Starting phenix.real_space_refine on Thu Jul 2 00:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkm_63182/07_2026/9lkm_63182.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkm_63182/07_2026/9lkm_63182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lkm_63182/07_2026/9lkm_63182.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkm_63182/07_2026/9lkm_63182.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lkm_63182/07_2026/9lkm_63182.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkm_63182/07_2026/9lkm_63182.map" } resolution = 3.34 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= 0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 25 5.16 5 C 2819 2.51 5 N 739 2.21 5 O 859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4445 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "B" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1017 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain breaks: 1 Chain: "D" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1333 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 206 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 0.80, per 1000 atoms: 0.18 Number of scatterers: 4445 At special positions: 0 Unit cell: (96.48, 62.176, 77.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 25 16.00 O 859 8.00 N 739 7.00 C 2819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 30 " - pdb=" SG CYS D 55 " distance=2.08 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 112 " distance=2.01 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 198 " distance=2.05 Simple disulfide: pdb=" SG CYS D 178 " - pdb=" SG CYS D 189 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 129.4 milliseconds 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 11 sheets defined 7.7% alpha, 46.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 102 through 105 Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 164 through 181 removed outlier: 3.534A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 155 removed outlier: 6.829A pdb=" N TYR A 133 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 154 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA A 131 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 173 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 155 removed outlier: 6.829A pdb=" N TYR A 133 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 154 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA A 131 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 173 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 181 " --> pdb=" O HIS A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 145 removed outlier: 3.747A pdb=" N GLU A 144 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS A 196 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 155 removed outlier: 4.981A pdb=" N VAL B 151 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY B 135 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 131 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR B 173 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.701A pdb=" N LYS B 165 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 196 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 199 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.701A pdb=" N LYS B 165 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 153 removed outlier: 6.806A pdb=" N TYR C 133 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 173 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP C 214 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.634A pdb=" N ILE C 232 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 165 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.634A pdb=" N ILE C 232 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 231 " --> pdb=" O CYS H 195 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP H 191 " --> pdb=" O ASP C 235 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS H 196 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.079A pdb=" N THR D 32 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLU D 60 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 34 " --> pdb=" O GLU D 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.515A pdb=" N VAL D 119 " --> pdb=" O PHE D 73 