Starting phenix.real_space_refine on Wed Sep 17 12:59:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vw3_43575/09_2025/8vw3_43575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vw3_43575/09_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_43575/09_2025/8vw3_43575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vw3_43575/09_2025/8vw3_43575.map" model { file = "/net/cci-nas-00/data/ceres_data/8vw3_43575/09_2025/8vw3_43575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vw3_43575/09_2025/8vw3_43575.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.34, per 1000 atoms: 0.26 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: 0.84 Conformation dependent library (CDL) restraints added in 352.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.30 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: 1.30 Time building geometry restraints manager: 1.11 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: 7.810 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.900 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- 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 : 5.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG C 99 TYR 0.009 0.001 TYR D 61 PHE 0.010 0.001 PHE F 120 TRP 0.005 0.001 TRP D 47 HIS 0.001 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 8982) covalent geometry : angle 0.38210 (12096) hydrogen bonds : bond 0.14063 ( 548) hydrogen bonds : angle 4.66654 ( 1608) *********************** 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 : 0.400 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: 0.7582 (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: 0.6418 (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: 0.8476 (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: 0.7859 (mp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1495 time to fit residues: 42.0415 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.109787 restraints weight = 11829.411| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.75 r_work: 0.3021 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8982 Z= 0.116 Angle : 0.449 4.892 12096 Z= 0.243 Chirality : 0.036 0.157 1428 Planarity : 0.003 0.029 1512 Dihedral : 3.215 16.615 1176 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.63 % Allowed : 7.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.26), residues: 1092 helix: 2.48 (0.19), residues: 753 sheet: None (None), residues: 0 loop : 0.53 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 23 TYR 0.012 0.002 TYR E 15 PHE 0.009 0.001 PHE E 20 TRP 0.006 0.001 TRP B 18 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8982) covalent geometry : angle 0.44930 (12096) hydrogen bonds : bond 0.04079 ( 548) hydrogen bonds : angle 3.98820 ( 1608) *********************** 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 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 39 MET cc_start: 0.5776 (mmm) cc_final: 0.5491 (mpp) REVERT: A 67 LEU cc_start: 0.9133 (mt) cc_final: 0.8520 (mt) REVERT: A 180 ILE cc_start: 0.9349 (mm) cc_final: 0.9144 (mt) REVERT: B 11 ASP cc_start: 0.8540 (t0) cc_final: 0.8177 (t0) REVERT: B 84 ASP cc_start: 0.7813 (t0) cc_final: 0.7545 (t0) REVERT: B 96 LEU cc_start: 0.8938 (mm) cc_final: 0.8602 (mm) REVERT: B 183 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8717 (mmmm) REVERT: B 184 ASN cc_start: 0.7506 (m-40) cc_final: 0.7223 (t0) REVERT: C 6 ASN cc_start: 0.8056 (t0) cc_final: 0.7795 (t0) REVERT: C 77 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.6734 (ttm170) REVERT: D 4 LYS cc_start: 0.7050 (mttt) cc_final: 0.6666 (mtpt) REVERT: D 11 ASP cc_start: 0.8092 (t0) cc_final: 0.7613 (t0) REVERT: D 146 THR cc_start: 0.9429 (t) cc_final: 0.8993 (p) REVERT: E 21 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8170 (mmt180) REVERT: E 30 ASP cc_start: 0.8141 (t0) cc_final: 0.7864 (t0) REVERT: F 6 ASN cc_start: 0.8707 (t0) cc_final: 0.8493 (t0) REVERT: F 30 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7791 (t0) REVERT: F 32 LEU cc_start: 0.9012 (tp) cc_final: 0.8644 (tp) REVERT: F 103 LEU cc_start: 0.8331 (mp) cc_final: 0.7978 (mp) outliers start: 16 outliers final: 9 residues processed: 186 average time/residue: 0.1479 time to fit residues: 34.6897 Evaluate side-chains 168 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain C residue 114 LEU 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 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 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.131566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.105890 restraints weight = 11753.631| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.69 r_work: 0.2967 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8982 Z= 0.110 Angle : 0.433 5.377 12096 Z= 0.233 Chirality : 0.036 0.175 1428 Planarity : 0.003 0.023 1512 Dihedral : 3.183 16.421 1176 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.52 % Allowed : 9.86 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.25), residues: 1092 helix: 2.46 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.42 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 23 TYR 0.011 0.002 TYR F 15 PHE 0.009 0.001 PHE E 20 TRP 0.006 0.001 TRP B 18 HIS 0.001 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8982) covalent geometry : angle 0.43347 (12096) hydrogen bonds : bond 0.03747 ( 548) hydrogen bonds : angle 3.82170 ( 1608) *********************** 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 179 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9060 (mt) cc_final: 0.8469 (mt) REVERT: B 5 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7686 (tpt170) REVERT: B 11 ASP cc_start: 0.8546 (t0) cc_final: 0.8205 (t0) REVERT: B 84 ASP cc_start: 0.7911 (t0) cc_final: 0.7598 (t0) REVERT: B 96 LEU cc_start: 0.8852 (mm) cc_final: 0.8578 (mm) REVERT: B 184 ASN cc_start: 0.7697 (m-40) cc_final: 0.7310 (t0) REVERT: C 6 ASN cc_start: 0.8004 (t0) cc_final: 0.7773 (t0) REVERT: C 77 ARG cc_start: 0.7598 (ttm-80) cc_final: 0.6357 (ttm170) REVERT: C 81 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5767 (mp0) REVERT: D 4 LYS cc_start: 0.7121 (mttt) cc_final: 0.6746 (mttt) REVERT: D 11 ASP cc_start: 0.8096 (t0) cc_final: 0.7638 (t0) REVERT: E 21 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8182 (mmt180) REVERT: E 30 ASP cc_start: 0.8091 (t0) cc_final: 0.7844 (t0) REVERT: F 6 ASN cc_start: 0.8710 (t0) cc_final: 0.8497 (t0) REVERT: F 30 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7826 (t0) REVERT: F 32 LEU cc_start: 0.9054 (tp) cc_final: 0.8627 (tp) REVERT: F 103 LEU cc_start: 0.8362 (mp) cc_final: 0.7991 (mp) outliers start: 15 outliers final: 7 residues processed: 170 average time/residue: 0.1379 time to fit residues: 29.9535 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.0470 chunk 95 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.7082 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.129839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.104078 restraints weight = 12013.203| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.69 r_work: 0.2957 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8982 Z= 0.126 Angle : 0.438 5.606 12096 Z= 0.234 Chirality : 0.036 0.180 1428 Planarity : 0.003 0.023 1512 Dihedral : 3.193 15.865 1176 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.63 % Allowed : 11.08 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.25), residues: 1092 helix: 2.39 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.36 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 23 TYR 0.015 0.002 TYR E 87 PHE 0.009 0.001 PHE E 20 TRP 0.007 0.001 TRP B 18 HIS 0.002 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8982) covalent geometry : angle 0.43847 (12096) hydrogen bonds : bond 0.03694 ( 548) hydrogen bonds : angle 3.75054 ( 1608) *********************** 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 175 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8994 (mt) cc_final: 0.8589 (mt) REVERT: B 11 ASP cc_start: 0.8532 (t0) cc_final: 0.8113 (t0) REVERT: B 84 ASP cc_start: 0.8004 (t0) cc_final: 0.7737 (t0) REVERT: B 96 LEU cc_start: 0.8835 (mm) cc_final: 0.8569 (mm) REVERT: B 179 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: C 