Starting phenix.real_space_refine on Tue Apr 29 16:14:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vw3_43575/04_2025/8vw3_43575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vw3_43575/04_2025/8vw3_43575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vw3_43575/04_2025/8vw3_43575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vw3_43575/04_2025/8vw3_43575.map" model { file = "/net/cci-nas-00/data/ceres_data/8vw3_43575/04_2025/8vw3_43575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vw3_43575/04_2025/8vw3_43575.cif" } resolution = 3.47 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= -0.002 sd= 0.053 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 30 5.16 5 C 5658 2.51 5 N 1488 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8856 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "B" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "C" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "D" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1476 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Time building chain proxies: 7.58, per 1000 atoms: 0.86 Number of scatterers: 8856 At special positions: 0 Unit cell: (108.054, 119.016, 106.488, 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 30 16.00 O 1680 8.00 N 1488 7.00 C 5658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 31 through 37 removed outlier: 4.101A pdb=" N VAL A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 63 through 70 removed outlier: 3.602A pdb=" N LEU A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 91 through 104 Processing helix chain 'A' and resid 112 through 130 Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.649A pdb=" N ILE A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.672A pdb=" N ALA A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 184 removed outlier: 3.842A pdb=" N ASN A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 31 through 37 removed outlier: 4.306A pdb=" N VAL B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 Processing helix chain 'B' and resid 63 through 70 removed outlier: 4.538A pdb=" N ASN B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 88 Processing helix chain 'B' and resid 91 through 103 removed outlier: 3.571A pdb=" N LYS B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 130 removed outlier: 3.518A pdb=" N ALA B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.501A pdb=" N THR B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 185 removed outlier: 3.583A pdb=" N ASN B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 29 Processing helix chain 'C' and resid 31 through 36 removed outlier: 4.260A pdb=" N VAL C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.544A pdb=" N SER C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 91 through 104 Processing helix chain 'C' and resid 112 through 131 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 167 through 185 removed outlier: 3.508A pdb=" N LYS C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 29 Processing helix chain 'D' and resid 31 through 36 removed outlier: 4.261A pdb=" N VAL D 35 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 67 through 72 removed outlier: 4.575A pdb=" N SER D 72 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 88 Processing helix chain 'D' and resid 91 through 104 Processing helix chain 'D' and resid 112 through 130 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 161 removed outlier: 3.557A pdb=" N THR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 185 removed outlier: 3.540A pdb=" N LYS D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.840A pdb=" N LEU E 67 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASN E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR E 71 " --> pdb=" O ASN E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 91 through 104 removed outlier: 3.667A pdb=" N ALA E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 130 Processing helix chain 'E' and resid 135 through 145 Processing helix chain 'E' and resid 