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 489 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: 0.73 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1147 1.33 - 1.45: 1039 1.45 - 1.58: 2329 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 4549 Sorted by residual: bond pdb=" C LEU D 85 " pdb=" O LEU D 85 " ideal model delta sigma weight residual 1.235 1.299 -0.064 1.18e-02 7.18e+03 2.97e+01 bond pdb=" CA SER D 188 " pdb=" CB SER D 188 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.35e-02 5.49e+03 1.45e+01 bond pdb=" N GLN D 89 " pdb=" CA GLN D 89 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.21e-02 6.83e+03 1.35e+01 bond pdb=" N LEU D 85 " pdb=" CA LEU D 85 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.20e-02 6.94e+03 1.15e+01 bond pdb=" C GLN D 89 " pdb=" O GLN D 89 " ideal model delta sigma weight residual 1.233 1.275 -0.042 1.28e-02 6.10e+03 1.08e+01 ... (remaining 4544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 5213 1.62 - 3.24: 781 3.24 - 4.86: 124 4.86 - 6.48: 22 6.48 - 8.09: 8 Bond angle restraints: 6148 Sorted by residual: angle pdb=" N VAL D 170 " pdb=" CA VAL D 170 " pdb=" C VAL D 170 " ideal model delta sigma weight residual 110.53 104.63 5.90 9.40e-01 1.13e+00 3.94e+01 angle pdb=" N ASN B 169 " pdb=" CA ASN B 169 " pdb=" C ASN B 169 " ideal model delta sigma weight residual 114.31 106.62 7.69 1.29e+00 6.01e-01 3.56e+01 angle pdb=" CA GLN D 89 " pdb=" C GLN D 89 " pdb=" O GLN D 89 " ideal model delta sigma weight residual 121.72 115.46 6.26 1.18e+00 7.18e-01 2.81e+01 angle pdb=" N LYS D 104 " pdb=" CA LYS D 104 " pdb=" C LYS D 104 " ideal model delta sigma weight residual 111.75 105.40 6.35 1.28e+00 6.10e-01 2.46e+01 angle pdb=" C CYS D 30 " pdb=" CA CYS D 30 " pdb=" CB CYS D 30 " ideal model delta sigma weight residual 110.19 102.10 8.09 1.64e+00 3.72e-01 2.44e+01 ... (remaining 6143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 2372 15.95 - 31.89: 200 31.89 - 47.84: 47 47.84 - 63.78: 15 63.78 - 79.73: 1 Dihedral angle restraints: 2635 sinusoidal: 1010 harmonic: 1625 Sorted by residual: dihedral pdb=" CB CYS D 172 " pdb=" SG CYS D 172 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual -86.00 -139.81 53.81 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" C CYS D 30 " pdb=" N CYS D 30 " pdb=" CA CYS D 30 " pdb=" CB CYS D 30 " ideal model delta harmonic sigma weight residual -122.60 -108.00 -14.60 0 2.50e+00 1.60e-01 3.41e+01 dihedral pdb=" N CYS D 30 " pdb=" C CYS D 30 " pdb=" CA CYS D 30 " pdb=" CB CYS D 30 " ideal model delta harmonic sigma weight residual 122.80 108.60 14.20 0 2.50e+00 1.60e-01 3.23e+01 ... (remaining 2632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 551 0.098 - 0.197: 78 0.197 - 0.295: 12 0.295 - 0.394: 0 0.394 - 0.492: 1 Chirality restraints: 642 Sorted by residual: chirality pdb=" CA CYS D 30 " pdb=" N CYS D 30 " pdb=" C CYS D 30 " pdb=" CB CYS D 30 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA GLN D 89 " pdb=" N GLN D 89 " pdb=" C GLN D 89 " pdb=" CB GLN D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LEU D 121 " pdb=" N LEU D 121 " pdb=" C LEU D 121 " pdb=" CB LEU D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 639 not shown) Planarity restraints: 806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 131 " -0.428 9.50e-02 1.11e+02 1.92e-01 2.25e+01 pdb=" NE ARG D 131 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 131 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 131 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 131 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 91 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C ASP D 91 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP D 91 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS D 92 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 127 " -0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO B 128 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " -0.047 5.00e-02 4.00e+02 ... (remaining 803 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1493 2.83 - 3.35: 3934 3.35 - 3.86: 7367 3.86 - 4.38: 8638 4.38 - 4.90: 14934 Nonbonded interactions: 36366 Sorted by model distance: nonbonded pdb=" NE2 HIS B 223 " pdb=" OD2 ASP B 258 " model vdw 2.312 3.120 