6 ASN cc_start: 0.8040 (t0) cc_final: 0.7793 (t0) REVERT: C 77 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7275 (ttm170) REVERT: D 4 LYS cc_start: 0.7239 (mttt) cc_final: 0.6934 (mtpt) REVERT: D 11 ASP cc_start: 0.8146 (t0) cc_final: 0.7678 (t0) REVERT: D 155 ILE cc_start: 0.9290 (mm) cc_final: 0.9065 (mm) REVERT: E 21 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8533 (mmt90) REVERT: E 30 ASP cc_start: 0.8165 (t0) cc_final: 0.7918 (t0) REVERT: F 6 ASN cc_start: 0.8772 (t0) cc_final: 0.8543 (t0) REVERT: F 30 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7878 (t0) REVERT: F 77 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8180 (mmm-85) REVERT: F 103 LEU cc_start: 0.8405 (mp) cc_final: 0.7962 (mp) REVERT: F 159 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7641 (mt-10) outliers start: 16 outliers final: 10 residues processed: 167 average time/residue: 0.1361 time to fit residues: 29.2257 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 92 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.129133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.103208 restraints weight = 11932.684| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.69 r_work: 0.2934 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8982 Z= 0.140 Angle : 0.450 6.122 12096 Z= 0.240 Chirality : 0.037 0.190 1428 Planarity : 0.003 0.024 1512 Dihedral : 3.239 15.560 1176 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.93 % Allowed : 12.09 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.25), residues: 1092 helix: 2.33 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.35 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 23 TYR 0.016 0.002 TYR E 87 PHE 0.009 0.001 PHE E 20 TRP 0.008 0.001 TRP B 18 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8982) covalent geometry : angle 0.45046 (12096) hydrogen bonds : bond 0.03743 ( 548) hydrogen bonds : angle 3.73436 ( 1608) *********************** 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 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9007 (mt) cc_final: 0.8416 (mt) REVERT: A 185 ASP cc_start: 0.6667 (m-30) cc_final: 0.6384 (m-30) REVERT: B 11 ASP cc_start: 0.8676 (t0) cc_final: 0.8335 (t0) REVERT: B 84 ASP cc_start: 0.8061 (t0) cc_final: 0.7814 (t0) REVERT: B 96 LEU cc_start: 0.8824 (mm) cc_final: 0.8569 (mm) REVERT: B 151 TYR cc_start: 0.9378 (m-80) cc_final: 0.8949 (m-80) REVERT: B 179 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: C 6 ASN cc_start: 0.8057 (t0) cc_final: 0.7824 (t0) REVERT: C 77 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7384 (ttm170) REVERT: D 4 LYS cc_start: 0.7502 (mttt) cc_final: 0.7061 (mttt) REVERT: D 11 ASP cc_start: 0.8119 (t0) cc_final: 0.7645 (t0) REVERT: D 155 ILE cc_start: 0.9291 (mm) cc_final: 0.9056 (mm) REVERT: E 21 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8381 (mmt90) REVERT: E 30 ASP cc_start: 0.8295 (t0) cc_final: 0.8027 (t0) REVERT: F 30 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7915 (t0) REVERT: F 77 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8170 (mmm-85) REVERT: F 103 LEU cc_start: 0.8433 (mp) cc_final: 0.8057 (mp) REVERT: F 159 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7686 (mt-10) outliers start: 19 outliers final: 10 residues processed: 170 average time/residue: 0.1418 time to fit residues: 30.7235 Evaluate side-chains 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.130036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.104009 restraints weight = 11917.983| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.69 r_work: 0.2948 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8982 Z= 0.118 Angle : 0.444 6.647 12096 Z= 0.236 Chirality : 0.036 0.197 1428 Planarity : 0.003 0.026 1512 Dihedral : 3.207 15.091 1176 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.83 % Allowed : 13.