146 through 147 No H-bonds generated for 'chain 'E' and resid 146 through 147' Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 167 through 185 Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 31 through 37 removed outlier: 4.188A pdb=" N VAL F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 Processing helix chain 'F' and resid 63 through 66 Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.531A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 88 Processing helix chain 'F' and resid 91 through 104 Processing helix chain 'F' and resid 112 through 130 Processing helix chain 'F' and resid 135 through 146 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 160 removed outlier: 3.558A pdb=" N THR F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 185 removed outlier: 3.553A pdb=" N LYS F 181 " --> pdb=" O ASP F 177 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1608 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: 2.29 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2892 1.34 - 1.46: 1580 1.46 - 1.58: 4462 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8982 Sorted by residual: bond pdb=" CG GLU C 179 " pdb=" CD GLU C 179 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.41e-01 bond pdb=" CA GLU B 163 " pdb=" CB GLU B 163 " ideal model delta sigma weight residual 1.524 1.536 -0.013 1.31e-02 5.83e+03 9.36e-01 bond pdb=" N LYS A 106 " pdb=" CA LYS A 106 " ideal model delta sigma weight residual 1.467 1.476 -0.009 1.32e-02 5.74e+03 5.13e-01 bond pdb=" CG PRO A 40 " pdb=" CD PRO A 40 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.85e-01 bond pdb=" CA VAL A 43 " pdb=" CB VAL A 43 " ideal model delta sigma weight residual 1.540 1.548 -0.008 1.36e-02 5.41e+03 3.48e-01 ... (remaining 8977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 11670 0.86 - 1.73: 337 1.73 - 2.59: 51 2.59 - 3.45: 33 3.45 - 4.31: 5 Bond angle restraints: 12096 Sorted by residual: angle pdb=" C GLU A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta sigma weight residual 121.97 126.28 -4.31 1.80e+00 3.09e-01 5.74e+00 angle pdb=" N GLU C 179 " pdb=" CA GLU C 179 " pdb=" CB GLU C 179 " ideal model delta sigma weight residual 110.28 113.49 -3.21 1.55e+00 4.16e-01 4.29e+00 angle pdb=" N VAL E 31 " pdb=" CA VAL E 31 " pdb=" CB VAL E 31 " ideal model delta sigma weight residual 112.12 109.74 2.38 1.35e+00 5.49e-01 3.10e+00 angle pdb=" C GLN C 178 " pdb=" N GLU C 179 " pdb=" CA GLU C 179 " ideal model delta sigma weight residual 120.31 117.76 2.55 1.52e+00 4.33e-01 2.81e+00 angle pdb=" N VAL D 31 " pdb=" CA VAL D 31 " pdb=" CB VAL D 31 " ideal model delta sigma weight residual 112.33 110.39 1.94 1.19e+00 7.06e-01 2.66e+00 ... (remaining 12091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5106 17.80 - 35.59: 395 35.59 - 53.39: 57 53.39 - 71.19: 10 71.19 - 88.98: 6 Dihedral angle restraints: 5574 sinusoidal: 2292 harmonic: 3282 Sorted by residual: dihedral pdb=" CA ASP C 36 " pdb=" CB ASP C 36 " pdb=" CG ASP C 36 " pdb=" OD1 ASP C 36 " ideal model delta sinusoidal sigma weight residual -30.00 -89.53 59.53 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP E 45 " pdb=" CB ASP E 45 " pdb=" CG ASP E 45 " pdb=" OD1 ASP E 45 " ideal model delta sinusoidal sigma weight residual -30.00 -88.73 58.73 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CB GLU B 136 " pdb=" CG GLU B 136 " pdb=" CD GLU B 136 " pdb=" OE1 GLU B 136 " ideal model delta sinusoidal sigma weight residual 0.00 -88.98 88.98 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 5571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 909 0.026 - 0.053: 344 0.053 - 0.079: 132 0.079 - 0.106: 31 0.106 - 0.132: 12 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CB VAL A 43 " pdb=" CA VAL A 43 " pdb=" CG1 VAL A 43 " pdb=" CG2 VAL A 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE C 74 " pdb=" N ILE C 74 " pdb=" C ILE C 74 " pdb=" CB ILE C 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.61e-01 chirality pdb=" CA ILE F 134 " pdb=" N ILE F 134 " pdb=" C ILE F 134 " pdb=" CB ILE F 134 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 1425 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 31 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C VAL E 31 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL E 31 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU E 32 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 31 " 0.005 2.00e-02 2.50e+03 9.69e-03 9.38e-01 pdb=" C VAL F 31 " -0.017 2.00e-02 2.50e+03 pdb=" O VAL F 31 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU F 32 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 160 " 0.005 2.00e-02 2.50e+03 9.52e-03 9.07e-01 pdb=" C THR C 160 " -0.016 2.00e-02 2.50e+03 pdb=" O THR C 160 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU C 161 " 0.006 2.00e-02 2.50e+03 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 105 2.69 - 3.24: 8809 3.24 - 3.80: 13466 3.80 - 4.35: 17387 4.35 - 4.90: 29011 Nonbonded interactions: 68778 Sorted by model distance: nonbonded pdb=" O LYS C 4 " pdb=" OH TYR C 61 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR C 15 " pdb=" OD1 ASP C 84 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR E 15 " pdb=" OD1 ASP E 84 " model vdw 2.222 3.040 nonbonded pdb=" OG SER C 91 " pdb=" OG SER C 94 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 15 " pdb=" OD1 ASP A 84 " model vdw 2.262 3.040 ... (remaining 68773 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 210.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 238.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.002 0.024 8982 Z= 0.092 Angle : 0.382 4.314 12096 Z= 0.208 Chirality : 0.033 0.132 1428 Planarity : 0.002 0.020 1512 Dihedral : 12.881 88.982 3414 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.26), residues: 1092 helix: 2.51 (0.19), residues: 739 sheet: None (None), residues: 0 loop : 0.54 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 47 HIS 0.001 0.000 HIS C 142 PHE 0.010 0.001 PHE F 120 TYR 0.009 0.001 TYR D 61 ARG 0.002 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.14063 ( 548) hydrogen bonds : angle 4.66654 ( 1608) covalent geometry : bond 0.00198 ( 8982) covalent geometry : angle 0.38210 (12096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ASP cc_start: 0.7955 (p0) cc_final: 0.7702 (p0) REVERT: A 52 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7509 (ttp-110) REVERT: A 67 LEU cc_start: 0.9168 (mt) cc_final: 0.8438 (mt) REVERT: A 77 ARG cc_start: 0.8191 (ttt180) cc_final: 0.7948 (ttm-80) REVERT: A 180 ILE cc_start: 0.9360 (mm) cc_final: 0.9124 (mt) REVERT: B 11 ASP cc_start: 0.8399 (t0) cc_final: 0.7827 (t0) REVERT: B 48 LYS cc_start: 0.8603 (mttp) cc_final: 0.8275 (mmtm) REVERT: B 77 ARG cc_start: 0.8597 (ptm160) cc_final: 0.8265 (ptm160) REVERT: B 84 ASP cc_start: 0.7923 (t0) cc_final: 0.7583 (t0) REVERT: B 96 LEU cc_start: 0.8951 (mm) cc_final: 0.8622 (mm) REVERT: C 6 ASN cc_start: 0.7888 (t0) cc_final: 0.7566 (t0) REVERT: D 4 LYS cc_start: 0.6735 (mttt) cc_final: 0.6417 (mtpp) REVERT: D 11 ASP cc_start: 0.8066 (t0) cc_final: 0.7579 (t0) REVERT: D 176 LEU cc_start: 0.9166 (mt) cc_final: 0.8962 (mt) REVERT: E 181 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8229 (ttpp) REVERT: F 6 ASN cc_start: 0.8679 (t0) cc_final: 0.8478 (t0) REVERT: F 13 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7677 (pt0) REVERT: F 103 LEU cc_start: 0.8162 (mp) cc_final: 0.7858 (mp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2850 time to fit residues: 80.3322 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 6 ASN B 186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.131131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106596 restraints weight = 11790.640| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.81 r_work: 0.2997 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8982 Z= 0.131 Angle : 0.463 4.570 12096 Z= 0.250 Chirality : 0.036 0.149 1428 Planarity : 0.003 0.029 1512 Dihedral : 3.228 16.035 1176 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.52 % Allowed : 7.62 