nonbonded pdb=" OE1 GLN C 211 " pdb=" OH TYR C 213 " model vdw 2.319 3.040 nonbonded pdb=" O ILE A 170 " pdb=" OH TYR A 174 " model vdw 2.333 3.040 nonbonded pdb=" O ILE C 170 " pdb=" OH TYR C 174 " model vdw 2.342 3.040 nonbonded pdb=" N ASN A 243 " pdb=" OD1 ASN A 243 " model vdw 2.357 3.120 ... (remaining 36361 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 127 through 258) selection = chain 'B' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.009 0.064 4554 Z= 0.631 Angle : 1.198 10.272 6158 Z= 0.843 Chirality : 0.073 0.492 642 Planarity : 0.011 0.192 806 Dihedral : 13.088 79.727 1590 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 31.72 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.68 % Favored : 90.60 % Rotamer: Outliers : 2.95 % Allowed : 4.64 % Favored : 92.41 % Cbeta Deviations : 0.19 % 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: -3.09 (0.30), residues: 553 helix: -3.73 (0.53), residues: 25 sheet: -0.84 (0.33), residues: 218 loop : -2.94 (0.27), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 131 TYR 0.016 0.001 TYR D 70 PHE 0.022 0.002 PHE D 73 TRP 0.010 0.002 TRP D 57 HIS 0.005 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00869 / 0.63 ( 4549) covalent geometry : angle 1.18928 / 0.84 ( 6148) SS BOND : bond 0.02652 / 1.36 ( 5) SS BOND : angle 3.83263 / 2.07 ( 10) hydrogen bonds : bond 0.19773 / 14.12 ( 163) hydrogen bonds : angle 8.70107 / 6.47 ( 489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7356 (m-80) cc_final: 0.6742 (m-80) REVERT: D 45 SER cc_start: 0.8007 (t) cc_final: 0.7759 (p) REVERT: D 62 PRO cc_start: 0.8000 (Cg_exo) cc_final: 0.7563 (Cg_endo) REVERT: D 63 ASP cc_start: 0.7761 (t0) cc_final: 0.7479 (t70) REVERT: D 67 TYR cc_start: 0.8069 (m-80) cc_final: 0.7780 (m-10) REVERT: D 73 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.5727 (m-80) REVERT: D 125 LYS cc_start: 0.8045 (mttm) cc_final: 0.7575 (mttm) outliers start: 14 outliers final: 6 residues processed: 147 average time/residue: 0.0579 time to fit residues: 10.6022 Evaluate side-chains 137 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 73 PHE Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN B 138 ASN C 158 ASN D 105 ASN D 110 GLN D 113 ASN D 129 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.153477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132060 restraints weight = 6554.536| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.78 r_work: 0.3575 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4554 Z= 0.223 Angle : 0.660 6.463 6158 Z= 0.367 Chirality : 0.045 0.144 642 Planarity : 0.004 0.033 806 Dihedral : 6.587 55.463 624 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.01 % Allowed : 13.29 % Favored : 82.70 % 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: -2.16 (0.32), residues: 553 helix: -2.46 (0.72), residues: 34 sheet: -0.51 (0.31), residues: 249 loop : -2.22 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 131 TYR 0.016 0.002 TYR D 88 PHE 0.024 0.003 PHE A 250 TRP 0.011 0.002 TRP B 191 HIS 0.008 0.002 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 ( 4549) covalent geometry : angle 0.65855 / 0.37 ( 6148) SS BOND : bond 0.01479 / 0.74 ( 5) SS BOND : angle 1.41496 / 0.77 ( 10) hydrogen bonds : bond 0.05048 / 3.50 ( 163) hydrogen bonds : angle 6.67948 / 4.87 ( 489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8131 (tt0) cc_final: 0.7750 (tt0) REVERT: C 181 LEU cc_start: 0.7007 (tp) cc_final: 0.6675 (tp) REVERT: C 212 ASN cc_start: 0.5862 (m-40) cc_final: 0.5461 (m-40) REVERT: C 232 ILE cc_start: 0.8234 (mm) cc_final: 0.7971 (mt) REVERT: D 134 PHE cc_start: 0.6530 (t80) cc_final: 0.6311 (t80) REVERT: D 159 ASN cc_start: 0.7778 (t0) cc_final: 0.7515 (t0) outliers start: 19 outliers final: 13 residues processed: 140 average time/residue: 0.0566 time to fit residues: 10.0197 Evaluate side-chains 137 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 27 optimal weight: 0.0050 chunk 17 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 122 GLN H 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.157811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134780 restraints weight = 6462.526| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.02 r_work: 0.3581 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4554 