Starting phenix.real_space_refine on Thu Jul 2 01:46:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t05_40935/07_2026/8t05_40935.cif" } resolution = 3.22 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= 0.004 sd= 0.066 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 22 5.16 5 C 3387 2.51 5 N 798 2.21 5 O 893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 5104 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "B" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1592 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain: "C" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 0.89, per 1000 atoms: 0.17 Number of scatterers: 5104 At special positions: 0 Unit cell: (81.34, 88.81, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 22 16.00 P 2 15.00 O 893 8.00 N 798 7.00 C 3387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 60 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 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: 0.30 Conformation dependent library (CDL) restraints added in 123.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 182 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 186 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 186 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 182 " 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1158 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 55.6% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.844A pdb=" N VAL A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.546A pdb=" N GLY A 22 " --> pdb=" O PHE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 51 removed outlier: 4.083A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.692A pdb=" N MET A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 86 removed outlier: 3.738A pdb=" N THR A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 removed outlier: 3.555A pdb=" N GLU A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 142 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.787A pdb=" N SER A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.721A pdb=" N GLY B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 63 through 86 removed outlier: 3.628A pdb=" N PHE B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 112 Processing helix chain 'B' and resid 119 through 141 Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 177 through 197 removed outlier: 3.965A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.885A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 11 removed outlier: 5.688A pdb=" N GLU C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 92 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.072A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.533A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 864 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: 0.44 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 746 1.31 - 1.44: 1499 1.44 - 1.56: 2946 1.56 - 1.69: 14 1.69 - 1.82: 32 Bond restraints: 5237 Sorted by residual: bond pdb=" C GLY C 8 " pdb=" N ALA C 9 " ideal model delta sigma weight residual 1.331 1.409 -0.077 1.30e-02 5.92e+03 3.53e+01 bond pdb=" C25 LBN A 303 " pdb=" O5 LBN A 303 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C25 LBN B 303 " pdb=" O5 LBN B 303 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C34 LBN A 303 " pdb=" O7 LBN A 303 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 303 " pdb=" O7 LBN B 303 " ideal model delta sigma weight residual 1.331 1.424 -0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 5232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 6281 2.92 - 5.84: 805 5.84 - 8.76: 12 8.76 - 11.68: 5 11.68 - 14.60: 2 Bond angle restraints: 7105 Sorted by residual: angle pdb=" N PHE C 109 " pdb=" CA PHE C 109 " pdb=" C PHE C 109 " ideal model delta sigma weight residual 111.24 118.85 -7.61 1.38e+00 5.25e-01 3.04e+01 angle pdb=" C GLY A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta sigma weight residual 120.03 125.59 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N THR D 94 " pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 108.82 117.00 -8.18 1.65e+00 3.67e-01 2.46e+01 angle pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O2 LBN B 303 " ideal model delta sigma weight residual 93.45 108.05 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O1 LBN A 303 " pdb=" P1 LBN A 303 " pdb=" O2 LBN A 303 " ideal model delta sigma weight residual 93.45 107.88 -14.43 3.00e+00 1.11e-01 2.31e+01 ... (remaining 7100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.48: 2918 30.48 - 60.96: 86 60.96 - 91.44: 9 91.44 - 121.92: 5 121.92 - 152.40: 4 Dihedral angle restraints: 3022 sinusoidal: 1207 harmonic: 1815 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 180.00 70.79 109.21 0 5.00e+00 4.00e-02 4.77e+02 dihedral pdb=" CA ALA D 50 " pdb=" C ALA D 50 " pdb=" N ALA D 51 " pdb=" CA ALA D 51 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA SER B 56 " pdb=" C SER B 56 " pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.12 -24.88 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 3019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.985: 803 0.985 - 1.969: 0 1.969 - 2.954: 0 2.954 - 3.938: 0 3.938 - 4.923: 2 Chirality restraints: 805 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.56 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" C14 CLR A 302 " pdb=" C13 CLR A 302 " pdb=" C15 CLR A 302 " pdb=" C8 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.97e+00 ... (remaining 802 not shown) Planarity restraints: 848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 145 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO B 146 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 13 " -0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO C 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " -0.042 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO D 95 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " -0.036 5.00e-02 4.00e+02 ... (remaining 845 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 71 2.68 - 3.23: 4609 3.23 - 3.79: 7701 3.79 - 4.34: 10686 4.34 - 4.90: 18018 Nonbonded interactions: 41085 Sorted by model distance: nonbonded pdb=" OE1 GLN A 44 " pdb="ZN ZN A 301 " model vdw 2.120 2.230 nonbonded pdb=" OE1 GLN B 44 " pdb="ZN ZN B 301 " model vdw 2.172 2.230 nonbonded pdb=" NH2 ARG D 61 " pdb=" OE2 GLU D 81 " model vdw 2.356 3.120 nonbonded pdb=" NH2 ARG A 108 " pdb=" O PRO A 116 " model vdw 2.413 3.120 nonbonded pdb=" O HIS D 90 " pdb=" ND1 HIS D 90 " model vdw 2.433 3.120 ... (remaining 41080 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' 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: 1.630 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: 0.010 Set scattering table: 0.020 Process input model: 4.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 7.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.015 0.181 5247 Z= 1.079 Angle : 1.851 14.605 7113 Z= 1.349 Chirality : 0.259 4.923 805 Planarity : 0.006 0.091 848 Dihedral : 16.609 152.400 1852 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.94 % Favored : 93.90 % Rotamer: Outliers : 0.93 % Allowed : 6.16 % Favored : 92.91 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: -2.10 (0.31), residues: 623 helix: -1.21 (0.25), residues: 313 sheet: -1.44 (0.49), residues: 86 loop : -1.32 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 108 TYR 0.043 0.003 TYR D 49 PHE 0.019 0.002 PHE B 43 TRP 0.027 0.003 TRP A 151 HIS 0.007 0.002 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.01446 / 1.07 ( 5237) covalent geometry : angle 1.85126 / 1.35 ( 7105) SS BOND : bond 0.01077 / 0.70 ( 4) SS BOND : angle 1.19535 / 0.63 ( 8) hydrogen bonds : bond 0.19464 / 12.57 ( 298) hydrogen bonds : angle 9.16980 / 6.60 ( 864) metal coordination : bond 0.11605 / 6.