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.25), residues: 1092 helix: 2.37 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.36 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 23 TYR 0.012 0.002 TYR E 87 PHE 0.008 0.001 PHE E 20 TRP 0.007 0.001 TRP B 18 HIS 0.001 0.000 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8982) covalent geometry : angle 0.44439 (12096) hydrogen bonds : bond 0.03585 ( 548) hydrogen bonds : angle 3.68531 ( 1608) *********************** 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 183 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9072 (mt) cc_final: 0.8501 (mt) REVERT: A 185 ASP cc_start: 0.6802 (m-30) cc_final: 0.6549 (m-30) REVERT: B 11 ASP cc_start: 0.8696 (t0) cc_final: 0.8369 (t0) REVERT: B 84 ASP cc_start: 0.7988 (t0) cc_final: 0.7677 (t0) REVERT: B 96 LEU cc_start: 0.8907 (mm) cc_final: 0.8628 (mm) REVERT: B 151 TYR cc_start: 0.9369 (m-80) cc_final: 0.8893 (m-80) REVERT: B 179 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8172 (tp30) REVERT: C 6 ASN cc_start: 0.8115 (t0) cc_final: 0.7805 (t0) REVERT: C 77 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7695 (ttm170) REVERT: D 4 LYS cc_start: 0.7463 (mttt) cc_final: 0.7087 (mtpt) REVERT: D 11 ASP cc_start: 0.8126 (t0) cc_final: 0.7654 (t0) REVERT: D 155 ILE cc_start: 0.9349 (mm) cc_final: 0.9105 (mm) REVERT: E 21 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8388 (mmt90) REVERT: E 30 ASP cc_start: 0.8311 (t0) cc_final: 0.8054 (t0) REVERT: F 77 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8098 (mmm-85) REVERT: F 87 TYR cc_start: 0.8798 (m-80) cc_final: 0.8536 (m-80) REVERT: F 103 LEU cc_start: 0.8425 (mp) cc_final: 0.8111 (mp) REVERT: F 159 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7727 (mt-10) outliers start: 18 outliers final: 11 residues processed: 176 average time/residue: 0.1342 time to fit residues: 30.2026 Evaluate side-chains 166 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.0980 chunk 94 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 86 optimal weight: 0.0000 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.1660 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.132272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.107677 restraints weight = 11915.726| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.77 r_work: 0.2984 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8982 Z= 0.094 Angle : 0.450 5.942 12096 Z= 0.242 Chirality : 0.035 0.192 1428 Planarity : 0.003 0.029 1512 Dihedral : 3.148 17.526 1176 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.52 % Allowed : 14.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.26), residues: 1092 helix: 2.53 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.32 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 23 TYR 0.014 0.002 TYR E 87 PHE 0.007 0.001 PHE E 20 TRP 0.008 0.001 TRP C 47 HIS 0.001 0.000 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 8982) covalent geometry : angle 0.45014 (12096) hydrogen bonds : bond 0.03250 ( 548) hydrogen bonds : angle 3.63687 ( 1608) *********************** 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 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9031 (mt) cc_final: 0.8476 (mt) REVERT: A 164 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7506 (tm-30) REVERT: B 11 ASP cc_start: 0.8597 (t0) cc_final: 0.7983 (t0) REVERT: B 31 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8898 (t) REVERT: B 78 GLN cc_start: 0.8923 (mt0) cc_final: 0.8673 (mp10) REVERT: B 84 ASP cc_start: 0.7858 (t0) cc_final: 0.7449 (t0) REVERT: B 96 LEU cc_start: 0.8893 (mm) cc_final: 0.8660 (mm) REVERT: C 6 ASN cc_start: 0.8108 (t0) cc_final: 0.7826 (t0) REVERT: D 4 LYS cc_start: 0.7424 (mttt) cc_final: 0.6975 (mtpt) REVERT: D 11 ASP cc_start: 0.8056 (t0) cc_final: 0.7595 (t0) REVERT: D 39 MET cc_start: 0.8157 (tpt) cc_final: 0.7938 (tpt) REVERT: E 21 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8393 (mmt180) REVERT: F 77 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8099 (mmm-85) REVERT: F 87 TYR cc_start: 0.8795 (m-80) cc_final: 0.8586 (m-80) REVERT: F 103 LEU cc_start: 0.8375 (mp) cc_final: 0.8069 (mp) REVERT: F 159 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7785 (mt-10) outliers start: 15 outliers final: 9 residues processed: 174 average time/residue: 0.1301 time to fit residues: 29.3430 Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.129816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105007 restraints weight = 12005.230| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.79 r_work: 0.2943 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8982 Z= 0.123 Angle : 0.481 8.988 12096 Z= 0.254 Chirality : 0.036 0.216 1428 Planarity : 0.003 0.030 1512 Dihedral : 3.178 16.673 1176 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 14.