Z= 0.105 Angle : 0.548 7.193 6158 Z= 0.294 Chirality : 0.043 0.140 642 Planarity : 0.003 0.032 806 Dihedral : 5.754 59.229 620 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.16 % Allowed : 15.82 % Favored : 81.01 % 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: -1.55 (0.33), residues: 553 helix: -0.85 (0.83), residues: 34 sheet: 0.07 (0.34), residues: 220 loop : -1.98 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 131 TYR 0.017 0.001 TYR C 247 PHE 0.044 0.002 PHE B 250 TRP 0.007 0.001 TRP D 174 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 4549) covalent geometry : angle 0.54601 / 0.29 ( 6148) SS BOND : bond 0.00410 / 0.22 ( 5) SS BOND : angle 1.23652 / 0.63 ( 10) hydrogen bonds : bond 0.03666 / 2.49 ( 163) hydrogen bonds : angle 5.97423 / 4.19 ( 489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.7933 (mmp80) cc_final: 0.7570 (mmt-90) REVERT: B 182 MET cc_start: 0.7348 (ttp) cc_final: 0.7011 (ttt) REVERT: B 196 LYS cc_start: 0.8098 (pttm) cc_final: 0.7860 (pttt) REVERT: B 199 GLN cc_start: 0.7835 (mp10) cc_final: 0.7632 (mp10) REVERT: C 181 LEU cc_start: 0.6887 (tp) cc_final: 0.6504 (tp) REVERT: C 212 ASN cc_start: 0.5989 (m-40) cc_final: 0.5595 (m-40) REVERT: C 232 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7884 (mt) REVERT: C 233 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7972 (ttmt) REVERT: D 134 PHE cc_start: 0.6623 (t80) cc_final: 0.6315 (t80) REVERT: D 159 ASN cc_start: 0.7777 (t0) cc_final: 0.7471 (t0) outliers start: 15 outliers final: 6 residues processed: 125 average time/residue: 0.0776 time to fit residues: 12.1430 Evaluate side-chains 124 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 44 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131735 restraints weight = 6453.000| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.97 r_work: 0.3556 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4554 Z= 0.146 Angle : 0.569 8.165 6158 Z= 0.301 Chirality : 0.043 0.147 642 Planarity : 0.003 0.030 806 Dihedral : 4.981 57.044 614 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.95 % Allowed : 17.72 % Favored : 79.32 % 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: -1.33 (0.33), residues: 553 helix: -0.38 (0.84), residues: 34 sheet: 0.19 (0.33), residues: 245 loop : -2.03 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 201 TYR 0.019 0.002 TYR B 133 PHE 0.033 0.002 PHE B 250 TRP 0.009 0.001 TRP B 191 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 4549) covalent geometry : angle 0.56667 / 0.30 ( 6148) SS BOND : bond 0.00392 / 0.20 ( 5) SS BOND : angle 1.43220 / 0.78 ( 10) hydrogen bonds : bond 0.03904 / 2.69 ( 163) hydrogen bonds : angle 5.97185 / 4.20 ( 489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8074 (mmp80) cc_final: 0.7695 (mmt-90) REVERT: A 207 GLN cc_start: 0.8229 (tt0) cc_final: 0.8027 (tt0) REVERT: B 182 MET cc_start: 0.7347 (ttp) cc_final: 0.7018 (ttt) REVERT: C 181 LEU cc_start: 0.6968 (tp) cc_final: 0.6586 (tp) REVERT: C 212 ASN cc_start: 0.6339 (m-40) cc_final: 0.6053 (m-40) REVERT: C 232 ILE cc_start: 0.8287 (mm) cc_final: 0.8045 (mt) REVERT: D 134 PHE cc_start: 0.6583 (t80) cc_final: 0.6263 (t80) REVERT: D 159 ASN cc_start: 0.7919 (t0) cc_final: 0.7641 (t0) REVERT: D 175 LEU cc_start: 0.7858 (mp) cc_final: 0.7537 (mt) outliers start: 14 outliers final: 10 residues processed: 124 average time/residue: 0.0759 time to fit residues: 11.7418 Evaluate side-chains 126 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128048 restraints weight = 6453.918| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.94 r_work: 0.3491 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4554 Z= 0.282 Angle : 0.658 7.533 6158 Z= 0.354 Chirality : 0.046 0.194 642 Planarity : 0.004 0.036 806 Dihedral : 4.960 16.859 611 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.22 % Allowed : 17.72 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.45 (0.34), residues: 553 helix: -0.45 (0.86), residues: 34 sheet: 0.34 (0.34), residues: 239 loop : -2.30 (0.31), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 201 TYR 0.017 0.002 TYR D 88 PHE 0.037 0.003 PHE B 250 TRP 0.021 0.003 TRP A 191 HIS 0.008 0.002 HIS D 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 ( 