Starting phenix.real_space_refine on Mon May 12 06:19:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vw3_43575/05_2025/8vw3_43575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vw3_43575/05_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_43575/05_2025/8vw3_43575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vw3_43575/05_2025/8vw3_43575.map" model { file = "/net/cci-nas-00/data/ceres_data/8vw3_43575/05_2025/8vw3_43575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vw3_43575/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.82, per 1000 atoms: 0.77 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: 2.43 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: 0.82 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: 2.23 Time building geometry restraints manager: 2.81 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: 0.01 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: 6.030 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.700 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- 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 : 1.235 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: 0.2963 time to fit residues: 83.8122 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 : 1.019 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.130174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.105900 restraints weight = 11804.172| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.85 r_work: 0.2989 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8982 Z= 0.153 Angle : 0.484 5.198 12096 Z= 0.259 Chirality : 0.037 0.158 1428 Planarity : 0.003 0.034 1512 Dihedral : 3.296 16.470 1176 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.52 % Allowed : 7.83 % Favored : 90.65 % 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: 2.65 (0.26), residues: 1092 helix: 2.34 (0.19), residues: 753 sheet: None (None), residues: 0 loop : 0.51 (0.34), residues: 339 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 B 66 TYR 0.014 0.002 TYR E 15 ARG 0.007 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.04342 ( 548) hydrogen bonds : angle 4.05613 ( 1608) covalent geometry : bond 0.00362 ( 8982) covalent geometry : angle 0.48357 (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 : 0.952 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.5816 (mmm) cc_final: 0.5495 (mpp) REVERT: A 67 LEU cc_start: 0.9166 (mt) cc_final: 0.8541 (mt) REVERT: B 11 ASP cc_start: 0.8629 (t0) cc_final: 0.8275 (t0) REVERT: B 84 ASP cc_start: 0.7939 (t0) cc_final: 0.7731 (t0) REVERT: B 96 LEU cc_start: 0.8944 (mm) cc_final: 0.8582 (mm) REVERT: B 183 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8723 (mmmm) REVERT: B 184 ASN cc_start: 0.7691 (m-40) cc_final: 0.7383 (t0) REVERT: C 6 ASN cc_start: 0.8086 (t0) cc_final: 0.7853 (t0) REVERT: C 77 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.6971 (ttm170) REVERT: D 4 LYS cc_start: 0.7137 (mttt) cc_final: 0.6780 (mtpt) REVERT: D 11 ASP cc_start: 0.8093 (t0) cc_final: 0.7635 (t0) REVERT: D 146 THR cc_start: 0.9475 (t) cc_final: 0.9044 (p) REVERT: E 21 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8278 (mmt90) REVERT: E 30 ASP cc_start: 0.8171 (t0) cc_final: 0.7893 (t0) REVERT: F 6 ASN cc_start: 0.8713 (t0) cc_final: 0.8468 (t0) REVERT: F 30 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7793 (t0) REVERT: F 39 MET cc_start: 0.7715 (tmm) cc_final: 0.7503 (tmm) REVERT: F 103 LEU cc_start: 0.8399 (mp) cc_final: 0.7991 (mp) outliers start: 15 outliers final: 7 residues processed: 176 average time/residue: 0.2973 time to fit residues: 66.5052 Evaluate side-chains 155 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain B residue 65 SER 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: 0.9980 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.130205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.107047 restraints weight = 11921.647| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.82 r_work: 0.2969 