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.143 Fit side-chains REVERT: A 137 GLU cc_start: 0.6864 (tp30) cc_final: 0.6262 (mm-30) REVERT: A 198 ARG cc_start: 0.6886 (ttm170) cc_final: 0.6588 (ttp80) REVERT: B 62 MET cc_start: 0.6309 (mtt) cc_final: 0.6034 (mtm) REVERT: B 184 ILE cc_start: 0.7178 (mm) cc_final: 0.6907 (mt) REVERT: C 10 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7500 (mp0) REVERT: C 28 THR cc_start: 0.8525 (m) cc_final: 0.8298 (t) REVERT: C 32 TYR cc_start: 0.8080 (m-80) cc_final: 0.7604 (m-80) REVERT: C 34 MET cc_start: 0.8066 (mmm) cc_final: 0.7480 (tpt) REVERT: D 30 TYR cc_start: 0.8035 (m-80) cc_final: 0.7673 (m-80) REVERT: D 71 TYR cc_start: 0.7538 (m-80) cc_final: 0.7100 (m-80) REVERT: D 100 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7906 (tp30) outliers start: 5 outliers final: 4 residues processed: 92 average time/residue: 0.0736 time to fit residues: 8.3687 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 PRO Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain D residue 90 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 113 ASN B 186 HIS D 6 GLN D 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.172036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.140814 restraints weight = 5992.936| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.14 r_work: 0.3616 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 5247 Z= 0.192 Angle : 0.644 7.989 7113 Z= 0.335 Chirality : 0.043 0.202 805 Planarity : 0.005 0.077 848 Dihedral : 15.772 139.321 760 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.49 % Allowed : 10.82 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 0.22 (0.34), residues: 623 helix: 1.26 (0.28), residues: 310 sheet: -0.94 (0.47), residues: 117 loop : -0.84 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.012 0.001 TYR B 37 PHE 0.016 0.002 PHE D 91 TRP 0.022 0.002 TRP C 47 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 5237) covalent geometry : angle 0.64367 / 0.33 ( 7105) SS BOND : bond 0.00208 / 0.14 ( 4) SS BOND : angle 1.03599 / 0.50 ( 8) hydrogen bonds : bond 0.04494 / 2.90 ( 298) hydrogen bonds : angle 4.97420 / 3.50 ( 864) metal coordination : bond 0.09473 / 7.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.173 Fit side-chains REVERT: A 112 GLU cc_start: 0.7408 (tt0) cc_final: 0.7205 (tt0) REVERT: A 137 GLU cc_start: 0.7914 (tp30) cc_final: 0.7397 (mm-30) REVERT: B 62 MET cc_start: 0.6938 (mtt) cc_final: 0.6735 (mtm) REVERT: B 184 ILE cc_start: 0.8275 (mm) cc_final: 0.7949 (mt) REVERT: B 198 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8386 (mtp85) REVERT: D 30 TYR cc_start: 0.8910 (m-80) cc_final: 0.8557 (m-80) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.0729 time to fit residues: 8.5361 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 HIS B 95 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.173318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.141752 restraints weight = 5912.989| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.16 r_work: 0.3638 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5247 Z= 0.131 Angle : 0.570 6.449 7113 Z= 0.290 Chirality : 0.040 0.197 805 Planarity : 0.005 0.078 848 Dihedral : 13.414 116.589 751 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.87 % Allowed : 13.06 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.02 (0.36), residues: 623 helix: 2.11 (0.29), residues: 312 sheet: -0.82 (0.49), residues: 110 loop : -0.71 (0.50), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 140 TYR 0.013 0.001 TYR D 49 PHE 0.015 0.001 PHE B 70 TRP 0.017 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 5237) covalent geometry : angle 0.56927 / 0.29 ( 7105) SS BOND : bond 0.00247 / 0.17 ( 4) SS BOND : angle 0.95059 / 0.47 ( 8) hydrogen bonds : bond 0.04010 / 2.61 ( 298) hydrogen bonds : angle 4.38854 / 3.05 ( 864) metal coordination : bond 0.00434 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8606 (tmmt) cc_final: 0.8129 (tptt) REVERT: A 88 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7734 (mmm-85) REVERT: A 137 GLU cc_start: 0.7856 (tp30) cc_final: 0.7115 (mm-30) REVERT: B 27 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8014 (ttpt) REVERT: C 5 GLN cc_start: 0.8176 (tt0) cc_final: 0.7944 (tt0) REVERT: C 90 ASP cc_start: 0.8697 (m-30) cc_final: 0.8484 (m-30) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.0774 time to fit residues: 8.1377 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.175719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144222 restraints weight = 5986.740| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.13 r_work: 0.3527 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5247 