Starting phenix.real_space_refine on Fri Sep 11 00:36:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sau_24957/09_2026/7sau_24957.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sau_24957/09_2026/7sau_24957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sau_24957/09_2026/7sau_24957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sau_24957/09_2026/7sau_24957.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sau_24957/09_2026/7sau_24957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sau_24957/09_2026/7sau_24957.map" } resolution = 3.0 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= 0.000 sd= 0.005 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 24 5.16 5 C 4140 2.51 5 N 1018 2.21 5 O 1135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6317 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1749 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1731 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "C" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 564 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "G" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 1.48, per 1000 atoms: 0.23 Number of scatterers: 6317 At special positions: 0 Unit cell: (70.72, 69.056, 134.784, 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 24 16.00 O 1135 8.00 N 1018 7.00 C 4140 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: 0.49 Conformation dependent library (CDL) restraints added in 321.6 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 1 sheets defined 76.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 29 through 68 removed outlier: 3.795A pdb=" N PHE A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 104 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 190 through 219 Proline residue: A 196 - end of helix removed outlier: 3.697A pdb=" N ASN A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 4.738A pdb=" N LEU B 18 " --> pdb=" O ASN B 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 19 " --> pdb=" O MET B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 66 removed outlier: 3.781A pdb=" N PHE B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 103 removed outlier: 3.567A pdb=" N ALA B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TRP B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 152 removed outlier: 4.309A pdb=" N GLU B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.537A pdb=" N PHE B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 187' Processing helix chain 'B' and resid 190 through 218 Proline residue: B 196 - end of helix removed outlier: 3.689A pdb=" N HIS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 36 Processing helix chain 'C' and resid 39 through 59 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'D' and resid 9 through 36 Processing helix chain 'D' and resid 39 through 58 removed outlier: 3.623A pdb=" N ILE D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'E' and resid 8 through 36 removed outlier: 3.614A pdb=" N LYS E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE E 14 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 58 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'F' and resid 9 through 36 removed outlier: 3.517A pdb=" N PHE F 14 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 3.532A pdb=" N MET F 43 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA F 59 " --> pdb=" O PHE F 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 36 removed outlier: 3.503A pdb=" N PHE G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.727A pdb=" N VAL A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1979 1.34 - 1.46: 920 1.46 - 1.57: 3508 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 6455 Sorted by residual: bond pdb=" CB PRO C 74 " pdb=" CG PRO C 74 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.35e+00 bond pdb=" CG1 ILE B 28 " pdb=" CD1 ILE B 28 " ideal model delta sigma weight residual 1.513 1.455 0.058 3.90e-02 6.57e+02 2.23e+00 bond pdb=" CB VAL A 82 " pdb=" CG1 VAL A 82 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB MET A 16 " pdb=" CG MET A 16 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB ARG A 139 " pdb=" CG ARG A 139 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.61e+00 ... (remaining 6450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8448 1.47 - 2.95: 200 2.95 - 4.42: 57 4.42 - 5.90: 7 5.90 - 7.37: 5 Bond angle restraints: 8717 Sorted by residual: angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" N GLU B 121 " ideal model delta sigma weight residual 116.84 122.70 -5.86 1.71e+00 3.42e-01 1.17e+01 angle pdb=" C MET B 16 " pdb=" N TYR B 17 " pdb=" CA TYR B 17 " ideal model delta sigma weight residual 120.31 115.17 5.14 1.52e+00 4.33e-01 1.14e+01 angle pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" C LEU A 128 " ideal model delta sigma weight residual 110.80 117.77 -6.97 2.13e+00 2.20e-01 1.07e+01 angle pdb=" CA ARG B 120 " pdb=" C ARG B 120 " pdb=" O ARG B 120 " ideal model delta sigma weight residual 120.51 116.47 4.04 1.43e+00 4.89e-01 7.97e+00 angle pdb=" CB ARG B 76 " pdb=" CG ARG B 76 " pdb=" CD ARG B 76 " ideal model delta sigma weight residual 111.30 117.73 -6.43 2.30e+00 1.89e-01 7.82e+00 ... (remaining 8712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 3427 17.04 - 34.07: 343 34.07 - 51.11: 48 51.11 - 68.15: 14 68.15 - 85.19: 5 Dihedral angle restraints: 3837 sinusoidal: 1542 harmonic: 2295 Sorted by residual: dihedral pdb=" CA GLU A 131 " pdb=" C GLU A 131 " pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TRP D 37 " pdb=" C TRP D 37 " pdb=" N THR D 38 " pdb=" CA THR D 38 " ideal model delta harmonic sigma weight residual 180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N THR F 38 " pdb=" CA THR F 38 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 539 0.029 - 0.058: 304 0.058 - 0.086: 89 0.086 - 0.115: 37 0.115 - 0.144: 5 Chirality restraints: 974 Sorted by residual: chirality pdb=" CA ASP A 211 " pdb=" N ASP A 211 " pdb=" C ASP A 211 " pdb=" CB ASP A 211 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA GLN B 151 " pdb=" N GLN B 151 " pdb=" C GLN B 151 " pdb=" CB GLN B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA PRO A 196 " pdb=" N PRO A 196 " pdb=" C PRO A 196 " pdb=" CB PRO A 196 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 971 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 73 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO G 74 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO G 74 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 74 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 73 " 0.055 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO C 74 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 73 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO E 74 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " -0.025 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 66 2.68 - 3.23: 6309 3.23 - 3.79: 9837 3.79 - 4.34: 13280 4.34 - 4.90: 21807 Nonbonded interactions: 51299 Sorted by model distance: nonbonded pdb=" OH TYR B 58 " pdb=" OE2 GLU B 209 " model vdw 2.122 3.040 nonbonded pdb=" OD2 ASP A 62 " pdb=" OH TYR A 80 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 58 " pdb=" OE2 GLU A 209 " model vdw 2.238 3.040 nonbonded pdb=" O ASN B 119 " pdb=" ND2 ASN B 119 " model vdw 2.314 3.120 nonbonded pdb=" OD1 ASN B 125 " pdb=" N TYR B 126 " model vdw 2.359 3.120 ... (remaining 51294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 220) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'E' and resid 6 through 76) selection = (chain 'F' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'G' and (resid 6 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.250 Find NCS groups from input model: 0.110 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6455 Z= 0.195 Angle : 0.606 7.370 8717 Z= 0.331 Chirality : 0.040 0.144 974 Planarity : 0.005 0.110 1095 Dihedral : 13.767 85.186 2353 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.15 % Allowed : 0.00 % Favored : 99.85 % 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 are not related in a simple way. whole: 0.64 (0.30), residues: 777 helix: 0.82 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.46 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 76 TYR 0.031 0.002 TYR B 17 PHE 0.012 0.001 PHE G 55 TRP 0.007 0.001 TRP A 75 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 ( 6455) covalent geometry : angle 0.60648 / 0.33 ( 8717) hydrogen bonds : bond 0.17038 / 11.18 ( 448) hydrogen bonds : angle 6.07327 / 4.21 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.234 Fit side-chains REVERT: A 30 LYS cc_start: 0.7710 (tmmt) cc_final: 0.7429 (ttmm) REVERT: A 38 LYS cc_start: 0.7866 (mmmt) cc_final: 0.7155 (mmtp) REVERT: A 59 GLN cc_start: 0.7322 (mt0) cc_final: 0.6849 (mp10) REVERT: A 84 LYS cc_start: 0.7920 (tttp) cc_final: 0.7515 (ttmp) REVERT: A 118 ASP cc_start: 0.8119 (p0) cc_final: 0.7883 (p0) REVERT: B 34 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6806 (mm-30) REVERT: B 80 TYR cc_start: 0.6974 (m-80) cc_final: 0.6663 (m-10) REVERT: B 85 