Starting phenix.real_space_refine on Tue Jan 14 00:19:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v93_43048/01_2025/8v93_43048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v93_43048/01_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_43048/01_2025/8v93_43048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v93_43048/01_2025/8v93_43048.map" model { file = "/net/cci-nas-00/data/ceres_data/8v93_43048/01_2025/8v93_43048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v93_43048/01_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-5571/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: 3.43, per 1000 atoms: 0.73 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: 1.08 Conformation dependent library (CDL) restraints added in 565.1 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: 0.67 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: 1.19 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: 1.290 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.860 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- 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 4799 Z= 0.320 Angle : 0.979 12.038 6531 Z= 0.529 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 *********************** 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 : 0.538 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: 0.1799 time to fit residues: 25.5665 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 : 0.528 ------------------------------------------------------------------------------- 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 4799 Z= 0.227 Angle : 0.622 8.446 6531 Z= 0.329 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 *********************** 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 : 0.536 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: 0.1626 time to fit residues: 20.1057 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 : 0.462 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 0.0970 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: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** 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 = 0.4621 r_free = 0.4621 target = 0.222066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.193394 restraints weight = 5924.366| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.73 r_work: 0.4231 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 4799 Z= 0.357 Angle : 0.753 8.992 6531 Z= 0.393 Chirality : 0.048 0.147 724 Planarity : 0.006 0.121 838 Dihedral : 5.321 21.199 660 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.81 % Favored : 91.86 % Rotamer: Outliers : 3.70 % Allowed : 10.92 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.33), residues: 602 helix: None (None), residues: 0 sheet: -0.02 (0.34), residues: 236 loop : -2.11 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 107 HIS 0.006 0.002 HIS A 35 PHE 0.018 0.003 PHE B 107 TYR 0.021 0.003 TYR A 50 ARG 0.010 0.001 ARG B 72 *********************** 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 121 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.472 Fit side-chains REVERT: A 66 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: B 106 TYR cc_start: 0.5600 (p90) cc_final: 0.5398 (p90) REVERT: C 106 MET cc_start: 0.6331 (mmm) cc_final: 0.5984 (mmp) REVERT: D 20 VAL cc_start: 0.7129 (p) cc_final: 0.6122 (m) REVERT: D 53 THR cc_start: 0.8380 (m) cc_final: 0.8093 (p) REVERT: D 71 PHE cc_start: 0.4955 (m-10) cc_final: 0.4735 (m-10) REVERT: L 102 THR cc_start: 0.7479 (m) cc_final: 0.6952 (p) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.1582 time to fit residues: 23.4141 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 : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR 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 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: 0.8980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.215896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.188493 restraints weight = 5954.384| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.66 r_work: 0.4203 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.6975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 4799 Z= 0.254 Angle : 0.639 7.081 6531 Z= 0.334 Chirality : 0.044 0.157 724 Planarity : 0.006 0.120 838 Dihedral : 4.683 20.076 660 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 3.51 % Allowed : 12.28 % Favored : 84.21 % 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: 