Z= 0.139 Angle : 0.564 6.186 7113 Z= 0.286 Chirality : 0.040 0.200 805 Planarity : 0.005 0.078 848 Dihedral : 11.556 107.781 751 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.87 % Allowed : 13.99 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.19 (0.36), residues: 623 helix: 2.33 (0.29), residues: 306 sheet: -0.83 (0.47), residues: 122 loop : -0.57 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 198 TYR 0.012 0.001 TYR D 49 PHE 0.015 0.001 PHE D 91 TRP 0.010 0.001 TRP C 112 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5237) covalent geometry : angle 0.56095 / 0.28 ( 7105) SS BOND : bond 0.00346 / 0.23 ( 4) SS BOND : angle 1.69656 / 0.67 ( 8) hydrogen bonds : bond 0.04000 / 2.60 ( 298) hydrogen bonds : angle 4.27154 / 2.96 ( 864) metal coordination : bond 0.00227 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8593 (tmmt) cc_final: 0.8088 (tptt) REVERT: A 88 ARG cc_start: 0.8066 (mtp-110) cc_final: 0.7793 (mmm-85) REVERT: A 137 GLU cc_start: 0.7827 (tp30) cc_final: 0.7150 (mm-30) REVERT: B 27 LYS cc_start: 0.8312 (mmmt) cc_final: 0.7957 (ttpt) REVERT: C 5 GLN cc_start: 0.8101 (tt0) cc_final: 0.7830 (tt0) REVERT: C 90 ASP cc_start: 0.8725 (m-30) cc_final: 0.8453 (m-30) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 0.0790 time to fit residues: 7.6536 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.173391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.140854 restraints weight = 6061.190| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.22 r_work: 0.3619 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5247 Z= 0.159 Angle : 0.575 6.613 7113 Z= 0.293 Chirality : 0.041 0.204 805 Planarity : 0.005 0.082 848 Dihedral : 10.400 106.138 751 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.49 % Allowed : 15.67 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.12 (0.36), residues: 623 helix: 2.28 (0.29), residues: 306 sheet: -0.85 (0.47), residues: 122 loop : -0.62 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 13 TYR 0.015 0.001 TYR D 49 PHE 0.016 0.002 PHE D 91 TRP 0.012 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 5237) covalent geometry : angle 0.57392 / 0.29 ( 7105) SS BOND : bond 0.00356 / 0.24 ( 4) SS BOND : angle 1.35808 / 0.57 ( 8) hydrogen bonds : bond 0.04078 / 2.65 ( 298) hydrogen bonds : angle 4.28685 / 2.98 ( 864) metal coordination : bond 0.00201 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.158 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8673 (tmmt) cc_final: 0.8120 (tptt) REVERT: A 88 ARG cc_start: 0.8085 (mtp-110) cc_final: 0.7831 (mmm-85) REVERT: A 137 GLU cc_start: 0.7857 (tp30) cc_final: 0.7084 (mm-30) REVERT: B 27 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8014 (ttpt) REVERT: C 5 GLN cc_start: 0.8151 (tt0) cc_final: 0.7902 (tt0) outliers start: 8 outliers final: 8 residues processed: 71 average time/residue: 0.0718 time to fit residues: 6.5166 Evaluate side-chains 74 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.174507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143330 restraints weight = 6108.206| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.14 r_work: 0.3589 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.830 5247 Z= 0.408 Angle : 0.546 6.028 7113 Z= 0.278 Chirality : 0.040 0.204 805 Planarity : 0.005 0.080 848 Dihedral : 9.515 96.765 751 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.61 % Allowed : 14.18 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.19 (0.36), residues: 623 helix: 2.34 (0.29), residues: 306 sheet: -0.80 (0.47), residues: 122 loop : -0.61 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 13 TYR 0.014 0.001 TYR D 49 PHE 0.014 0.001 PHE B 70 TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 5237) covalent geometry : angle 0.54531 / 0.28 ( 7105) SS BOND : bond 0.00226 / 0.16 ( 4) SS BOND : angle 1.19677 / 0.50 ( 8) hydrogen bonds : bond 0.03928 / 2.56 ( 298) hydrogen bonds : angle 4.19136 / 2.91 ( 864) metal coordination : bond 0.33877 / 27.