GLN cc_start: 0.7652 (mt0) cc_final: 0.7330 (mt0) REVERT: B 91 ASN cc_start: 0.7662 (m-40) cc_final: 0.7425 (m-40) REVERT: B 113 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6588 (mtt90) REVERT: B 122 LYS cc_start: 0.7702 (mttp) cc_final: 0.7426 (mtmt) REVERT: B 126 TYR cc_start: 0.8093 (t80) cc_final: 0.7632 (t80) REVERT: B 143 GLU cc_start: 0.6765 (mt-10) cc_final: 0.6409 (mt-10) REVERT: B 149 MET cc_start: 0.7400 (mmp) cc_final: 0.7137 (mpm) REVERT: C 33 LYS cc_start: 0.8531 (tptm) cc_final: 0.8318 (tptp) REVERT: D 38 THR cc_start: 0.8002 (p) cc_final: 0.7799 (m) REVERT: D 43 MET cc_start: 0.8181 (mtp) cc_final: 0.7950 (mtp) REVERT: E 33 LYS cc_start: 0.8641 (tptt) cc_final: 0.8297 (tppt) REVERT: E 41 ASP cc_start: 0.7976 (m-30) cc_final: 0.7751 (m-30) REVERT: F 13 ASN cc_start: 0.7162 (t0) cc_final: 0.6864 (m110) REVERT: F 61 GLU cc_start: 0.7110 (pt0) cc_final: 0.6890 (pt0) REVERT: G 7 ASN cc_start: 0.6154 (m110) cc_final: 0.5763 (m-40) REVERT: G 62 LYS cc_start: 0.5998 (mppt) cc_final: 0.5785 (mttp) REVERT: G 67 TYR cc_start: 0.7524 (m-80) cc_final: 0.7272 (m-80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.6085 time to fit residues: 99.1377 Evaluate side-chains 115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097921 restraints weight = 7421.026| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.78 r_work: 0.2860 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6455 Z= 0.152 Angle : 0.555 7.582 8717 Z= 0.293 Chirality : 0.039 0.141 974 Planarity : 0.005 0.077 1095 Dihedral : 4.234 20.071 833 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.97 % Allowed : 9.85 % Favored : 88.18 % 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 are not related in a simple way. whole: 1.46 (0.30), residues: 777 helix: 1.48 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.015 0.001 TYR A 80 PHE 0.015 0.001 PHE G 55 TRP 0.006 0.001 TRP E 69 HIS 0.002 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 6455) covalent geometry : angle 0.55491 / 0.29 ( 8717) hydrogen bonds : bond 0.05025 / 3.35 ( 448) hydrogen bonds : angle 4.06822 / 2.89 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.248 Fit side-chains REVERT: A 30 LYS cc_start: 0.7449 (tmmt) cc_final: 0.6976 (ttmm) REVERT: A 34 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7625 (mm-30) REVERT: A 38 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7229 (mmtp) REVERT: A 59 GLN cc_start: 0.7651 (mt0) cc_final: 0.6983 (mp10) REVERT: A 84 LYS cc_start: 0.8049 (tttp) cc_final: 0.7715 (ttmp) REVERT: A 214 SER cc_start: 0.8150 (m) cc_final: 0.7732 (p) REVERT: B 34 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7240 (mm-30) REVERT: B 80 TYR cc_start: 0.7058 (m-80) cc_final: 0.6706 (m-10) REVERT: B 91 ASN cc_start: 0.7702 (m-40) cc_final: 0.7481 (m-40) REVERT: B 113 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6449 (mtt90) REVERT: B 126 TYR cc_start: 0.8015 (t80) cc_final: 0.7436 (t80) REVERT: B 131 GLU cc_start: 0.6990 (mp0) cc_final: 0.6734 (mp0) REVERT: B 143 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6657 (mt-10) REVERT: B 149 MET cc_start: 0.7455 (mmp) cc_final: 0.7051 (mpm) REVERT: B 163 LEU cc_start: 0.7083 (mt) cc_final: 0.6785 (mp) REVERT: B 182 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7962 (pm20) REVERT: C 33 LYS cc_start: 0.8641 (tptm) cc_final: 0.8387 (tptp) REVERT: E 10 LYS cc_start: 0.7506 (mtmt) cc_final: 0.7047 (mttm) REVERT: E 25 ILE cc_start: 0.8691 (mm) cc_final: 0.8417 (mt) REVERT: E 33 LYS cc_start: 0.8750 (tptt) cc_final: 0.8473 (tppt) REVERT: F 61 GLU cc_start: 0.7491 (pt0) cc_final: 0.7190 (pt0) REVERT: G 7 ASN cc_start: 0.6174 (m110) cc_final: 0.5724 (m-40) REVERT: G 62 LYS cc_start: 0.6500 (mppt) cc_final: 0.6099 (mttp) outliers start: 13 outliers final: 5 residues processed: 130 average time/residue: 0.6177 time to fit residues: 83.8265 Evaluate side-chains 114 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 70 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 66 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.2208 > 50:) chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 85 GLN D 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.137142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.096774 restraints weight = 7446.617| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.79 r_work: 0.2770 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 6455 Z= 0.209 Angle : 0.610 8.417 8717 Z= 0.318 Chirality : 0.042 0.187 974 Planarity : 0.005 0.066 1095 Dihedral : 4.450 21.817 833 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.24 % Allowed : 12.88 % Favored : 82.88 % 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 are not related in a simple way. whole: 1.56 (0.30), residues: 777 helix: 1.63 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.50 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 218 TYR 0.015 0.002 TYR B 17 PHE 0.026 0.002 PHE G 55 TRP 0.007 0.001 TRP C 69 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.21 ( 6455) covalent geometry : angle 0.60954 / 0.32 ( 8717) hydrogen bonds : bond 0.05096 / 3.39 ( 448) hydrogen bonds : angle 4.07814 / 2.92 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.256 Fit side-chains REVERT: A 30 LYS cc_start: 0.7697 (tmmt) cc_final: 0.7250 (ttmm) REVERT: A 38 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7274 (mmtp) REVERT: A 59 GLN cc_start: 0.7658 (mt0) cc_final: 0.6972 (mp10) REVERT: A 84 LYS cc_start: 0.8119 (tttp) cc_final: 0.7726 (ttmp) REVERT: A 88 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7856 (mm-30) REVERT: A 214 SER cc_start: 0.7998 (m) cc_final: 0.7647 (p) REVERT: B 34 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7343 (mm-30) REVERT: B 80 TYR cc_start: 0.7001 (m-80) cc_final: 0.6630 (m-10) REVERT: B 91 ASN cc_start: 0.7667 (m-40) cc_final: 0.7452 (m-40) REVERT: B 113 ARG cc_start: 0.7077 (mtt180) cc_final: 0.6507 (mtt90) REVERT: B 115 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6459 (mttt) REVERT: B 126 TYR cc_start: 0.8040 (t80) cc_final: 0.7597 (t80) REVERT: B 136 ARG cc_start: 0.7552 (mtp85) cc_final: 0.6956 (mtm110) REVERT: B 162 MET cc_start: 0.7114 (tmm) cc_final: 0.6893 (tmm) REVERT: B 163 LEU cc_start: 0.6941 (mt) cc_final: 0.6683 (mp) REVERT: B 182 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: C 62 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6624 (mtmt) REVERT: E 25 ILE cc_start: 0.8798 (mm) cc_final: 0.8564 (mt) REVERT: E 33 LYS cc_start: 0.8762 (tptt) cc_final: 0.8501 (tppt) REVERT: G 41 ASP cc_start: 0.7749 (m-30) cc_final: 0.7381 (m-30) REVERT: G 62 LYS cc_start: 0.6555 (mppt) cc_final: 0.6093 (mttp) REVERT: G 67 TYR cc_start: 0.7618 (m-80) cc_final: 0.7212 (m-80) outliers start: 28 outliers final: 10 residues processed: 125 average time/residue: 0.5977 time to fit residues: 78.0679 Evaluate side-chains 117 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 HIS B 85 GLN D 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100475 restraints weight = 7380.150| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.83 r_work: 0.2873 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6455 Z= 0.119 Angle : 0.515 7.965 8717 Z= 0.270 Chirality : 0.038 0.129 974 Planarity : 0.004 0.059 1095 Dihedral : 4.138 19.730 833 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.18 % Allowed : 14.70 % Favored : 82.12 % 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 are not related in a simple way. whole: 1.97 (0.31), residues: 777 helix: 1.98 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -0.52 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 218 TYR 0.015 0.001 TYR A 80 PHE 0.012 0.001 PHE E 55 TRP 0.005 0.000 TRP A 75 HIS 0.002 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6455) covalent geometry : angle 0.51499 / 0.27 ( 8717) hydrogen bonds : bond 0.04181 / 2.76 ( 448) hydrogen bonds : angle 3.83905 / 2.75 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.221 Fit side-chains REVERT: A 30 LYS cc_start: 0.7598 (tmmt) cc_final: 0.7042 (ttmm) REVERT: A 34 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7598 (mm-30) REVERT: A 38 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7054 (mmtp) REVERT: A 42 ASP cc_start: 0.7987 (m-30) cc_final: 0.7473 (m-30) REVERT: A 59 GLN cc_start: 0.7725 (mt0) cc_final: 0.7050 (mp10) REVERT: A 84 LYS cc_start: 0.8127 (tttp) cc_final: 0.7777 (ttmp) REVERT: A 211 ASP cc_start: 0.7700 (p0) cc_final: 0.7360 (p0) REVERT: A 214 SER cc_start: 0.8032 (m) cc_final: 0.7649 (p) REVERT: B 34 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7301 (mm-30) REVERT: B 80 TYR cc_start: 0.7012 (m-80) cc_final: 0.6734 (m-10) REVERT: B 91 ASN cc_start: 0.7782 (m-40) cc_final: 0.7581 (m-40) REVERT: B 113 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6612 (mtt90) REVERT: B 126 TYR cc_start: 0.8051 (t80) cc_final: 0.7590 (t80) REVERT: B 182 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: C 62 LYS cc_start: 0.7076 (mtpt) cc_final: 0.6625 (mtmt) REVERT: E 25 ILE cc_start: 0.8787 (mm) cc_final: 0.8519 (mt) REVERT: E 33 LYS cc_start: 0.8770 (tptt) cc_final: 0.8487 (tppt) REVERT: G 27 ILE cc_start: 