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.26), residues: 1092 helix: 2.44 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.30 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 23 TYR 0.019 0.002 TYR E 87 PHE 0.008 0.001 PHE E 20 TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8982) covalent geometry : angle 0.48146 (12096) hydrogen bonds : bond 0.03468 ( 548) hydrogen bonds : angle 3.66555 ( 1608) *********************** 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 173 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7539 (tm-30) REVERT: B 11 ASP cc_start: 0.8724 (t0) cc_final: 0.8206 (t0) REVERT: B 31 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8925 (t) REVERT: B 78 GLN cc_start: 0.9058 (mt0) cc_final: 0.8768 (mp10) REVERT: B 84 ASP cc_start: 0.7982 (t0) cc_final: 0.7629 (t0) REVERT: B 96 LEU cc_start: 0.8892 (mm) cc_final: 0.8620 (mm) REVERT: C 6 ASN cc_start: 0.8121 (t0) cc_final: 0.7875 (t0) REVERT: D 4 LYS cc_start: 0.7471 (mttt) cc_final: 0.7037 (mtpt) REVERT: D 11 ASP cc_start: 0.8089 (t0) cc_final: 0.7622 (t0) REVERT: E 21 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8393 (mmt90) REVERT: F 77 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8124 (mmm-85) REVERT: F 87 TYR cc_start: 0.8797 (m-80) cc_final: 0.8582 (m-80) REVERT: F 103 LEU cc_start: 0.8436 (mp) cc_final: 0.8123 (mp) REVERT: F 159 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7814 (mt-10) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 0.1400 time to fit residues: 29.6023 Evaluate side-chains 163 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 105 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 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 71 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.0050 chunk 100 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- 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 F 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105615 restraints weight = 11919.035| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.75 r_work: 0.2956 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2133 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= 0.113 Angle : 0.472 7.045 12096 Z= 0.249 Chirality : 0.036 0.215 1428 Planarity : 0.003 0.030 1512 Dihedral : 3.152 15.986 1176 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.52 % Allowed : 14.13 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.26), residues: 1092 helix: 2.45 (0.19), residues: 757 sheet: None (None), residues: 0 loop : 0.28 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 52 TYR 0.016 0.002 TYR E 87 PHE 0.008 0.001 PHE E 20 TRP 0.008 0.001 TRP C 47 HIS 0.003 0.000 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8982) covalent geometry : angle 0.47231 (12096) hydrogen bonds : bond 0.03372 ( 548) hydrogen bonds : angle 3.65743 ( 1608) *********************** 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 167 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ASP cc_start: 0.8624 (t0) cc_final: 0.8031 (t0) REVERT: B 31 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8914 (t) REVERT: B 78 GLN cc_start: 0.9090 (mt0) cc_final: 0.8818 (mp10) REVERT: B 84 ASP cc_start: 0.7946 (t0) cc_final: 0.7557 (t0) REVERT: B 96 LEU cc_start: 0.8901 (mm) cc_final: 0.8640 (mm) REVERT: C 6 ASN cc_start: 0.8090 (t0) cc_final: 0.7849 (t0) REVERT: C 111 MET cc_start: 0.6910 (tpt) cc_final: 0.6680 (tpt) REVERT: D 4 LYS cc_start: 0.7441 (mttt) cc_final: 0.7015 (mtpt) REVERT: D 11 ASP cc_start: 0.8049 (t0) cc_final: 0.7585 (t0) REVERT: E 21 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8382 (mmt90) REVERT: F 77 ARG cc_start: 0.8349 (mtp85) cc_final: 0.8081 (mmm-85) REVERT: F 87 TYR cc_start: 0.8784 (m-80) cc_final: 0.8578 (m-80) REVERT: F 103 LEU cc_start: 0.8420 (mp) cc_final: 0.8121 (mp) REVERT: F 159 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7818 (mt-10) outliers start: 15 outliers final: 11 residues processed: 160 average time/residue: 0.1385 time to fit residues: 28.3560 Evaluate side-chains 158 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 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 16 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.0870 chunk 22 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.129422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104521 restraints weight = 11977.241| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.83 r_work: 0.2935 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2187 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= 0.125 Angle : 0.482 7.509 12096 Z= 0.254 Chirality : 0.036 0.217 1428 Planarity : 0.003 0.030 1512 Dihedral : 3.172 15.029 1176 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.73 % Allowed : 13.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.25), residues: 1092 helix: 2.43 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.25 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 23 TYR 0.017 0.002 TYR E 87 PHE 0.009 0.001 PHE E 20 TRP 0.007 0.001 TRP B 18 HIS 0.003 0.001 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8982) covalent geometry : angle 0.48181 (12096) hydrogen bonds : bond 0.03461 ( 548) hydrogen bonds : angle 3.66930 ( 1608) ********************** 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: 17 poor density : 148 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.9026 (mt) cc_final: 0.8455 (mt) REVERT: B 11 ASP cc_start: 0.8658 (t0) cc_final: 0.8081 (t0) REVERT: B 31 VAL cc_start: 0.9224 (OUTLIER) cc_final: 0.8917 (t) REVERT: B 84 ASP cc_start: 0.7994 (t0) cc_final: 0.7638 (t0) REVERT: B 96 LEU cc_start: 0.8907 (mm) cc_final: 0.8641 (mm) REVERT: C 6 ASN cc_start: 0.8127 (t0) cc_final: 0.7874 (t0) REVERT: C 111 MET cc_start: 0.6845 (tpt) cc_final: 0.6634 (tpt) REVERT: D 4 LYS cc_start: 0.7488 (mttt) cc_final: 0.7051 (mtpt) REVERT: D 11 ASP cc_start: 0.8048 (t0) cc_final: 0.7604 (t0) REVERT: E 21 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8402 (mmt180) REVERT: F 77 ARG cc_start: 0.8393 (mtp85) cc_final: 0.8128 (mmm-85) REVERT: F 87 TYR cc_start: 0.8796 (m-80) cc_final: 0.8581 (m-80) REVERT: F 103 LEU cc_start: 0.8451 (mp) cc_final: 0.8106 (mp) REVERT: F 159 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7859 (mt-10) outliers start: 17 outliers final: 12 residues processed: 158 average time/residue: 0.1404 time to fit residues: 28.3164 Evaluate side-chains 160 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain B residue 179 GLU 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 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 22 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 F 6 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104893 restraints weight = 11877.413| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.82 r_work: 0.2941 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2205 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 : 0.477 7.379 12096 Z= 0.252 Chirality : 0.036 0.218 1428 Planarity : 0.003 0.031 1512 Dihedral : 3.183 16.591 1176 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.63 % Allowed : 13.72 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.25), residues: 1092 helix: 2.42 (0.19), residues: 755 sheet: None (None), residues: 0 loop : 0.27 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 23 TYR 0.016 0.002 TYR E 87 PHE 0.009 0.001 PHE E 20 TRP 0.007 0.001 TRP B 18 HIS 0.003 0.000 HIS B 186 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8982) covalent geometry : angle 0.47727 (12096) hydrogen bonds : bond 0.03431 ( 548) hydrogen bonds : angle 3.66384 ( 1608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2574.41 seconds wall clock time: 45 minutes 0.28 seconds (2700.28 seconds total)