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.26), residues: 1092 helix: 2.42 (0.19), residues: 753 sheet: None (None), residues: 0 loop : 0.53 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 HIS 0.003 0.001 HIS B 186 PHE 0.008 0.001 PHE E 20 TYR 0.013 0.002 TYR E 15 ARG 0.006 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 548) hydrogen bonds : angle 4.06195 ( 1608) covalent geometry : bond 0.00303 ( 8982) covalent geometry : angle 0.46314 (12096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.5812 (mmm) cc_final: 0.5485 (mpp) REVERT: A 67 LEU cc_start: 0.9158 (mt) cc_final: 0.8518 (mt) REVERT: A 180 ILE cc_start: 0.9359 (mm) cc_final: 0.9155 (mt) REVERT: B 11 ASP cc_start: 0.8591 (t0) cc_final: 0.8232 (t0) REVERT: B 84 ASP cc_start: 0.7869 (t0) cc_final: 0.7610 (t0) REVERT: B 96 LEU cc_start: 0.8939 (mm) cc_final: 0.8578 (mm) REVERT: B 183 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8716 (mmmm) REVERT: B 184 ASN cc_start: 0.7511 (m-40) cc_final: 0.7208 (t0) REVERT: C 6 ASN cc_start: 0.8065 (t0) cc_final: 0.7799 (t0) REVERT: C 77 ARG cc_start: 0.7833 (ttm-80) cc_final: 0.6959 (ttm170) REVERT: D 4 LYS cc_start: 0.7152 (mttt) cc_final: 0.6766 (mtpt) REVERT: D 11 ASP cc_start: 0.8084 (t0) cc_final: 0.7620 (t0) REVERT: D 146 THR cc_start: 0.9444 (t) cc_final: 0.9010 (p) REVERT: E 21 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8266 (mmt180) REVERT: E 30 ASP cc_start: 0.8145 (t0) cc_final: 0.7866 (t0) REVERT: F 6 ASN cc_start: 0.8782 (t0) cc_final: 0.8530 (t0) REVERT: F 30 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7782 (t0) REVERT: F 32 LEU cc_start: 0.9181 (tp) cc_final: 0.8956 (tp) REVERT: F 39 MET cc_start: 0.7703 (tmm) cc_final: 0.7481 (tmm) REVERT: F 103 LEU cc_start: 0.8366 (mp) cc_final: 0.7997 (mp) outliers start: 15 outliers final: 6 residues processed: 175 average time/residue: 0.3198 time to fit residues: 71.1178 Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 128 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 57 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN F 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.130479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107123 restraints weight = 11917.513| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.80 r_work: 0.2978 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8982 Z= 0.119 Angle : 0.437 4.226 12096 Z= 0.236 Chirality : 0.036 0.180 1428 Planarity : 0.003 0.023 1512 Dihedral : 3.228 16.559 1176 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.52 % Allowed : 9.96 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.25), residues: 1092 helix: 2.37 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.37 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 HIS 0.001 0.000 HIS E 142 PHE 0.010 0.001 PHE E 20 TYR 0.012 0.002 TYR C 61 ARG 0.006 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.03835 ( 548) hydrogen bonds : angle 3.83807 ( 1608) covalent geometry : bond 0.00275 ( 8982) covalent geometry : angle 0.43660 (12096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9050 (mt) cc_final: 0.8463 (mt) REVERT: B 11 ASP cc_start: 0.8547 (t0) cc_final: 0.8185 (t0) REVERT: B 84 ASP cc_start: 0.7894 (t0) cc_final: 0.7608 (t0) REVERT: B 96 LEU cc_start: 0.8834 (mm) cc_final: 0.8562 (mm) REVERT: B 184 ASN cc_start: 0.7696 (m-40) cc_final: 0.7350 (t0) REVERT: C 6 ASN cc_start: 0.7961 (t0) cc_final: 0.7722 (t0) REVERT: C 77 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.6343 (ttm170) REVERT: D 4 LYS cc_start: 0.7160 (mttt) cc_final: 0.6766 (mttt) REVERT: D 11 ASP cc_start: 0.8097 (t0) cc_final: 0.7632 (t0) REVERT: E 21 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8137 (mmt90) REVERT: E 30 ASP cc_start: 0.8084 (t0) cc_final: 0.7831 (t0) REVERT: F 6 ASN cc_start: 0.8709 (t0) cc_final: 0.8488 (t0) REVERT: F 29 GLN cc_start: 0.8125 (mt0) cc_final: 0.7769 (mt0) REVERT: F 30 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7806 (t0) REVERT: F 32 LEU cc_start: 0.9183 (tp) cc_final: 0.8899 (tp) REVERT: F 39 MET cc_start: 