0.8968 (mm) cc_final: 0.8574 (mt) REVERT: G 41 ASP cc_start: 0.7752 (m-30) cc_final: 0.7440 (m-30) REVERT: G 62 LYS cc_start: 0.6472 (mppt) cc_final: 0.6008 (mttp) REVERT: G 67 TYR cc_start: 0.7639 (m-80) cc_final: 0.7385 (m-80) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.5499 time to fit residues: 74.9297 Evaluate side-chains 125 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.140712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100264 restraints weight = 7457.799| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.82 r_work: 0.2912 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6455 Z= 0.117 Angle : 0.508 7.962 8717 Z= 0.265 Chirality : 0.037 0.135 974 Planarity : 0.004 0.052 1095 Dihedral : 4.011 19.259 833 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.18 % Allowed : 16.36 % Favored : 80.45 % 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 are not related in a simple way. whole: 2.18 (0.31), residues: 777 helix: 2.15 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -0.51 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 218 TYR 0.014 0.001 TYR A 80 PHE 0.011 0.001 PHE G 55 TRP 0.004 0.000 TRP C 69 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6455) covalent geometry : angle 0.50766 / 0.27 ( 8717) hydrogen bonds : bond 0.03988 / 2.63 ( 448) hydrogen bonds : angle 3.76674 / 2.72 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.170 Fit side-chains REVERT: A 30 LYS cc_start: 0.7687 (tmmt) cc_final: 0.7158 (ttmm) REVERT: A 34 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 38 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7399 (mmtp) REVERT: A 59 GLN cc_start: 0.7717 (mt0) cc_final: 0.7051 (mp10) REVERT: A 84 LYS cc_start: 0.8109 (tttp) cc_final: 0.7702 (ttmp) REVERT: A 87 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8218 (m-30) REVERT: A 88 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7859 (mm-30) REVERT: A 214 SER cc_start: 0.8091 (m) cc_final: 0.7715 (p) REVERT: B 34 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7367 (mm-30) REVERT: B 80 TYR cc_start: 0.7066 (m-80) cc_final: 0.6817 (m-10) REVERT: B 91 ASN cc_start: 0.7796 (m-40) cc_final: 0.7589 (m-40) REVERT: B 113 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6606 (mtt90) REVERT: B 122 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6922 (mtmt) REVERT: B 126 TYR cc_start: 0.8093 (t80) cc_final: 0.7664 (t80) REVERT: B 182 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: C 62 LYS cc_start: 0.7070 (mtpt) cc_final: 0.6644 (mtmt) REVERT: E 25 ILE cc_start: 0.8823 (mm) cc_final: 0.8567 (mt) REVERT: E 33 LYS cc_start: 0.8803 (tptt) cc_final: 0.8545 (tppt) REVERT: F 15 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7056 (mt) REVERT: G 27 ILE cc_start: 0.8951 (mm) cc_final: 0.8549 (mt) REVERT: G 41 ASP cc_start: 0.7693 (m-30) cc_final: 0.7382 (m-30) REVERT: G 62 LYS cc_start: 0.6464 (mppt) cc_final: 0.6024 (mttp) REVERT: G 67 TYR cc_start: 0.7692 (m-80) cc_final: 0.7445 (m-80) outliers start: 21 outliers final: 9 residues processed: 128 average time/residue: 0.5794 time to fit residues: 77.6471 Evaluate side-chains 127 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 122 LYS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 85 GLN B 148 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.100605 restraints weight = 7420.507| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.83 r_work: 0.2924 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6455 Z= 0.112 Angle : 0.497 8.354 8717 Z= 0.260 Chirality : 0.037 0.135 974 Planarity : 0.004 0.048 1095 Dihedral : 3.941 19.148 833 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.18 % Allowed : 17.58 % Favored : 79.24 % 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 are not related in a simple way. whole: 2.28 (0.31), residues: 777 helix: 2.24 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.56 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 218 TYR 0.014 0.001 TYR A 80 PHE 0.011 0.001 PHE G 55 TRP 0.004 0.000 TRP C 69 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 6455) covalent geometry : angle 0.49700 / 0.26 ( 8717) hydrogen bonds : bond 0.03897 / 2.56 ( 448) hydrogen bonds : angle 3.70697 / 2.68 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.7676 (tmmt) cc_final: 0.7179 (ttmm) REVERT: A 34 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 38 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7413 (mmtp) REVERT: A 84 LYS cc_start: 0.8080 (tttp) cc_final: 0.7659 (ttmp) REVERT: A 87 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: A 88 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7871 (mm-30) REVERT: A 162 MET cc_start: 0.8108 (pp-130) cc_final: 0.7760 (ppp) REVERT: A 214 SER cc_start: 0.8077 (m) cc_final: 0.7725 (p) REVERT: B 34 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7348 (mm-30) REVERT: B 80 TYR cc_start: 0.7130 (m-80) cc_final: 0.6866 (m-10) REVERT: B 113 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6590 (mtt90) REVERT: B 126 TYR cc_start: 0.8050 (t80) cc_final: 0.7642 (t80) REVERT: B 136 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7202 (mtp85) REVERT: B 139 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6844 (ttm-80) REVERT: E 25 ILE cc_start: 0.8814 (mm) cc_final: 0.8558 (mt) REVERT: E 33 LYS cc_start: 0.8804 (tptt) cc_final: 0.8549 (tppt) REVERT: F 15 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6962 (mt) REVERT: G 27 ILE cc_start: 0.8971 (mm) cc_final: 0.8640 (mt) REVERT: G 41 ASP cc_start: 0.7689 (m-30) cc_final: 0.7410 (m-30) REVERT: G 62 LYS cc_start: 0.6405 (mppt) cc_final: 0.5940 (mttp) REVERT: G 67 TYR cc_start: 0.7698 (m-80) cc_final: 0.7381 (m-80) outliers start: 21 outliers final: 7 residues processed: 122 average time/residue: 0.5706 time to fit residues: 72.8959 Evaluate side-chains 121 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 152 TYR Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 32 optimal weight: 0.0170 chunk 11 optimal weight: 0.0010 chunk 68 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 0.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 85 GLN G 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103758 restraints weight = 7369.107| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.78 r_work: 0.2987 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6455 Z= 0.100 Angle : 0.477 8.801 8717 Z= 0.250 Chirality : 0.036 0.129 974 Planarity : 0.004 0.054 1095 Dihedral : 3.813 19.246 833 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.88 % Allowed : 17.73 % Favored : 79.39 % 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 are not related in a simple way. whole: 2.42 (0.31), residues: 777 helix: 2.34 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.55 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 218 TYR 0.013 0.001 TYR A 80 PHE 0.006 0.001 PHE E 55 TRP 0.004 0.000 TRP B 75 HIS 0.002 0.000 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 6455) covalent geometry : angle 0.47675 / 0.25 ( 8717) hydrogen bonds : bond 0.03571 / 2.34 ( 448) hydrogen bonds : angle 3.63372 / 2.64 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.235 Fit side-chains REVERT: A 30 LYS cc_start: 0.7399 (tmmt) cc_final: 0.6985 (ttmm) REVERT: A 34 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 38 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7310 (mmtp) REVERT: A 42 ASP cc_start: 0.7879 (m-30) cc_final: 0.7558 (m-30) REVERT: A 63 LEU cc_start: 0.7664 (mp) cc_final: 0.7433 (mt) REVERT: A 84 LYS cc_start: 0.7950 (tttp) cc_final: 0.7530 (ttmp) REVERT: A 87 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: A 88 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7767 (mm-30) REVERT: A 162 MET cc_start: 0.8074 (pp-130) cc_final: 0.7804 (ppp) REVERT: A 214 SER cc_start: 0.7934 (m) cc_final: 0.7553 (p) REVERT: A 217 GLN cc_start: 0.7997 (tt0) cc_final: 0.7233 (pt0) REVERT: B 34 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7179 (mm-30) REVERT: B 80 TYR cc_start: 0.7040 (m-80) cc_final: 0.6751 (m-80) REVERT: B 113 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6592 (mtt90) REVERT: B 126 TYR cc_start: 0.7918 (t80) cc_final: 0.7480 (t80) REVERT: B 136 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7155 (mtp85) REVERT: B 182 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: E 25 ILE cc_start: 0.8782 (mm) cc_final: 0.8530 (mt) REVERT: E 33 LYS cc_start: 0.8726 (tptt) cc_final: 0.8460 (tppt) REVERT: G 27 ILE cc_start: 0.8960 (mm) cc_final: 0.8585 (mt) REVERT: G 41 ASP cc_start: 0.7636 (m-30) cc_final: 0.7330 (m-30) REVERT: G 62 LYS cc_start: 0.6359 (mppt) cc_final: 0.5965 (mttp) outliers start: 19 outliers final: 5 residues processed: 123 average time/residue: 0.5572 time to fit residues: 71.8551 Evaluate side-chains 115 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain D residue 58 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 76 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 0.0570 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN G 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.105055 restraints weight = 