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8982 Z= 0.119 Angle : 0.440 4.238 12096 Z= 0.238 Chirality : 0.036 0.182 1428 Planarity : 0.003 0.023 1512 Dihedral : 3.260 16.044 1176 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.42 % Allowed : 10.16 % Favored : 88.41 % 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: 2.33 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.38 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.001 0.000 HIS E 116 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 0.03904 ( 548) hydrogen bonds : angle 3.85810 ( 1608) covalent geometry : bond 0.00272 ( 8982) covalent geometry : angle 0.43963 (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 176 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9058 (mt) cc_final: 0.8468 (mt) REVERT: B 11 ASP cc_start: 0.8558 (t0) cc_final: 0.8205 (t0) REVERT: B 84 ASP cc_start: 0.7907 (t0) cc_final: 0.7625 (t0) REVERT: B 96 LEU cc_start: 0.8838 (mm) cc_final: 0.8557 (mm) REVERT: B 184 ASN cc_start: 0.7715 (m-40) cc_final: 0.7364 (t0) REVERT: C 6 ASN cc_start: 0.7986 (t0) cc_final: 0.7777 (t0) REVERT: C 77 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.6285 (ttm170) REVERT: C 81 GLU cc_start: 0.6282 (mt-10) cc_final: 0.5844 (mp0) REVERT: D 4 LYS cc_start: 0.7181 (mttt) cc_final: 0.6781 (mttt) REVERT: D 11 ASP cc_start: 0.8096 (t0) cc_final: 0.7632 (t0) REVERT: E 11 ASP cc_start: 0.8442 (p0) cc_final: 0.8239 (p0) REVERT: E 21 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8184 (mmt90) REVERT: E 30 ASP cc_start: 0.8088 (t0) cc_final: 0.7833 (t0) REVERT: F 30 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7799 (t0) REVERT: F 39 MET cc_start: 0.7328 (tmm) cc_final: 0.7068 (tmm) REVERT: F 77 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.8053 (mtp85) REVERT: F 103 LEU cc_start: 0.8383 (mp) cc_final: 0.8012 (mp) REVERT: F 159 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7600 (mt-10) outliers start: 14 outliers final: 8 residues processed: 169 average time/residue: 0.2710 time to fit residues: 58.9083 Evaluate side-chains 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0000 chunk 100 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.129973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.106742 restraints weight = 11873.746| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.74 r_work: 0.2974 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1760 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= 0.117 Angle : 0.427 4.267 12096 Z= 0.230 Chirality : 0.036 0.187 1428 Planarity : 0.003 0.024 1512 Dihedral : 3.211 15.891 1176 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.03 % Allowed : 10.98 % Favored : 86.99 % 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: 2.37 (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 0.007 0.001 TRP B 18 HIS 0.001 0.000 HIS C 142 PHE 0.010 0.001 PHE E 20 TYR 0.015 0.002 TYR E 87 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 548) hydrogen bonds : angle 3.73966 ( 1608) covalent geometry : bond 0.00270 ( 8982) covalent geometry : angle 0.42698 (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: 20 poor density : 164 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.5773 (mmm) cc_final: 0.5463 (mpp) REVERT: A 67 LEU cc_start: 0.8963 (mt) cc_final: 0.8538 (mt) REVERT: B 11 ASP cc_start: 0.8583 (t0) cc_final: 0.8240 (t0) REVERT: B 84 ASP cc_start: 0.7915 (t0) cc_final: 0.7630 (t0) REVERT: B 96 LEU cc_start: 0.8870 (mm) cc_final: 0.8623 (mm) REVERT: B 179 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8155 (tp30) REVERT: B 184 ASN cc_start: 0.7957 (m-40) cc_final: 0.7390 (t0) REVERT: C 6 ASN cc_start: 0.7990 (t0) cc_final: 0.7776 (t0) REVERT: C 77 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.6970 (ttm170) REVERT: D 4 LYS cc_start: 0.7228 (mttt) cc_final: 0.6918 (mtpt) REVERT: D 11 ASP cc_start: 0.8067 (t0) cc_final: 0.7606 (t0) REVERT: D 155 ILE cc_start: 0.9263 (mm) cc_final: 0.9028 (mm) REVERT: E 21 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8514 (mmt90) REVERT: E 30 ASP cc_start: 0.8082 (t0) cc_final: 0.7841 (t0) REVERT: E 84 ASP cc_start: 0.8930 (m-30) cc_final: 0.8715 (m-30) REVERT: F 30 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7869 (t0) REVERT: F 39 MET cc_start: 0.7269 (tmm) cc_final: 0.6947 (tmm) REVERT: F 103 LEU cc_start: 0.8392 (mp) cc_final: 0.8037 (mp) REVERT: F 159 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7684 (mt-10) outliers start: 20 outliers final: 11 residues processed: 175 average time/residue: 0.2571 time to fit residues: 58.0715 Evaluate side-chains 170 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 4 optimal weight: 0.0060 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.3954 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.130840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.105988 restraints weight = 11716.240| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.74 r_work: 0.2967 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8982 Z= 0.099 Angle : 0.423 5.100 12096 Z= 0.228 Chirality : 0.036 0.186 1428 Planarity : 0.003 0.026 1512 Dihedral : 3.167 15.505 1176 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.73 % Allowed : 11.79 % Favored : 86.48 % 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: 2.72 (0.25), residues: 1092 helix: 2.45 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.33 (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 0.007 0.001 PHE E 20 TYR 0.014 0.002 TYR E 87 ARG 0.006 0.000 ARG F 77 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 548) hydrogen bonds : angle 3.67276 ( 1608) covalent geometry : bond 0.00220 ( 8982) covalent geometry : angle 0.42268 (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 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 MET cc_start: 0.5945 (mmm) cc_final: 0.5574 (mpp) REVERT: A 67 LEU cc_start: 0.8819 (mt) cc_final: 0.8487 (mt) REVERT: A 185 ASP cc_start: 0.6750 (m-30) cc_final: 0.6481 (m-30) REVERT: B 11 ASP cc_start: 0.8665 (t0) cc_final: 0.8338 (t0) REVERT: B 84 ASP cc_start: 0.7886 (t0) cc_final: 0.7552 (t0) REVERT: B 96 LEU cc_start: 0.8913 (mm) cc_final: 0.8659 (mm) REVERT: B 184 ASN cc_start: 0.7978 (m-40) cc_final: 0.7736 (m-40) REVERT: C 6 ASN cc_start: 0.7994 (t0) cc_final: 0.7775 (t0) REVERT: C 77 ARG cc_start: 0.7878 (ttm-80) cc_final: 0.7483 (ttm170) REVERT: D 4 LYS cc_start: 0.7443 (mttt) cc_final: 0.6999 (mttt) REVERT: D 11 ASP cc_start: 0.8084 (t0) cc_final: 0.7614 (t0) REVERT: D 155 ILE cc_start: 0.9293 (mm) cc_final: 0.9018 (mm) REVERT: E 14 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8691 (mmtp) REVERT: E 21 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8408 (mmt90) REVERT: E 30 ASP cc_start: 0.8088 (t0) cc_final: 0.7862 (t0) REVERT: F 30 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7879 (t0) REVERT: F 87 TYR cc_start: 0.8802 (m-80) cc_final: 0.8596 (m-80) REVERT: F 159 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7747 (mt-10) outliers start: 17 outliers final: 11 residues processed: 172 average time/residue: 0.2898 time to fit residues: 63.7524 Evaluate side-chains 171 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.128462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103375 restraints weight = 11803.086| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.77 r_work: 0.2924 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8982 Z= 0.150 Angle : 0.470 5.045 12096 Z= 0.250 Chirality : 0.037 0.203 1428 Planarity : 0.003 0.026 1512 Dihedral : 3.270 15.676 1176 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.13 % Allowed : 13.31 % Favored : 84.55 % 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: 2.52 (0.25), residues: 1092 helix: 2.29 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.30 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 HIS 0.002 0.001 HIS C 142 PHE 0.010 0.001 PHE E 20 TYR 0.019 0.003 TYR E 87 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 548) hydrogen bonds : angle 3.73960 ( 1608) covalent