0.01 (0.34), residues: 241 loop : -1.94 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 107 HIS 0.003 0.001 HIS A 35 PHE 0.016 0.002 PHE A 104 TYR 0.023 0.002 TYR A 50 ARG 0.006 0.001 ARG B 72 *********************** 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 116 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.524 Fit side-chains REVERT: A 18 VAL cc_start: 0.6178 (OUTLIER) cc_final: 0.5965 (p) REVERT: A 66 ASP cc_start: 0.7496 (m-30) cc_final: 0.7223 (m-30) REVERT: A 98 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6084 (ttt-90) REVERT: C 81 GLU cc_start: 0.7165 (pp20) cc_final: 0.6522 (pp20) REVERT: C 82 ASP cc_start: 0.6210 (m-30) cc_final: 0.6001 (m-30) REVERT: C 106 MET cc_start: 0.6619 (mmm) cc_final: 0.5884 (mmt) REVERT: D 53 THR cc_start: 0.8397 (m) cc_final: 0.8093 (p) REVERT: L 79 GLU cc_start: 0.6297 (pp20) cc_final: 0.6049 (pp20) REVERT: L 102 THR cc_start: 0.7656 (m) cc_final: 0.7354 (p) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.1894 time to fit residues: 26.4862 Evaluate side-chains 101 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 90 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: 10.0000 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 D 33 ASN D 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.215232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.187567 restraints weight = 5934.377| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.67 r_work: 0.4186 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 4799 Z= 0.236 Angle : 0.613 7.020 6531 Z= 0.320 Chirality : 0.044 0.167 724 Planarity : 0.006 0.117 838 Dihedral : 4.585 19.152 660 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.31 % Favored : 93.36 % Rotamer: Outliers : 3.70 % Allowed : 14.81 % Favored : 81.48 % 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: -1.60 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.06 (0.35), residues: 240 loop : -1.86 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 107 HIS 0.002 0.001 HIS D 45 PHE 0.019 0.002 PHE A 60 TYR 0.032 0.002 TYR A 50 ARG 0.005 0.001 ARG B 72 *********************** 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 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: 0.7395 (m-30) cc_final: 0.7136 (m-30) REVERT: B 34 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4443 (mmm) REVERT: B 83 MET cc_start: 0.3413 (mtm) cc_final: 0.3130 (mtm) REVERT: C 24 ARG cc_start: 0.5777 (mmm-85) cc_final: 0.5569 (mmm-85) REVERT: C 81 GLU cc_start: 0.7145 (pp20) cc_final: 0.6498 (pp20) REVERT: C 82 ASP cc_start: 0.6921 (m-30) cc_final: 0.6589 (m-30) REVERT: C 106 MET cc_start: 0.6361 (mmm) cc_final: 0.6157 (mmp) REVERT: D 53 THR cc_start: 0.8313 (m) cc_final: 0.8069 (p) REVERT: L 79 GLU cc_start: 0.6483 (pp20) cc_final: 0.6169 (pp20) REVERT: L 102 THR cc_start: 0.7677 (m) cc_final: 0.7362 (p) outliers start: 19 outliers final: 13 residues processed: 102 average time/residue: 0.1923 time to fit residues: 24.3766 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 : 0.521 ------------------------------------------------------------------------------- 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 B residue 2 VAL Chi-restraints excluded: chain B residue 34 MET 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 116 LEU 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 126 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 82 GLN B 77 ASN D 135 ASN D 147 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.212442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.185113 restraints weight = 5932.761| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.63 r_work: 0.4166 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 4799 Z= 0.258 Angle : 0.624 8.826 6531 Z= 0.324 Chirality : 0.044 0.166 724 Planarity : 0.006 0.118 838 Dihedral : 4.521 20.250 660 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.31 % Favored : 93.36 % Rotamer: Outliers : 3.90 % Allowed : 15.59 % 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: -1.58 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.25 (0.34), residues: 247 loop : -1.69 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 107 HIS 0.003 0.001 HIS D 45 PHE 0.015 0.002 PHE L 86 TYR 0.025 0.002 TYR A 50 ARG 0.006 0.001 ARG D 60 *********************** 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 105 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.524 Fit side-chains REVERT: A 66 ASP cc_start: 0.7479 (m-30) cc_final: 