7298.173| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.76 r_work: 0.2969 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6455 Z= 0.104 Angle : 0.492 8.122 8717 Z= 0.254 Chirality : 0.036 0.130 974 Planarity : 0.004 0.056 1095 Dihedral : 3.757 18.692 833 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.42 % Allowed : 18.33 % Favored : 79.24 % 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 are not related in a simple way. whole: 2.49 (0.31), residues: 777 helix: 2.39 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.56 (0.47), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 218 TYR 0.013 0.001 TYR A 80 PHE 0.006 0.001 PHE E 55 TRP 0.005 0.000 TRP A 75 HIS 0.002 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6455) covalent geometry : angle 0.49152 / 0.25 ( 8717) hydrogen bonds : bond 0.03571 / 2.34 ( 448) hydrogen bonds : angle 3.61191 / 2.63 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.299 Fit side-chains REVERT: A 30 LYS cc_start: 0.7397 (tmmt) cc_final: 0.6971 (ttmm) REVERT: A 34 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7387 (mm-30) REVERT: A 38 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7242 (mmtp) REVERT: A 42 ASP cc_start: 0.7850 (m-30) cc_final: 0.7494 (m-30) REVERT: A 63 LEU cc_start: 0.7650 (mp) cc_final: 0.7422 (mt) REVERT: A 84 LYS cc_start: 0.7895 (tttp) cc_final: 0.7624 (ttmp) REVERT: A 87 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8186 (m-30) REVERT: A 162 MET cc_start: 0.8064 (pp-130) cc_final: 0.7802 (ppp) REVERT: A 214 SER cc_start: 0.7947 (m) cc_final: 0.7558 (p) REVERT: A 217 GLN cc_start: 0.8014 (tt0) cc_final: 0.7229 (pt0) REVERT: B 34 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7190 (mm-30) REVERT: B 113 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6564 (mtt90) REVERT: B 126 TYR cc_start: 0.7911 (t80) cc_final: 0.7498 (t80) REVERT: B 136 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7179 (mtp85) REVERT: E 10 LYS cc_start: 0.7268 (mtpp) cc_final: 0.6694 (mtmm) REVERT: E 25 ILE cc_start: 0.8811 (mm) cc_final: 0.8535 (mt) REVERT: E 33 LYS cc_start: 0.8716 (tptt) cc_final: 0.8458 (tppt) REVERT: G 27 ILE cc_start: 0.8955 (mm) cc_final: 0.8627 (mt) REVERT: G 41 ASP cc_start: 0.7682 (m-30) cc_final: 0.7389 (m-30) REVERT: G 62 LYS cc_start: 0.6329 (mppt) cc_final: 0.5928 (mttp) outliers start: 16 outliers final: 6 residues processed: 122 average time/residue: 0.5437 time to fit residues: 69.6248 Evaluate side-chains 116 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 85 GLN B 148 ASN G 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103061 restraints weight = 7426.026| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.80 r_work: 0.2898 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6455 Z= 0.113 Angle : 0.506 9.212 8717 Z= 0.261 Chirality : 0.037 0.131 974 Planarity : 0.004 0.051 1095 Dihedral : 3.771 18.307 833 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.27 % Allowed : 18.79 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.31), residues: 777 helix: 2.37 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -0.49 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 218 TYR 0.013 0.001 TYR A 80 PHE 0.010 0.001 PHE G 55 TRP 0.004 0.000 TRP B 75 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 6455) covalent geometry : angle 0.50584 / 0.26 ( 8717) hydrogen bonds : bond 0.03726 / 2.44 ( 448) hydrogen bonds : angle 3.64447 / 2.65 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.247 Fit side-chains REVERT: A 30 LYS cc_start: 0.7369 (tmmt) cc_final: 0.6835 (ttmm) REVERT: A 34 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 38 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7214 (mmtp) REVERT: A 42 ASP cc_start: 0.7806 (m-30) cc_final: 0.7447 (m-30) REVERT: A 84 LYS cc_start: 0.7780 (tttp) cc_final: 0.7505 (ttmp) REVERT: A 87 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: A 104 THR cc_start: 0.8294 (m) cc_final: 0.7949 (t) REVERT: A 162 MET cc_start: 0.8058 (pp-130) cc_final: 0.7823 (ppp) REVERT: A 214 SER cc_start: 0.7969 (m) cc_final: 0.7528 (p) REVERT: A 217 GLN cc_start: 0.8004 (tt0) cc_final: 0.7194 (pt0) REVERT: B 34 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7213 (mm-30) REVERT: B 41 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: B 103 ILE cc_start: 0.7883 (pt) cc_final: 0.7594 (pp) REVERT: B 113 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6538 (mtt90) REVERT: B 126 TYR cc_start: 0.7903 (t80) cc_final: 0.7570 (t80) REVERT: B 136 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7147 (mtp85) REVERT: E 