geometry : bond 0.00363 ( 8982) covalent geometry : angle 0.47038 (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 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.6317 (mmm) cc_final: 0.6108 (mpp) REVERT: A 67 LEU cc_start: 0.8933 (mt) cc_final: 0.8487 (mt) REVERT: B 11 ASP cc_start: 0.8715 (t0) cc_final: 0.8187 (t0) REVERT: B 84 ASP cc_start: 0.8038 (t0) cc_final: 0.7657 (t0) REVERT: B 96 LEU cc_start: 0.8922 (mm) cc_final: 0.8638 (mm) REVERT: B 151 TYR cc_start: 0.9397 (m-80) cc_final: 0.8949 (m-80) REVERT: B 179 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: B 184 ASN cc_start: 0.8121 (m-40) cc_final: 0.7918 (m-40) REVERT: C 6 ASN cc_start: 0.8092 (t0) cc_final: 0.7876 (t0) REVERT: C 77 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7451 (ttm170) REVERT: D 4 LYS cc_start: 0.7538 (mttt) cc_final: 0.7076 (mttt) REVERT: D 11 ASP cc_start: 0.8106 (t0) cc_final: 0.7634 (t0) REVERT: D 146 THR cc_start: 0.9444 (t) cc_final: 0.8968 (p) REVERT: D 155 ILE cc_start: 0.9369 (mm) cc_final: 0.9132 (mm) REVERT: E 21 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8314 (mmt90) REVERT: E 30 ASP cc_start: 0.8138 (t0) cc_final: 0.7909 (t0) REVERT: F 30 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7898 (t0) REVERT: F 77 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8205 (mmm-85) REVERT: F 159 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7794 (mt-10) outliers start: 21 outliers final: 12 residues processed: 167 average time/residue: 0.2860 time to fit residues: 61.0911 Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 127 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 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 Chi-restraints excluded: chain F residue 128 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.129629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.103256 restraints weight = 11918.187| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.71 r_work: 0.2934 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2015 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= 0.127 Angle : 0.452 5.366 12096 Z= 0.242 Chirality : 0.036 0.210 1428 Planarity : 0.003 0.028 1512 Dihedral : 3.220 14.956 1176 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 14.13 % Favored : 83.94 % 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: 2.56 (0.25), residues: 1092 helix: 2.34 (0.18), residues: 756 sheet: None (None), residues: 0 loop : 0.27 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.002 0.000 HIS C 142 PHE 0.021 0.001 PHE C 170 TYR 0.019 0.002 TYR E 87 ARG 0.006 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 548) hydrogen bonds : angle 3.70573 ( 1608) covalent geometry : bond 0.00301 ( 8982) covalent geometry : angle 0.45240 (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 177 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8973 (mt) cc_final: 0.8425 (mt) REVERT: A 185 ASP cc_start: 0.6825 (m-30) cc_final: 0.6614 (m-30) REVERT: B 11 ASP cc_start: 0.8739 (t0) cc_final: 0.8220 (t0) REVERT: B 84 ASP cc_start: 0.8023 (t0) cc_final: 0.7763 (t0) REVERT: B 96 LEU cc_start: 0.8893 (mm) cc_final: 0.8622 (mm) REVERT: B 151 TYR cc_start: 0.9400 (m-80) cc_final: 0.8964 (m-80) REVERT: B 179 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: B 184 ASN cc_start: 0.8018 (m-40) cc_final: 0.7787 (m-40) REVERT: C 6 ASN cc_start: 0.8110 (t0) cc_final: 0.7885 (t0) REVERT: C 77 ARG cc_start: 0.8068 (ttm-80) cc_final: 0.7769 (ttm170) REVERT: D 4 LYS cc_start: 0.7531 (mttt) cc_final: 0.7124 (mtpt) REVERT: D 11 ASP cc_start: 0.8132 (t0) cc_final: 0.7722 (t0) REVERT: D 146 THR cc_start: 0.9486 (t) cc_final: 0.9020 (p) REVERT: D 155 ILE cc_start: 0.9328 (mm) cc_final: 0.9066 (mm) REVERT: E 21 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8311 (mmt90) REVERT: E 30 ASP cc_start: 0.8278 (t0) cc_final: 0.8028 (t0) REVERT: F 77 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8176 (mmm-85) outliers start: 19 outliers final: 13 residues processed: 168 average