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8654 (tmmt) cc_final: 0.8092 (tptt) REVERT: A 88 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7811 (mmm-85) REVERT: A 137 GLU cc_start: 0.7861 (tp30) cc_final: 0.7035 (mm-30) REVERT: B 27 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7973 (ttpt) REVERT: C 5 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: D 30 TYR cc_start: 0.8924 (m-80) cc_final: 0.8652 (m-10) REVERT: D 74 LYS cc_start: 0.8548 (ptmm) cc_final: 0.8147 (ptmm) REVERT: D 100 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8006 (mm-30) outliers start: 14 outliers final: 13 residues processed: 77 average time/residue: 0.0768 time to fit residues: 7.4443 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.175488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143289 restraints weight = 5985.283| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.30 r_work: 0.3645 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.915 5247 Z= 0.441 Angle : 0.530 6.101 7113 Z= 0.269 Chirality : 0.039 0.203 805 Planarity : 0.005 0.079 848 Dihedral : 9.006 86.253 751 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.43 % Allowed : 14.18 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.25 (0.36), residues: 623 helix: 2.42 (0.29), residues: 308 sheet: -0.49 (0.50), residues: 108 loop : -0.89 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 13 TYR 0.013 0.001 TYR D 49 PHE 0.014 0.001 PHE B 70 TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5237) covalent geometry : angle 0.52877 / 0.27 ( 7105) SS BOND : bond 0.00182 / 0.13 ( 4) SS BOND : angle 1.16093 / 0.52 ( 8) hydrogen bonds : bond 0.03810 / 2.48 ( 298) hydrogen bonds : angle 4.10806 / 2.85 ( 864) metal coordination : bond 0.37352 / 30.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8695 (tmmt) cc_final: 0.8145 (tptt) REVERT: A 137 GLU cc_start: 0.7864 (tp30) cc_final: 0.7153 (mm-30) REVERT: B 27 LYS cc_start: 0.8343 (mmmt) cc_final: 0.8004 (ttpt) REVERT: B 62 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6848 (ttm) REVERT: C 5 GLN cc_start: 0.8125 (tt0) cc_final: 0.7904 (tt0) REVERT: D 30 TYR cc_start: 0.8945 (m-80) cc_final: 0.8688 (m-10) REVERT: D 74 LYS cc_start: 0.8598 (ptmm) cc_final: 0.8217 (ptmm) outliers start: 13 outliers final: 10 residues processed: 76 average time/residue: 0.0780 time to fit residues: 7.5592 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.4202 r_free = 0.4202 target = 0.178025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146766 restraints weight = 6064.863| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.18 r_work: 0.3670 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5247 Z= 0.110 Angle : 0.507 5.862 7113 Z= 0.255 Chirality : 0.038 0.202 805 Planarity : 0.005 0.076 848 Dihedral : 8.502 71.185 751 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.05 % Allowed : 15.30 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.43 (0.36), residues: 623 helix: 2.55 (0.29), residues: 317 sheet: -0.43 (0.51), residues: 108 loop : -0.93 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 13 TYR 0.012 0.001 TYR D 49 PHE 0.013 0.001 PHE A 39 TRP 0.008 0.001 TRP C 47 HIS 0.004 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 5237) covalent geometry : angle 0.50553 / 0.25 ( 7105) SS BOND : bond 0.00196 / 0.14 ( 4) SS BOND : angle 1.11365 / 0.50 ( 8) hydrogen bonds : bond 0.03619 / 2.36 ( 298) hydrogen bonds : angle 3.99163 / 2.77 ( 864) metal coordination : bond 0.00662 / 0.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8656 (tmmt) cc_final: 0.8086 (tptt) REVERT: A 88 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7919 (mtp-110) REVERT: A 137 GLU cc_start: 0.7693 (tp30) cc_final: 0.7113 (mm-30) REVERT: B 27 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7784 (mptt) REVERT: D 30 TYR cc_start: 0.8847 (m-80) cc_final: 0.8585 (m-10) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.0766 time to fit residues: 7.7133 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.174980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.142870 restraints weight = 6056.449| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.24 r_work: 0.3642 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5247 Z= 0.139 Angle : 0.540 6.078 7113 Z= 0.272 Chirality : 0.040 0.204 805 Planarity : 0.005 0.080 848 Dihedral : 