0.7319 (tmm) cc_final: 0.7049 (tmm) REVERT: F 77 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.8039 (mtp85) REVERT: F 103 LEU cc_start: 0.8378 (mp) cc_final: 0.7974 (mp) outliers start: 15 outliers final: 8 residues processed: 174 average time/residue: 0.3245 time to fit residues: 72.7440 Evaluate side-chains 162 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106570 restraints weight = 11964.898| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.81 r_work: 0.2958 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8982 Z= 0.127 Angle : 0.439 4.468 12096 Z= 0.237 Chirality : 0.036 0.185 1428 Planarity : 0.003 0.025 1512 Dihedral : 3.232 15.639 1176 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.13 % Allowed : 11.79 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.25), residues: 1092 helix: 2.35 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.34 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.002 0.000 HIS C 142 PHE 0.009 0.001 PHE E 20 TYR 0.013 0.002 TYR C 61 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 548) hydrogen bonds : angle 3.76097 ( 1608) covalent geometry : bond 0.00300 ( 8982) covalent geometry : angle 0.43867 (12096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8969 (mt) cc_final: 0.8555 (mt) REVERT: B 11 ASP cc_start: 0.8613 (t0) cc_final: 0.8272 (t0) REVERT: B 84 ASP cc_start: 0.7959 (t0) cc_final: 0.7698 (t0) REVERT: B 96 LEU cc_start: 0.8865 (mm) cc_final: 0.8617 (mm) REVERT: B 179 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8176 (tp30) REVERT: B 184 ASN cc_start: 0.8109 (m-40) cc_final: 0.7500 (t0) REVERT: C 6 ASN cc_start: 0.7957 (t0) cc_final: 0.7717 (t0) REVERT: C 77 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.6531 (ttm170) REVERT: D 4 LYS cc_start: 0.7249 (mttt) cc_final: 0.6852 (mttt) REVERT: D 11 ASP cc_start: 0.8086 (t0) cc_final: 0.7613 (t0) REVERT: D 155 ILE cc_start: 0.9265 (mm) cc_final: 0.9027 (mm) REVERT: E 21 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8516 (mmt90) REVERT: E 30 ASP cc_start: 0.8098 (t0) cc_final: 0.7852 (t0) REVERT: F 30 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7890 (t0) REVERT: F 32 LEU cc_start: 0.9161 (tp) cc_final: 0.8868 (tp) REVERT: F 39 MET cc_start: 0.7257 (tmm) cc_final: 0.6936 (tmm) REVERT: F 159 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7588 (mt-10) outliers start: 21 outliers final: 11 residues processed: 173 average time/residue: 0.2750 time to fit residues: 61.1935 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 30 ASP Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN F 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104794 restraints weight = 11806.815| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.71 r_work: 0.2941 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8982 Z= 0.129 Angle : 0.448 4.937 12096 Z= 0.240 Chirality : 0.037 0.193 1428 Planarity : 0.003 0.024 1512 Dihedral : 3.250 15.502 1176 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.24 % Allowed : 12.09 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.25), residues: 1092 helix: 2.31 (0.18), residues: 757 sheet: None (None), residues: 0 loop : 0.30 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.002 0.000 HIS C 142 PHE 0.009 0.001 PHE E 20 TYR 0.013 0.002 TYR C 61 ARG 0.007 0.000 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 548) hydrogen bonds : angle 3.72641 ( 1608) covalent geometry : bond 0.00306 ( 8982) covalent geometry : angle 0.44763 (12096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8948 (mt) cc_final: 0.8558 (mt) REVERT: A 185 ASP cc_start: 0.6782 (m-30) cc_final: 0.6508 (m-30) REVERT: B 11 ASP cc_start: 0.8693 (t0) cc_final: 0.8152 (t0) REVERT: B 78 GLN cc_start: 0.9085 (mt0) cc_final: 0.8882 (mp10) REVERT: B 84 ASP cc_start: 0.7969 (t0) cc_final: 0.7697 (t0) REVERT: B 96 LEU cc_start: 0.8925 (mm) cc_final: 0.8646 (mm) REVERT: B 179 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8276 (tp30) REVERT: C 6 ASN cc_start: 0.7972 (t0) cc_final: 0.7750 (t0) REVERT: C 77 