10 LYS cc_start: 0.7311 (mtpp) cc_final: 0.6712 (mtmm) REVERT: E 25 ILE cc_start: 0.8756 (mm) cc_final: 0.8474 (mt) REVERT: E 33 LYS cc_start: 0.8705 (tptt) cc_final: 0.8394 (tppt) REVERT: F 15 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6598 (mt) REVERT: G 27 ILE cc_start: 0.8921 (mm) cc_final: 0.8588 (mt) REVERT: G 41 ASP cc_start: 0.7721 (m-30) cc_final: 0.7408 (m-30) REVERT: G 62 LYS cc_start: 0.6342 (mppt) cc_final: 0.5930 (mttp) outliers start: 15 outliers final: 6 residues processed: 116 average time/residue: 0.5418 time to fit residues: 66.0817 Evaluate side-chains 116 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 85 GLN G 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101979 restraints weight = 7314.559| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.76 r_work: 0.2938 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6455 Z= 0.129 Angle : 0.526 7.934 8717 Z= 0.271 Chirality : 0.038 0.137 974 Planarity : 0.004 0.048 1095 Dihedral : 3.872 18.928 833 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 19.24 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.31), residues: 777 helix: 2.32 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.53 (0.48), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 218 TYR 0.013 0.001 TYR A 80 PHE 0.015 0.001 PHE G 55 TRP 0.005 0.001 TRP B 75 HIS 0.003 0.001 HIS E 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 6455) covalent geometry : angle 0.52598 / 0.27 ( 8717) hydrogen bonds : bond 0.03992 / 2.62 ( 448) hydrogen bonds : angle 3.70425 / 2.69 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.201 Fit side-chains REVERT: A 30 LYS cc_start: 0.7524 (tmmt) cc_final: 0.7000 (ttmm) REVERT: A 34 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 38 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7336 (mmtp) REVERT: A 59 GLN cc_start: 0.7617 (mt0) cc_final: 0.6833 (mp10) REVERT: A 84 LYS cc_start: 0.7909 (tttp) cc_final: 0.7632 (ttmp) REVERT: A 87 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: A 104 THR cc_start: 0.8351 (m) cc_final: 0.8016 (t) REVERT: A 214 SER cc_start: 0.8102 (m) cc_final: 0.7748 (p) REVERT: A 218 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.6789 (ptm160) REVERT: B 34 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7327 (mm-30) REVERT: B 41 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: B 113 ARG cc_start: 0.7093 (mtt180) cc_final: 0.6547 (mtt90) REVERT: B 126 TYR cc_start: 0.7989 (t80) cc_final: 0.7669 (t80) REVERT: B 136 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7212 (mtp85) REVERT: D 62 LYS cc_start: 0.7138 (mppt) cc_final: 0.6375 (mmtp) REVERT: E 10 LYS cc_start: 0.7266 (mtpp) cc_final: 0.6691 (mtmm) REVERT: E 25 ILE cc_start: 0.8861 (mm) cc_final: 0.8590 (mt) REVERT: E 33 LYS cc_start: 0.8771 (tptt) cc_final: 0.8479 (tppt) REVERT: F 15 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6736 (mt) REVERT: G 27 ILE cc_start: 0.8965 (mm) cc_final: 0.8659 (mt) REVERT: G 41 ASP cc_start: 0.7652 (m-30) cc_final: 0.7327 (m-30) REVERT: G 62 LYS cc_start: 0.6333 (mppt) cc_final: 0.5919 (mttp) outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 0.5449 time to fit residues: 65.6824 Evaluate side-chains 114 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 41 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain F residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 ASN B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.140512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098961 restraints weight = 7364.845| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.82 r_work: 0.2910 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6455 Z= 0.125 Angle : 0.530 9.436 8717 Z= 0.271 Chirality : 0.038 0.129 974 Planarity : 0.004 0.046 1095 Dihedral : 3.899 18.840 833 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.97 % Allowed : 19.70 % Favored : 78.33 % 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 are not related in a simple way. whole: 2.36 (0.31), residues: 777 helix: 2.26 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.48 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 218 TYR 0.013 0.001 TYR A 80 PHE 0.014 0.001 PHE G 55 TRP 0.005 0.001 TRP B 75 HIS 0.003 0.001 HIS G 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6455) covalent geometry : angle 0.52959 / 0.27 ( 8717) hydrogen bonds : bond 0.03937 / 2.58 ( 448) hydrogen bonds : angle 3.71624 / 2.70 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2392.14 seconds wall clock time: 41 minutes 33.77 seconds (2493.77 seconds total)