4549) covalent geometry : angle 0.65474 / 0.35 ( 6148) SS BOND : bond 0.00478 / 0.25 ( 5) SS BOND : angle 1.74992 / 0.88 ( 10) hydrogen bonds : bond 0.05110 / 3.53 ( 163) hydrogen bonds : angle 6.37831 / 4.52 ( 489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8526 (mttp) cc_final: 0.8183 (mttp) REVERT: A 201 ARG cc_start: 0.8226 (mmp80) cc_final: 0.7863 (mmt-90) REVERT: B 233 LYS cc_start: 0.7710 (tmtt) cc_final: 0.7399 (tmtt) REVERT: C 154 ASN cc_start: 0.8185 (t0) cc_final: 0.7971 (t0) REVERT: C 212 ASN cc_start: 0.6620 (m-40) cc_final: 0.6165 (m-40) REVERT: D 88 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6672 (p90) REVERT: D 109 MET cc_start: 0.6813 (tmm) cc_final: 0.6466 (tmm) REVERT: D 134 PHE cc_start: 0.6557 (t80) cc_final: 0.6268 (t80) REVERT: D 159 ASN cc_start: 0.8041 (t0) cc_final: 0.7650 (t0) REVERT: D 192 MET cc_start: 0.6097 (mmt) cc_final: 0.5871 (mmp) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.0678 time to fit residues: 10.5666 Evaluate side-chains 131 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 HIS D 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.127635 restraints weight = 6590.201| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.96 r_work: 0.3488 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4554 Z= 0.233 Angle : 0.629 7.187 6158 Z= 0.333 Chirality : 0.045 0.213 642 Planarity : 0.003 0.035 806 Dihedral : 4.870 17.265 611 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.43 % Allowed : 19.62 % Favored : 75.95 % 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: -1.36 (0.34), residues: 553 helix: -0.36 (0.90), residues: 34 sheet: 0.48 (0.34), residues: 234 loop : -2.30 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 201 TYR 0.014 0.002 TYR D 39 PHE 0.032 0.002 PHE B 250 TRP 0.014 0.002 TRP A 191 HIS 0.006 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 ( 4549) covalent geometry : angle 0.62700 / 0.33 ( 6148) SS BOND : bond 0.00425 / 0.21 ( 5) SS BOND : angle 1.30631 / 0.66 ( 10) hydrogen bonds : bond 0.04630 / 3.19 ( 163) hydrogen bonds : angle 6.17124 / 4.40 ( 489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8532 (mttp) cc_final: 0.8185 (mttp) REVERT: A 201 ARG cc_start: 0.8219 (mmp80) cc_final: 0.7889 (mmt-90) REVERT: A 210 ASP cc_start: 0.7909 (m-30) cc_final: 0.7644 (m-30) REVERT: A 256 TYR cc_start: 0.8571 (m-10) cc_final: 0.8306 (m-10) REVERT: C 154 ASN cc_start: 0.8082 (t0) cc_final: 0.7849 (t0) REVERT: C 181 LEU cc_start: 0.7265 (tp) cc_final: 0.7051 (tt) REVERT: C 212 ASN cc_start: 0.6566 (m-40) cc_final: 0.6292 (m-40) REVERT: C 213 TYR cc_start: 0.8396 (m-80) cc_final: 0.8180 (m-80) REVERT: D 88 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6626 (p90) REVERT: D 109 MET cc_start: 0.6733 (tmm) cc_final: 0.6404 (tmm) REVERT: D 159 ASN cc_start: 0.8114 (t0) cc_final: 0.7794 (t0) REVERT: D 162 SER cc_start: 0.7444 (p) cc_final: 0.6905 (p) REVERT: D 192 MET cc_start: 0.6125 (mmt) cc_final: 0.5881 (mmp) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.0744 time to fit residues: 12.3982 Evaluate side-chains 140 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 88 TYR Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 8 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 1 optimal weight: 0.0060 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.130570 restraints weight = 6488.632| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.84 r_work: 0.3541 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4554 Z= 0.124 Angle : 0.562 7.244 6158 Z= 0.293 Chirality : 0.044 0.227 642 Planarity : 0.003 0.061 806 Dihedral : 4.482 15.974 611 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.01 % Allowed : 21.73 % Favored : 74.26 % 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: -1.32 (0.34), residues: 553 helix: -0.56 (0.80), residues: 40 sheet: 0.53 (0.34), residues: 234 loop : -2.29 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.016 0.001 TYR D 39 PHE 0.025 0.002 PHE B 250 TRP 0.006 0.001 TRP D 174 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4549) covalent geometry : angle 0.56144 / 0.29 ( 6148) SS BOND : bond 0.00288 / 0.14 ( 5) SS BOND : angle 0.83403 / 0.45 ( 10) hydrogen bonds : bond 0.03560 / 2.41 ( 163) hydrogen bonds : angle 5.82205 / 4.16 ( 