0.7221 (m-30) REVERT: B 83 MET cc_start: 0.3630 (mtm) cc_final: 0.3246 (mtm) REVERT: C 24 ARG cc_start: 0.5973 (mmm-85) cc_final: 0.5518 (mmm-85) REVERT: C 81 GLU cc_start: 0.7099 (pp20) cc_final: 0.6398 (pp20) REVERT: C 82 ASP cc_start: 0.6698 (m-30) cc_final: 0.6384 (m-30) REVERT: D 37 ASP cc_start: 0.8110 (t0) cc_final: 0.7829 (t0) REVERT: D 53 THR cc_start: 0.8371 (m) cc_final: 0.8138 (p) REVERT: L 65 SER cc_start: 0.6521 (t) cc_final: 0.5664 (p) REVERT: L 79 GLU cc_start: 0.6868 (pp20) cc_final: 0.5749 (pp20) REVERT: L 102 THR cc_start: 0.7765 (m) cc_final: 0.7442 (p) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.1793 time to fit residues: 21.6487 Evaluate side-chains 93 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 54 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 B residue 2 VAL Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.208720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.183114 restraints weight = 5877.026| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.49 r_work: 0.4145 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 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 : 0.004 0.094 4799 Z= 0.264 Angle : 0.630 8.487 6531 Z= 0.329 Chirality : 0.044 0.163 724 Planarity : 0.006 0.119 838 Dihedral : 4.721 20.059 660 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 3.90 % Allowed : 15.79 % 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 (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: -1.59 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.35 (0.35), residues: 242 loop : -1.60 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 107 HIS 0.003 0.001 HIS A 35 PHE 0.020 0.002 PHE A 60 TYR 0.028 0.002 TYR B 105 ARG 0.005 0.001 ARG B 72 *********************** 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 106 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.483 Fit side-chains REVERT: B 83 MET cc_start: 0.4103 (mtm) cc_final: 0.3798 (mtm) REVERT: C 24 ARG cc_start: 0.5940 (mmm-85) cc_final: 0.5729 (mmm-85) REVERT: C 81 GLU cc_start: 0.7358 (pp20) cc_final: 0.6368 (pp20) REVERT: C 82 ASP cc_start: 0.6467 (m-30) cc_final: 0.6149 (m-30) REVERT: D 37 ASP cc_start: 0.8062 (t0) cc_final: 0.7827 (t0) REVERT: D 53 THR cc_start: 0.8465 (m) cc_final: 0.8232 (p) REVERT: L 79 GLU cc_start: 0.7054 (pp20) cc_final: 0.6007 (pp20) REVERT: L 102 THR cc_start: 0.7792 (m) cc_final: 0.7465 (p) outliers start: 20 outliers final: 15 residues processed: 98 average time/residue: 0.1916 time to fit residues: 23.3735 Evaluate side-chains 94 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 B residue 2 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 4 MET 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 L residue 2 ILE Chi-restraints excluded: chain L residue 13 VAL 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: 0.1980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.207535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.181669 restraints weight = 5987.380| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.53 r_work: 0.4144 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.8610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 4799 Z= 0.237 Angle : 0.618 7.756 6531 Z= 0.324 Chirality : 0.044 0.159 724 Planarity : 0.006 0.118 838 Dihedral : 4.631 21.127 660 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 3.90 % Allowed : 16.37 % Favored : 79.73 % 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: -1.52 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.33 (0.35), residues: 247 loop : -1.56 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 94 HIS 0.003 0.001 HIS A 35 PHE 0.014 0.002 PHE A 104 TYR 0.022 0.002 TYR B 105 ARG 0.003 0.001 ARG C 61 *********************** 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 103 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.477 Fit side-chains REVERT: B 83 MET cc_start: 0.4096 (mtm) cc_final: 0.3778 (mtm) REVERT: C 24 ARG cc_start: 0.5882 (mmm-85) cc_final: 0.5579 (mmm-85) REVERT: C 81 GLU cc_start: 0.7317 (pp20) cc_final: 0.6448 (pp20) REVERT: C 82 ASP cc_start: 0.6345 (m-30) cc_final: 0.6014 (m-30) REVERT: L 79 GLU cc_start: 0.7211 (pp20) cc_final: 0.6273 (pp20) REVERT: L 102 THR cc_start: 0.7738 (m) cc_final: 0.7487 (p) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.1936 time to fit residues: 22.8203 Evaluate side-chains 93 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU 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 