time/residue: 0.2763 time to fit residues: 59.3671 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 0.0020 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.129678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.103593 restraints weight = 11952.262| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.68 r_work: 0.2939 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8982 Z= 0.120 Angle : 0.462 9.326 12096 Z= 0.245 Chirality : 0.036 0.213 1428 Planarity : 0.003 0.028 1512 Dihedral : 3.202 15.008 1176 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.24 % Allowed : 13.72 % Favored : 84.04 % 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: 2.39 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.23 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.002 0.000 HIS B 186 PHE 0.018 0.001 PHE C 170 TYR 0.017 0.002 TYR E 87 ARG 0.007 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 548) hydrogen bonds : angle 3.68376 ( 1608) covalent geometry : bond 0.00284 ( 8982) covalent geometry : angle 0.46227 (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 181 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9000 (mt) cc_final: 0.8572 (mt) REVERT: A 185 ASP cc_start: 0.6850 (m-30) cc_final: 0.6631 (m-30) REVERT: B 11 ASP cc_start: 0.8751 (t0) cc_final: 0.8235 (t0) REVERT: B 31 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8920 (t) REVERT: B 84 ASP cc_start: 0.7980 (t0) cc_final: 0.7679 (t0) REVERT: B 96 LEU cc_start: 0.8907 (mm) cc_final: 0.8650 (mm) REVERT: B 151 TYR cc_start: 0.9392 (m-80) cc_final: 0.8930 (m-80) REVERT: B 179 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: B 184 ASN cc_start: 0.8005 (m-40) cc_final: 0.7769 (m-40) REVERT: C 6 ASN cc_start: 0.8091 (t0) cc_final: 0.7873 (t0) REVERT: D 4 LYS cc_start: 0.7543 (mttt) cc_final: 0.7136 (mtpt) REVERT: D 11 ASP cc_start: 0.8092 (t0) cc_final: 0.7690 (t0) REVERT: D 146 THR cc_start: 0.9481 (t) cc_final: 0.8993 (p) REVERT: E 21 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8304 (mmt90) REVERT: E 30 ASP cc_start: 0.8280 (t0) cc_final: 0.8044 (t0) REVERT: F 77 ARG cc_start: 0.8391 (mtp85) cc_final: 0.8105 (mmm-85) REVERT: F 87 TYR cc_start: 0.8809 (m-80) cc_final: 0.8556 (m-80) outliers start: 22 outliers final: 14 residues processed: 173 average time/residue: 0.2766 time to fit residues: 61.7042 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 0.0060 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.131273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.106715 restraints weight = 11897.542| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.77 r_work: 0.2963 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8982 Z= 0.101 Angle : 0.453 8.691 12096 Z= 0.242 Chirality : 0.036 0.207 1428 Planarity : 0.003 0.026 1512 Dihedral : 3.128 14.926 1176 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.73 % Allowed : 14.23 % Favored : 84.04 % 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: 2.68 (0.25), residues: 1092 helix: 2.48 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.19 (0.34), residues: 338 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 0.015 0.002 TYR E 87 ARG 0.007 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 548) hydrogen bonds : angle 3.65808 ( 1608) covalent geometry : bond 0.00227 ( 8982) covalent geometry : angle 0.45324 (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 180 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 4 LYS cc_start: 0.8116 (mmpt) cc_final: 0.7828 (mmtt) REVERT: B 11 ASP cc_start: 0.8698 (t0) cc_final: 0.8181 (t0) REVERT: B 31 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 84 ASP cc_start: 0.7902 (t0) cc_final: 0.7529 (t0) REVERT: B 96 LEU cc_start: 0.8902 (mm) cc_final: 0.8664 (mm) REVERT: B 184 ASN cc_start: 0.7995 (m-40) cc_final: 0.7715 (m-40) REVERT: C 6 ASN cc_start: 0.8070 (t0) cc_final: 0.7843 (t0) REVERT: C 77 ARG cc_start: 0.7739 (ttm-80) cc_final: 0.6997 (ttm170) REVERT: C 81 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6008 (mt-10) REVERT: D 4 LYS cc_start: 0.7492 (mttt) cc_final: 0.7069 (mtpt) REVERT: D 11 ASP cc_start: 0.8041 (t0) cc_final: 0.7702 (t0) REVERT: D 39 MET cc_start: 0.8108 (tpt) cc_final: 0.7895 (tpt) REVERT: D 146 THR cc_start: 0.9371 (t) cc_final: 0.8830 (p) REVERT: E 21 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8378 (mmt90) REVERT: F 77 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7973 (mmm-85) REVERT: F 78 GLN cc_start: 0.8307 (mt0) cc_final: 0.7910 (mp10) REVERT: F 87 TYR cc_start: 0.8797 (m-80) cc_final: 0.8549 (m-80) outliers start: 17 outliers final: 12 residues processed: 174 average time/residue: 0.2814 time to fit residues: 62.5529 Evaluate side-chains 165 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 167 THR Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 186 HIS 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 84 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 6 ASN E 29 GLN F 6 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103493 restraints weight = 11914.779| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.67 r_work: 0.2932 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8982 Z= 0.139 Angle : 0.496 7.367 12096 Z= 0.261 Chirality : 0.037 0.221 1428 Planarity : 0.003 0.041 1512 Dihedral : 3.189 15.136 1176 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.52 % Allowed : 14.63 % 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: 2.55 (0.25), residues: 1092 helix: 2.37 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.16 (0.34), residues: 338 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 0.019 0.002 TYR E 87 ARG 0.007 0.001 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 548) hydrogen bonds : angle 3.70461 ( 1608) covalent geometry : bond 0.00336 ( 8982) covalent geometry : angle 0.49551 (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 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 ASP cc_start: 0.8704 (t0) cc_final: 0.8212 (t0) REVERT: B 31 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8912 (t) REVERT: B 84 ASP cc_start: 0.7989 (t0) cc_final: 0.7684 (t0) REVERT: B 96 LEU cc_start: 0.8904 (mm) cc_final: 0.8649 (mm) REVERT: C 6 ASN cc_start: 0.8084 (t0) cc_final: 0.7869 (t0) REVERT: C 77 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7058 (ttm170) REVERT: C 81 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6003 (mt-10) REVERT: D 4 LYS cc_start: 0.7507 (mttt) cc_final: 0.7135 (mtpt) REVERT: D 11 ASP cc_start: 0.8048 (t0) cc_final: 0.7688 (t0) REVERT: D 146 THR cc_start: 0.9483 (t) cc_final: 0.9011 (p) REVERT: E 21 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8323 (mmt90) REVERT: F 77 ARG cc_start: 0.8368 (mtp85) cc_final: 0.8096 (mmm-85) REVERT: F 87 TYR cc_start: 0.8811 (m-80) cc_final: 0.8525 (m-80) outliers start: 15 outliers final: 9 residues processed: 164 average time/residue: 0.2789 time to fit residues: 58.4495 Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3427 r_free = 0.3427 target = 0.129953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.104673 restraints weight = 11905.802| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.85 r_work: 0.2938 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8982 Z= 0.121 Angle : 0.479 7.387 12096 Z= 0.255 Chirality : 0.036 0.222 1428 Planarity : 0.003 0.040 1512 Dihedral : 3.205 15.413 1176 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 14.74 % 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: 2.58 (0.25), residues: 1092 helix: 2.39 (0.19), residues: 754 sheet: None (None), residues: 0 loop : 0.17 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.003 0.001 HIS B 186 PHE 0.009 0.001 PHE E 20 TYR 0.015 0.002 TYR E 87 ARG 0.008 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 548) hydrogen bonds : angle 3.69013 ( 1608) covalent geometry : bond 0.00285 ( 8982) covalent geometry : angle 0.47937 (12096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4839.23 seconds wall clock time: 85 minutes 0.13 seconds (5100.13 seconds total)