489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7459 (ttm110) REVERT: A 147 LYS cc_start: 0.8507 (mttp) cc_final: 0.8185 (mttp) REVERT: A 201 ARG cc_start: 0.8148 (mmp80) cc_final: 0.7839 (mmt-90) REVERT: A 210 ASP cc_start: 0.7816 (m-30) cc_final: 0.7565 (m-30) REVERT: A 256 TYR cc_start: 0.8558 (m-10) cc_final: 0.8277 (m-10) REVERT: B 178 TYR cc_start: 0.8552 (p90) cc_final: 0.7997 (p90) REVERT: B 214 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: C 154 ASN cc_start: 0.7940 (t0) cc_final: 0.7690 (t0) REVERT: C 181 LEU cc_start: 0.7132 (tp) cc_final: 0.6887 (tt) REVERT: C 212 ASN cc_start: 0.6445 (m-40) cc_final: 0.6211 (m-40) REVERT: D 109 MET cc_start: 0.6650 (tmm) cc_final: 0.6374 (tmm) REVERT: D 162 SER cc_start: 0.7415 (p) cc_final: 0.6934 (p) REVERT: D 192 MET cc_start: 0.6041 (mmt) cc_final: 0.5835 (mmp) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.0763 time to fit residues: 12.4818 Evaluate side-chains 142 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 29 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.151658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129603 restraints weight = 6455.836| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.80 r_work: 0.3533 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4554 Z= 0.143 Angle : 0.577 7.356 6158 Z= 0.301 Chirality : 0.044 0.251 642 Planarity : 0.003 0.050 806 Dihedral : 4.385 15.908 611 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.59 % Allowed : 22.15 % Favored : 74.26 % 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: -1.30 (0.34), residues: 553 helix: -0.59 (0.79), residues: 41 sheet: 0.47 (0.34), residues: 231 loop : -2.16 (0.31), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 201 TYR 0.015 0.001 TYR B 256 PHE 0.023 0.002 PHE B 250 TRP 0.006 0.001 TRP D 57 HIS 0.005 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4549) covalent geometry : angle 0.57693 / 0.30 ( 6148) SS BOND : bond 0.00246 / 0.12 ( 5) SS BOND : angle 0.69429 / 0.38 ( 10) hydrogen bonds : bond 0.03564 / 2.38 ( 163) hydrogen bonds : angle 5.74683 / 4.09 ( 489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8513 (mttp) cc_final: 0.8202 (mttp) REVERT: A 201 ARG cc_start: 0.8161 (mmp80) cc_final: 0.7848 (mmt-90) REVERT: A 210 ASP cc_start: 0.7841 (m-30) cc_final: 0.7609 (m-30) REVERT: A 256 TYR cc_start: 0.8585 (m-10) cc_final: 0.8299 (m-10) REVERT: B 178 TYR cc_start: 0.8600 (p90) cc_final: 0.7991 (p90) REVERT: B 233 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7400 (tmtt) REVERT: C 154 ASN cc_start: 0.7929 (t0) cc_final: 0.7669 (t0) REVERT: C 181 LEU cc_start: 0.7110 (tp) cc_final: 0.6869 (tt) REVERT: C 212 ASN cc_start: 0.6407 (m-40) cc_final: 0.6199 (m-40) REVERT: D 109 MET cc_start: 0.6665 (tmm) cc_final: 0.6386 (tmm) REVERT: D 162 SER cc_start: 0.7491 (p) cc_final: 0.7172 (p) REVERT: D 192 MET cc_start: 0.6042 (mmt) cc_final: 0.5827 (mmp) outliers start: 17 outliers final: 14 residues processed: 125 average time/residue: 0.0721 time to fit residues: 11.1238 Evaluate side-chains 133 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125213 restraints weight = 6506.602| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.83 r_work: 0.3470 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 4554 Z= 0.335 Angle : 0.723 8.582 6158 Z= 0.382 Chirality : 0.049 0.271 642 Planarity : 0.004 0.059 806 Dihedral : 5.147 17.446 611 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.80 % Allowed : 22.78 % Favored : 73.42 % 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: -1.59 (0.34), residues: 553 helix: -0.51 (0.86), residues: 34 sheet: 0.19 (0.33), residues: 239 loop : -2.35 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.023 0.003 TYR D 88 PHE 0.033 0.003 PHE B 250 TRP 0.017 0.003 TRP B 191 HIS 0.008 0.002 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.34 ( 4549) covalent geometry : angle 0.72258 / 0.38 ( 6148) SS BOND : bond 0.00356 / 0.17 ( 5) SS BOND : angle 0.73365 / 0.38 ( 10) hydrogen bonds : bond 0.05198 / 3.52 ( 163) hydrogen bonds : angle 6.36873 / 4.58 ( 489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8543 (mttp) cc_final: 0.8189 (mttp) REVERT: A 201 ARG cc_start: 0.8233 (mmp80) cc_final: 0.7908 (mmt-90) REVERT: A 256 TYR cc_start: 0.8672 (m-10) cc_final: 