 0.613 8.519 6541 Z= 0.319 Chirality : 0.043 0.159 724 Planarity : 0.006 0.115 838 Dihedral : 4.521 20.864 660 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.98 % Favored : 93.85 % Rotamer: Outliers : 4.29 % Allowed : 16.18 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.44 (0.34), residues: 243 loop : -1.41 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 60 TYR 0.019 0.002 TYR A 50 PHE 0.016 0.002 PHE A 104 TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4799) covalent geometry : angle 0.61263 ( 6531) SS BOND : bond 0.00494 ( 5) SS BOND : angle 0.79049 ( 10) hydrogen bonds : bond 0.02975 ( 139) hydrogen bonds : angle 6.69383 ( 351) *********************** 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 107 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.150 Fit side-chains REVERT: C 24 ARG cc_start: 0.5642 (mmm-85) cc_final: 0.5398 (mmm-85) REVERT: C 81 GLU cc_start: 0.7065 (pp20) cc_final: 0.6108 (pp20) REVERT: C 82 ASP cc_start: 0.6112 (m-30) cc_final: 0.5842 (m-30) REVERT: C 106 MET cc_start: 0.7368 (mmm) cc_final: 0.6407 (mmt) REVERT: D 11 ILE cc_start: 0.6053 (mm) cc_final: 0.5837 (mt) REVERT: D 53 THR cc_start: 0.8424 (m) cc_final: 0.8107 (p) REVERT: L 42 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.5334 (pm20) REVERT: L 65 SER cc_start: 0.6482 (t) cc_final: 0.5692 (p) REVERT: L 102 THR cc_start: 0.7807 (m) cc_final: 0.7478 (p) outliers start: 22 outliers final: 16 residues processed: 99 average time/residue: 0.0806 time to fit residues: 10.0901 Evaluate side-chains 100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 26 optimal weight: 0.0020 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** L 34 HIS ** 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 = 0.4551 r_free = 0.4551 target = 0.212748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.186257 restraints weight = 5889.288| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.63 r_work: 0.4165 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.8387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 4804 Z= 0.131 Angle : 0.614 9.053 6541 Z= 0.318 Chirality : 0.043 0.158 724 Planarity : 0.006 0.114 838 Dihedral : 4.375 20.969 660 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.36 % Rotamer: Outliers : 3.31 % Allowed : 16.37 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.35), residues: 602 helix: None (None), residues: 0 sheet: -0.44 (0.34), residues: 243 loop : -1.36 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 60 TYR 0.019 0.002 TYR A 50 PHE 0.016 0.002 PHE B 27 TRP 0.010 0.001 TRP A 107 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4799) covalent geometry : angle 0.61412 ( 6531) SS BOND : bond 0.00510 ( 5) SS BOND : angle 0.79959 ( 10) hydrogen bonds : bond 0.02901 ( 139) hydrogen bonds : angle 6.62708 ( 351) *********************** 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 100 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.190 Fit side-chains REVERT: C 24 ARG cc_start: 0.5742 (mmm-85) cc_final: 0.5540 (mmm-85) REVERT: C 81 GLU cc_start: 0.7162 (pp20) cc_final: 0.6253 (pp20) REVERT: C 106 MET cc_start: 0.7449 (mmm) cc_final: 0.6537 (mmt) REVERT: D 11 ILE cc_start: 0.6066 (mm) cc_final: 0.5845 (mt) REVERT: D 53 THR cc_start: 0.8534 (m) cc_final: 0.8253 (p) REVERT: L 42 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5318 (pm20) REVERT: L 102 THR cc_start: 0.7837 (m) cc_final: 0.7543 (p) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.0796 time to fit residues: 9.2467 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 : 0.185 ------------------------------------------------------------------------------- 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 A residue 112 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN 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 = 0.4465 r_free = 0.4465 target = 0.202396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.177051 restraints weight = 6125.511| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 2.50 r_work: 0.4090 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.9003 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= 0.198 Angle : 0.691 9.203 6541 Z= 0.359 Chirality : 0.045 0.153 724 Planarity : 0.006 0.117 838 Dihedral : 4.815 22.319 660 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.14 % Favored : 91.69 % Rotamer: Outliers : 2.92 % Allowed : 17.74 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.60 (0.34), residues: 245 loop : -1.36 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 72 TYR 0.027 0.002 TYR A 50 PHE 0.016 0.002 PHE L 86 TRP 0.022 0.002 TRP L 94 HIS 0.004 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 4799) covalent geometry : angle 0.68920 ( 6531) SS BOND : bond 0.00737 ( 5) SS BOND : angle 1.48236 ( 10) hydrogen bonds : bond 0.03453 ( 139) hydrogen bonds : angle 7.03548 ( 351) ********************** 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 101 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.178 Fit side-chains REVERT: A 32 TYR cc_start: 0.6181 (m-10) cc_final: 0.5968 (m-80) REVERT: C 24 ARG cc_start: 0.5805 (mmm-85) cc_final: 0.5593 (mmm-85) REVERT: C 61 ARG cc_start: 0.5422 (mtm180) cc_final: 0.5100 (mtp180) REVERT: C 81 GLU cc_start: 0.7146 (pp20) cc_final: 0.6697 (pp20) REVERT: C 106 MET cc_start: 0.7787 (mmm) cc_final: 0.6841 (mmt) REVERT: D 11 ILE cc_start: 0.6360 (mm) cc_final: 0.6036 (mt) REVERT: D 53 THR cc_start: 0.8498 (m) cc_final: 0.8236 (p) REVERT: L 42 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5390 (pm20) REVERT: L 102 THR cc_start: 0.7712 (m) cc_final: 0.7351 (p) outliers start: 15 outliers final: 10 residues processed: 94 average time/residue: 0.0803 time to fit residues: 9.4570 Evaluate side-chains 92 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 112 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 42 GLU Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.206354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.180543 restraints weight = 5983.804| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.55 r_work: 0.4134 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.8987 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= 0.148 Angle : 0.650 9.235 6541 Z= 0.336 Chirality : 0.045 0.238 724 Planarity : 0.006 0.118 838 Dihedral : 4.611 22.840 660 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.31 % Favored : 92.52 % Rotamer: Outliers : 3.31 % Allowed : 17.35 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.35), residues: 602 helix: None (None), residues: 0 sheet: -0.47 (0.34), residues: 248 loop : -1.38 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 60 TYR 0.035 0.002 TYR B 106 PHE 0.020 0.002 PHE A 60 TRP 0.029 0.002 TRP B 47 HIS 0.004 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4799) covalent geometry : angle 0.64900 ( 6531) SS BOND : bond 0.00449 ( 5) SS BOND : angle 0.94673 ( 10) hydrogen bonds : bond 0.03051 ( 139) hydrogen bonds : angle 6.90795 ( 351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.09 seconds wall clock time: 22 minutes 37.34 seconds (1357.34 seconds total)