8.492 64.839 751 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.68 % Allowed : 15.49 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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: 1.35 (0.36), residues: 623 helix: 2.50 (0.29), residues: 308 sheet: -0.35 (0.51), residues: 108 loop : -0.90 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 13 TYR 0.014 0.001 TYR D 49 PHE 0.014 0.001 PHE A 39 TRP 0.009 0.001 TRP C 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5237) covalent geometry : angle 0.53837 / 0.27 ( 7105) SS BOND : bond 0.00232 / 0.16 ( 4) SS BOND : angle 1.22914 / 0.56 ( 8) hydrogen bonds : bond 0.03804 / 2.48 ( 298) hydrogen bonds : angle 4.06549 / 2.82 ( 864) metal coordination : bond 0.00146 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8702 (tmmt) cc_final: 0.8138 (tptt) REVERT: A 137 GLU cc_start: 0.7709 (tp30) cc_final: 0.7110 (mm-30) REVERT: A 172 PHE cc_start: 0.7924 (m-10) cc_final: 0.7683 (m-10) REVERT: B 27 LYS cc_start: 0.8356 (mmmt) cc_final: 0.8008 (ttpt) REVERT: D 30 TYR cc_start: 0.8953 (m-80) cc_final: 0.8687 (m-10) outliers start: 9 outliers final: 9 residues processed: 74 average time/residue: 0.0714 time to fit residues: 6.6447 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.174511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142383 restraints weight = 6108.922| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.23 r_work: 0.3515 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.848 5247 Z= 0.416 Angle : 0.549 5.937 7113 Z= 0.277 Chirality : 0.040 0.204 805 Planarity : 0.005 0.079 848 Dihedral : 8.452 57.304 751 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.05 % Allowed : 15.11 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.36), residues: 623 helix: 2.44 (0.29), residues: 308 sheet: -0.34 (0.51), residues: 108 loop : -0.86 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 88 TYR 0.015 0.001 TYR D 49 PHE 0.014 0.001 PHE A 39 TRP 0.010 0.001 TRP C 47 HIS 0.002 0.001 HIS B 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 5237) covalent geometry : angle 0.54745 / 0.28 ( 7105) SS BOND : bond 0.00227 / 0.15 ( 4) SS BOND : angle 1.34155 / 0.64 ( 8) hydrogen bonds : bond 0.03864 / 2.52 ( 298) hydrogen bonds : angle 4.11235 / 2.86 ( 864) metal coordination : bond 0.34628 / 28.15 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8667 (tmmt) cc_final: 0.8093 (tptt) REVERT: A 88 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7925 (mtp-110) REVERT: A 137 GLU cc_start: 0.7726 (tp30) cc_final: 0.7048 (mm-30) REVERT: A 172 PHE cc_start: 0.7903 (m-10) cc_final: 0.7672 (m-10) REVERT: B 27 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7927 (ttpt) REVERT: C 32 TYR cc_start: 0.8019 (m-80) cc_final: 0.7767 (m-10) outliers start: 11 outliers final: 10 residues processed: 77 average time/residue: 0.0814 time to fit residues: 7.9528 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.191020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.148046 restraints weight = 6456.110| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.34 r_work: 0.3509 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.891 5247 Z= 0.439 Angle : 0.563 6.294 7113 Z= 0.285 Chirality : 0.040 0.205 805 Planarity : 0.005 0.080 848 Dihedral : 8.469 54.812 751 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.05 % Allowed : 14.74 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % 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 (0.36), residues: 623 helix: 2.42 (0.29), residues: 306 sheet: -0.63 (0.49), residues: 122 loop : -0.62 (0.51), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 88 TYR 0.015 0.001 TYR D 49 PHE 0.016 0.001 PHE D 91 TRP 0.011 0.001 TRP C 47 HIS 0.004 0.001 HIS B 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 5237) covalent geometry : angle 0.56223 / 0.28 ( 7105) SS BOND : bond 0.00255 / 0.17 ( 4) SS BOND : angle 1.14327 / 0.52 ( 8) hydrogen bonds : bond 0.03949 / 2.57 ( 298) hydrogen bonds : angle 4.17290 / 2.91 ( 864) metal coordination : bond 0.36375 / 29.57 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1069.42 seconds wall clock time: 19 minutes 6.24 seconds (1146.24 seconds total)