0.8326 (m-10) REVERT: B 190 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7517 (tpp) REVERT: B 233 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7532 (tmtt) REVERT: C 154 ASN cc_start: 0.8115 (t0) cc_final: 0.7862 (t0) REVERT: C 214 ASP cc_start: 0.8321 (t0) cc_final: 0.8070 (t0) REVERT: D 63 ASP cc_start: 0.7997 (t0) cc_final: 0.7678 (t0) REVERT: D 109 MET cc_start: 0.6695 (tmm) cc_final: 0.6439 (tmm) REVERT: D 162 SER cc_start: 0.7590 (p) cc_final: 0.7267 (p) REVERT: D 192 MET cc_start: 0.6074 (mmt) cc_final: 0.5823 (mmp) outliers start: 18 outliers final: 15 residues processed: 124 average time/residue: 0.0644 time to fit residues: 9.9701 Evaluate side-chains 134 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 141 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 83 PHE Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 199 GLN Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127981 restraints weight = 6429.310| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.95 r_work: 0.3503 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4554 Z= 0.154 Angle : 0.622 7.994 6158 Z= 0.321 Chirality : 0.045 0.243 642 Planarity : 0.003 0.053 806 Dihedral : 4.619 16.516 611 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.74 % Allowed : 24.89 % Favored : 72.36 % 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: -1.47 (0.33), residues: 553 helix: -0.57 (0.80), residues: 40 sheet: 0.31 (0.34), residues: 229 loop : -2.23 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.017 0.001 TYR D 39 PHE 0.024 0.002 PHE B 250 TRP 0.007 0.001 TRP B 191 HIS 0.005 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4549) covalent geometry : angle 0.62144 / 0.32 ( 6148) SS BOND : bond 0.00240 / 0.12 ( 5) SS BOND : angle 0.68938 / 0.39 ( 10) hydrogen bonds : bond 0.03761 / 2.49 ( 163) hydrogen bonds : angle 5.93378 / 4.25 ( 489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1106 Ramachandran restraints generated. 553 Oldfield, 0 Emsley, 553 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7386 (ttm110) REVERT: A 147 LYS cc_start: 0.8511 (mttp) cc_final: 0.8191 (mttp) REVERT: A 256 TYR cc_start: 0.8629 (m-10) cc_final: 0.8289 (m-10) REVERT: B 178 TYR cc_start: 0.8679 (p90) cc_final: 0.8066 (p90) REVERT: B 190 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7575 (tpp) REVERT: B 214 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: B 233 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7574 (tmtt) REVERT: C 137 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7768 (mtpp) REVERT: C 154 ASN cc_start: 0.8023 (t0) cc_final: 0.7772 (t0) REVERT: C 181 LEU cc_start: 0.7182 (tp) cc_final: 0.6945 (tt) REVERT: D 109 MET cc_start: 0.6600 (tmm) cc_final: 0.6282 (tmm) REVERT: D 162 SER cc_start: 0.7578 (p) cc_final: 0.7275 (p) REVERT: D 192 MET cc_start: 0.6129 (mmt) cc_final: 0.5881 (mmp) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.0642 time to fit residues: 9.4455 Evaluate side-chains 123 residues out of total 476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain H residue 200 VAL Chi-restraints excluded: chain H residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125963 restraints weight = 6468.570| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.99 r_work: 0.3481 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4554 Z= 0.230 Angle : 0.660 8.564 6158 Z= 0.345 Chirality : 0.046 0.287 642 Planarity : 0.004 0.052 806 Dihedral : 4.819 16.461 611 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.38 % Allowed : 23.21 % Favored : 73.42 % 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: -1.54 (0.34), residues: 553 helix: -0.73 (0.81), residues: 40 sheet: 0.26 (0.34), residues: 232 loop : -2.30 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 129 TYR 0.015 0.002 TYR D 88 PHE 0.025 0.002 PHE B 250 TRP 0.012 0.002 TRP B 191 HIS 0.006 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 ( 4549) covalent geometry : angle 0.65990 / 0.35 ( 6148) SS BOND : bond 0.00245 / 0.12 ( 5) SS BOND : angle 0.75056 / 0.42 ( 10) hydrogen bonds : bond 0.04335 / 2.90 ( 163) hydrogen bonds : angle 6.08330 / 4.35 ( 489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1041.85 seconds wall clock time: 18 minutes 34.03 seconds (1114.03 seconds total)