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7081 (ttm170) REVERT: D 4 LYS cc_start: 0.7485 (mttt) cc_final: 0.7051 (mttt) REVERT: D 11 ASP cc_start: 0.8059 (t0) cc_final: 0.7605 (t0) REVERT: D 155 ILE cc_start: 0.9317 (mm) cc_final: 0.9055 (mm) REVERT: E 21 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8350 (mmt90) REVERT: E 30 ASP cc_start: 0.8273 (t0) cc_final: 0.8012 (t0) REVERT: F 32 LEU cc_start: 0.9200 (tp) cc_final: 0.8896 (tp) REVERT: F 39 MET cc_start: 0.7610 (tmm) cc_final: 0.7167 (tmm) REVERT: F 159 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7647 (mt-10) outliers start: 22 outliers final: 13 residues processed: 171 average time/residue: 0.2815 time to fit residues: 61.5723 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 128 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 97 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103867 restraints weight = 11823.417| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.68 r_work: 0.2942 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8982 Z= 0.114 Angle : 0.440 4.903 12096 Z= 0.238 Chirality : 0.036 0.197 1428 Planarity : 0.003 0.025 1512 Dihedral : 3.217 15.196 1176 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.03 % Allowed : 12.91 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.25), residues: 1092 helix: 2.35 (0.18), residues: 757 sheet: None (None), residues: 0 loop : 0.31 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.001 0.000 HIS C 142 PHE 0.008 0.001 PHE E 20 TYR 0.014 0.002 TYR E 87 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 548) hydrogen bonds : angle 3.71811 ( 1608) covalent geometry : bond 0.00266 ( 8982) covalent geometry : angle 0.43999 (12096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8837 (mt) cc_final: 0.8495 (mt) REVERT: A 185 ASP cc_start: 0.6788 (m-30) cc_final: 0.6539 (m-30) REVERT: B 11 ASP cc_start: 0.8715 (t0) cc_final: 0.8185 (t0) REVERT: B 84 ASP cc_start: 0.7961 (t0) cc_final: 0.7676 (t0) REVERT: B 96 LEU cc_start: 0.8904 (mm) cc_final: 0.8636 (mm) REVERT: C 6 ASN cc_start: 0.8047 (t0) cc_final: 0.7801 (t0) REVERT: C 81 GLU cc_start: 0.6633 (mt-10) cc_final: 0.5769 (mp0) REVERT: D 4 LYS cc_start: 0.7489 (mttt) cc_final: 0.7104 (mtpt) REVERT: D 11 ASP cc_start: 0.8106 (t0) cc_final: 0.7633 (t0) REVERT: E 21 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8417 (mmt90) REVERT: E 30 ASP cc_start: 0.8303 (t0) cc_final: 0.8053 (t0) REVERT: F 39 MET cc_start: 0.7625 (tmm) cc_final: 0.7156 (tmm) REVERT: F 77 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8183 (mmm-85) REVERT: F 159 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7745 (mt-10) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.2896 time to fit residues: 63.7105 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.129240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104135 restraints weight = 12008.314| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.78 r_work: 0.2940 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8982 Z= 0.121 Angle : 0.452 5.365 12096 Z= 0.242 Chirality : 0.036 0.202 1428 Planarity : 0.003 0.027 1512 Dihedral : 3.229 16.987 1176 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.83 % Allowed : 14.02 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.25), residues: 1092 helix: 2.36 (0.18), residues: 757 sheet: None (None), residues: 0 loop : 0.27 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.001 0.000 HIS C 142 PHE 0.009 0.001 PHE E 20 TYR 0.013 0.002 TYR C 61 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 548) hydrogen bonds : angle 3.68432 ( 1608) covalent geometry : bond 0.00286 ( 8982) covalent geometry : angle 0.45221 (12096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8966 (mt) cc_final: 0.8425 (mt) REVERT: A 185 ASP cc_start: 0.6770 (m-30) cc_final: 0.6563 (m-30) REVERT: B 11 ASP cc_start: 0.8728 (t0) cc_final: 0.8203 (t0) REVERT: B 31 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8932 (t) REVERT: B 78 GLN cc_start: 0.9048 (mt0) cc_final: 0.8845 (mp10) REVERT: B 84 ASP