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain L residue 2 ILE 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: 0.6980 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 = 0.4494 r_free = 0.4494 target = 0.205569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.179512 restraints weight = 5975.484| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 2.54 r_work: 0.4122 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 4799 Z= 0.274 Angle : 0.646 8.307 6531 Z= 0.337 Chirality : 0.045 0.219 724 Planarity : 0.006 0.117 838 Dihedral : 4.724 21.942 660 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.64 % Favored : 92.19 % Rotamer: Outliers : 3.31 % Allowed : 16.57 % 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: -1.55 (0.34), residues: 602 helix: None (None), residues: 0 sheet: -0.45 (0.35), residues: 236 loop : -1.46 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 94 HIS 0.003 0.001 HIS A 35 PHE 0.016 0.002 PHE L 86 TYR 0.026 0.002 TYR B 105 ARG 0.005 0.001 ARG A 98 *********************** 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 99 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.475 Fit side-chains REVERT: C 24 ARG cc_start: 0.5814 (mmm-85) cc_final: 0.5613 (mmm-85) REVERT: C 81 GLU cc_start: 0.7360 (pp20) cc_final: 0.6468 (pp20) REVERT: C 82 ASP cc_start: 0.6483 (m-30) cc_final: 0.6211 (m-30) REVERT: L 79 GLU cc_start: 0.7254 (pp20) cc_final: 0.6388 (pp20) REVERT: L 102 THR cc_start: 0.7796 (m) cc_final: 0.7501 (p) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.1912 time to fit residues: 21.8275 Evaluate side-chains 94 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain L residue 2 ILE 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: 0.8980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 135 ASN L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.207199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.181566 restraints weight = 5974.122| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.53 r_work: 0.4130 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.8979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 4799 Z= 0.259 Angle : 0.678 8.562 6531 Z= 0.348 Chirality : 0.045 0.209 724 Planarity : 0.006 0.119 838 Dihedral : 4.783 23.159 660 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.81 % Favored : 93.02 % Rotamer: Outliers : 2.92 % Allowed : 17.15 % Favored : 79.92 % 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: -0.41 (0.35), residues: 236 loop : -1.42 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 94 HIS 0.003 0.001 HIS L 34 PHE 0.016 0.002 PHE L 86 TYR 0.037 0.002 TYR B 106 ARG 0.004 0.001 ARG C 61 ********************** 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 97 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.519 Fit side-chains REVERT: B 19 LYS cc_start: 0.7077 (tppt) cc_final: 0.6634 (mtpp) REVERT: C 24 ARG cc_start: 0.5827 (mmm-85) cc_final: 0.5617 (mmm-85) REVERT: C 81 GLU cc_start: 0.7365 (pp20) cc_final: 0.6418 (pp20) REVERT: L 79 GLU cc_start: 0.7298 (pp20) cc_final: 0.7004 (pp20) REVERT: L 102 THR cc_start: 0.7733 (m) cc_final: 0.7473 (p) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1986 time to fit residues: 21.5813 Evaluate side-chains 95 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 B residue 93 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain L residue 13 VAL 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: 7.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.201898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175809 restraints weight = 6028.341| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.52 r_work: 0.4071 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.9427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 4799 Z= 0.336 Angle : 0.721 8.313 6531 Z= 0.371 Chirality : 0.046 0.219 724 Planarity : 0.006 0.121 838 Dihedral : 5.077 23.188 660 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.30 % Favored : 90.53 % Rotamer: Outliers : 3.31 % Allowed : 16.57 % 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: -1.64 (0.35), residues: 602 helix: None (None), residues: 0 sheet: -0.64 (0.34), residues: 243 loop : -1.43 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 107 HIS 0.003 0.001 HIS L 34 PHE 0.019 0.002 PHE L 86 TYR 0.035 0.003 TYR B 106 ARG 0.006 0.001 ARG A 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.16 seconds wall clock time: 44 minutes 55.68 seconds (2695.68 seconds total)