cc_start: 0.7968 (t0) cc_final: 0.7676 (t0) REVERT: B 96 LEU cc_start: 0.8907 (mm) cc_final: 0.8650 (mm) REVERT: C 6 ASN cc_start: 0.8054 (t0) cc_final: 0.7813 (t0) REVERT: C 77 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7077 (ttm170) REVERT: D 4 LYS cc_start: 0.7510 (mttt) cc_final: 0.7126 (mtpt) REVERT: D 11 ASP cc_start: 0.8068 (t0) cc_final: 0.7667 (t0) REVERT: E 21 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8432 (mmt90) REVERT: E 30 ASP cc_start: 0.8270 (t0) cc_final: 0.8032 (t0) REVERT: F 39 MET cc_start: 0.7745 (tmm) cc_final: 0.7415 (tmm) REVERT: F 77 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8150 (mmm-85) REVERT: F 159 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7752 (mt-10) outliers start: 18 outliers final: 13 residues processed: 168 average time/residue: 0.2788 time to fit residues: 59.8365 Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.0170 chunk 44 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.104738 restraints weight = 12027.708| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.78 r_work: 0.2951 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8982 Z= 0.114 Angle : 0.460 6.220 12096 Z= 0.245 Chirality : 0.036 0.213 1428 Planarity : 0.003 0.027 1512 Dihedral : 3.178 15.205 1176 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.13 % Allowed : 14.13 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.25), residues: 1092 helix: 2.40 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.24 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.002 0.000 HIS B 186 PHE 0.008 0.001 PHE E 20 TYR 0.013 0.002 TYR C 61 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 548) hydrogen bonds : angle 3.68894 ( 1608) covalent geometry : bond 0.00266 ( 8982) covalent geometry : angle 0.45999 (12096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8989 (mt) cc_final: 0.8515 (mt) REVERT: A 185 ASP cc_start: 0.6772 (m-30) cc_final: 0.6567 (m-30) REVERT: B 11 ASP cc_start: 0.8735 (t0) cc_final: 0.8217 (t0) REVERT: B 31 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8919 (t) REVERT: B 84 ASP cc_start: 0.7948 (t0) cc_final: 0.7625 (t0) REVERT: B 96 LEU cc_start: 0.8900 (mm) cc_final: 0.8641 (mm) REVERT: C 6 ASN cc_start: 0.8055 (t0) cc_final: 0.7814 (t0) REVERT: C 77 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7505 (ttm170) REVERT: D 4 LYS cc_start: 0.7497 (mttt) cc_final: 0.7103 (mtpt) REVERT: D 11 ASP cc_start: 0.8037 (t0) cc_final: 0.7645 (t0) REVERT: D 39 MET cc_start: 0.8145 (tpt) cc_final: 0.7933 (tpt) REVERT: E 21 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8401 (mmt180) REVERT: F 39 MET cc_start: 0.7733 (tmm) cc_final: 0.7426 (tmm) REVERT: F 77 ARG cc_start: 0.8341 (mtp85) cc_final: 0.8072 (mmm-85) REVERT: F 159 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7772 (mt-10) outliers start: 21 outliers final: 15 residues processed: 166 average time/residue: 0.2838 time to fit residues: 60.9512 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.129217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104071 restraints weight = 11998.356| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.79 r_work: 0.2934 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8982 Z= 0.129 Angle : 0.505 13.400 12096 Z= 0.269 Chirality : 0.037 0.214 1428 Planarity : 0.003 0.031 1512 Dihedral : 3.187 15.036 1176 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.13 % Allowed : 14.23 % Favored : 83.64 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.25), residues: 1092 helix: 2.35 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.20 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.003 0.000 HIS B 186 PHE 0.008 0.001 PHE E 20 TYR 0.014 0.002 TYR E 87 ARG 0.007 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 548) hydrogen bonds : angle 3.71720 ( 1608) covalent geometry : bond 0.00306 ( 8982) covalent geometry : angle 0.50453 (12096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9060 (mt) cc_final: 0.8561 (mt) REVERT: A 185 ASP cc_start: 0.6791 (m-30) cc_final: 0.6581 (m-30) REVERT: B 11 ASP cc_start: 0.8741 (t0) cc_final: 0.8238 (t0) REVERT: B 31 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8910 (t) REVERT: B 84 ASP cc_start: 0.8007 (t0) cc_final: 0.7709 (t0) REVERT: B 96 LEU cc_start: 0.8902 (mm) cc_final: 0.8648 (mm) REVERT: C 6 ASN cc_start: 0.8073 (t0) cc_final: 0.7827 (t0) REVERT: C 77 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7684 (ttm-80) REVERT: D 4 LYS cc_start: 0.7546 (mttt) cc_final: 0.7148 (mtpt) REVERT: D 11 ASP cc_start: 0.8070 (t0) cc_final: 0.7713 (t0) REVERT: E 21 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8436 (mmt90) REVERT: F 39 MET cc_start: 0.8096 (tmm) cc_final: 0.7538 (tmm) REVERT: F 77 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8078 (mmm-85) REVERT: F 159 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7821 (mt-10) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 0.2902 time to fit residues: 60.2358 Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 chunk 33 optimal weight: 0.0040 chunk 59 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN E 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105879 restraints weight = 11916.712| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.75 r_work: 0.2963 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8982 Z= 0.109 Angle : 0.476 9.665 12096 Z= 0.255 Chirality : 0.036 0.210 1428 Planarity : 0.003 0.027 1512 Dihedral : 3.130 14.858 1176 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.32 % Allowed : 14.84 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.25), residues: 1092 helix: 2.41 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.23 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.003 0.000 HIS B 186 PHE 0.008 0.001 PHE E 20 TYR 0.014 0.002 TYR E 87 ARG 0.007 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 548) hydrogen bonds : angle 3.69875 ( 1608) covalent geometry : bond 0.00250 ( 8982) covalent geometry : angle 0.47618 (12096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASP cc_start: 0.6760 (m-30) cc_final: 0.6553 (m-30) REVERT: B 11 ASP cc_start: 0.8607 (t0) cc_final: 0.8043 (t0) REVERT: B 31 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8896 (t) REVERT: B 84 ASP cc_start: 0.8161 (t0) cc_final: 0.7829 (t0) REVERT: B 96 LEU cc_start: 0.8889 (mm) cc_final: 0.8645 (mm) REVERT: C 6 ASN cc_start: 0.8083 (t0) cc_final: 0.7851 (t0) REVERT: D 4 LYS cc_start: 0.7481 (mttt) cc_final: 0.7059 (mtpt) REVERT: D 11 ASP cc_start: 0.8044 (t0) cc_final: 0.7691 (t0) REVERT: E 21 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8371 (mmt90) REVERT: F 39 MET cc_start: 0.8103 (tmm) cc_final: 0.7562 (tmm) REVERT: F 159 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7861 (mt-10) outliers start: 13 outliers final: 10 residues processed: 160 average time/residue: 0.2860 time to fit residues: 58.8547 Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain F residue 111 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 38 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: B 6 ASN C 173 ASN E 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.103737 restraints weight = 12004.515| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.81 r_work: 0.2942 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8982 Z= 0.138 Angle : 0.506 8.958 12096 Z= 0.266 Chirality : 0.037 0.219 1428 Planarity : 0.003 0.041 1512 Dihedral : 3.189 14.956 1176 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.52 % Allowed : 14.84 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1092 helix: 2.31 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.21 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS B 186 PHE 0.009 0.001 PHE E 20 TYR 0.014 0.002 TYR C 61 ARG 0.007 0.001 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 548) hydrogen bonds : angle 3.73152 ( 1608) covalent geometry : bond 0.00331 ( 8982) covalent geometry : angle 0.50603 (12096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5753.82 seconds wall clock time: 101 minutes 24.90 seconds (6084.90 seconds total)