Starting phenix.real_space_refine on Tue Aug 4 14:58:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p1v_71135/08_2026/9p1v_71135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p1v_71135/08_2026/9p1v_71135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p1v_71135/08_2026/9p1v_71135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p1v_71135/08_2026/9p1v_71135.map" model { file = "/net/cci-nas-00/data/ceres_data/9p1v_71135/08_2026/9p1v_71135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p1v_71135/08_2026/9p1v_71135.cif" } resolution = 3.27 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= -0.069 sd= 0.295 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 Zn 1 6.06 5 S 12 5.16 5 C 2567 2.51 5 N 691 2.21 5 O 815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4086 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "L" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1650 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain: "H" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1672 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 212} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.14, per 1000 atoms: 0.28 Number of scatterers: 4086 At special positions: 0 Unit cell: (54.15, 68.4, 120.65, 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) Zn 1 29.99 S 12 16.00 O 815 8.00 N 691 7.00 C 2567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.15 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: 0.35 Conformation dependent library (CDL) restraints added in 177.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 83 " pdb="ZN ZN A1000 " - pdb=" NE2 HIS A 88 " pdb="ZN ZN A1000 " - pdb=" ND1 HIS A 86 " 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 988 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 12.0% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'L' and resid 28 through 31 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.796A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.657A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.762A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'H' and resid 201 through 204 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 75 removed outlier: 5.829A pdb=" N VAL A 71 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER A 82 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR A 87 " --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 6.569A pdb=" N ILE A 100 " --> pdb=" O ARG A 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.707A pdb=" N ILE A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 129 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.438A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.567A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.680A pdb=" N PHE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.370A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.080A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.080A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 151 through 154 187 hydrogen bonds defined for protein. 438 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: 0.66 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 842 1.33 - 1.45: 978 1.45 - 1.57: 2335 1.57 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 4172 Sorted by residual: bond pdb=" N HIS A 86 " pdb=" CA HIS A 86 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.22e-02 6.72e+03 9.82e+00 bond pdb=" CA GLU H 148 " pdb=" C GLU H 148 " ideal model delta sigma weight residual 1.522 1.553 -0.031 1.26e-02 6.30e+03 6.20e+00 bond pdb=" CG ASP H 86 " pdb=" OD2 ASP H 86 " ideal model delta sigma weight residual 1.249 1.203 0.046 1.90e-02 2.77e+03 5.75e+00 bond pdb=" NE ARG L 54 " pdb=" CZ ARG L 54 " ideal model delta sigma weight residual 1.326 1.352 -0.026 1.10e-02 8.26e+03 5.52e+00 bond pdb=" CD GLU A 152 " pdb=" OE1 GLU A 152 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 ... (remaining 4167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 5296 2.35 - 4.69: 304 4.69 - 7.04: 58 7.04 - 9.38: 4 9.38 - 11.73: 4 Bond angle restraints: 5666 Sorted by residual: angle pdb=" CB HIS A 86 " pdb=" CG HIS A 86 " pdb=" CD2 HIS A 86 " ideal model delta sigma weight residual 131.20 119.89 11.31 1.30e+00 5.92e-01 7.56e+01 angle pdb=" C HIS A 83 " pdb=" CA HIS A 83 " pdb=" CB HIS A 83 " ideal model delta sigma weight residual 111.82 100.67 11.15 1.38e+00 5.25e-01 6.52e+01 angle pdb=" CB HIS A 86 " pdb=" CG HIS A 86 " pdb=" ND1 HIS A 86 " ideal model delta sigma weight residual 122.70 134.43 -11.73 1.50e+00 4.44e-01 6.11e+01 angle pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta sigma weight residual 120.03 127.41 -7.38 9.90e-01 1.02e+00 5.56e+01 angle pdb=" C GLY H 118 " pdb=" N PRO H 119 " pdb=" CA PRO H 119 " ideal model delta sigma weight residual 119.85 127.22 -7.37 1.01e+00 9.80e-01 5.32e+01 ... (remaining 5661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 2405 15.65 - 31.30: 68 31.30 - 46.95: 23 46.95 - 62.60: 13 62.60 - 78.25: 6 Dihedral angle restraints: 2515 sinusoidal: 972 harmonic: 1543 Sorted by residual: dihedral pdb=" C HIS A 83 " pdb=" N HIS A 83 " pdb=" CA HIS A 83 " pdb=" CB HIS A 83 " ideal model delta harmonic sigma weight residual -122.60 -110.12 -12.48 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -123.92 37.92 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 57.64 35.36 1 1.00e+01 1.00e-02 1.77e+01 ... (remaining 2512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 459 0.062 - 0.124: 153 0.124 - 0.186: 23 0.186 - 0.248: 2 0.248 - 0.310: 2 Chirality restraints: 639 Sorted by residual: chirality pdb=" CA HIS A 83 " pdb=" N HIS A 83 " pdb=" C HIS A 83 " pdb=" CB HIS A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA ILE H 52 " pdb=" N ILE H 52 " pdb=" C ILE H 52 " pdb=" CB ILE H 52 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA VAL A 94 " pdb=" N VAL A 94 " pdb=" C VAL A 94 " pdb=" CB VAL A 94 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 636 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 140 " 0.034 2.00e-02 2.50e+03 1.78e-02 6.34e+00 pdb=" CG TYR L 140 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 140 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR L 140 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR L 140 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 140 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR L 140 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 140 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 36 " 0.026 2.00e-02 2.50e+03 1.49e-02 4.47e+00 pdb=" CG TYR L 36 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR L 36 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR L 36 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 36 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR L 36 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR L 36 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 36 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 32 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C PHE H 32 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE H 32 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA H 33 " 0.011 2.00e-02 2.50e+03 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1790 2.93 - 3.43: 3324 3.43 - 3.92: 6450 3.92 - 4.41: 7131 4.41 - 4.90: 12145 Nonbonded interactions: 30840 Sorted by model distance: nonbonded pdb=" O SER H 130 " pdb=" OG1 THR H 131 " model vdw 2.442 3.040 nonbonded pdb=" O HIS A 83 " pdb=" CB HIS A 83 " model vdw 2.473 2.752 nonbonded pdb=" NE2 GLN L 90 " pdb=" OG1 THR L 97 " model vdw 2.504 3.120 nonbonded pdb=" OG1 THR L 29 " pdb=" NE2 GLN L 92 " model vdw 2.509 3.120 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.562 3.040 ... (remaining 30835 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.350 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.720 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.012 0.287 4179 Z= 0.641 Angle : 1.303 11.726 5674 Z= 0.887 Chirality : 0.062 0.310 639 Planarity : 0.006 0.031 730 Dihedral : 10.452 78.251 1515 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.44 % Allowed : 0.88 % Favored : 98.68 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 11.54 % 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: 3.58 (0.39), residues: 526 helix: -1.91 (0.67), residues: 27 sheet: 2.53 (0.35), residues: 214 loop : 3.00 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 45 TYR 0.034 0.005 TYR L 140 PHE 0.022 0.004 PHE L 98 TRP 0.017 0.004 TRP L 35 HIS 0.008 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.01105 / 0.61 ( 4172) covalent geometry : angle 1.29437 / 0.88 ( 5666) SS BOND : bond 0.08074 / 3.96 ( 4) SS BOND : angle 4.14135 / 2.56 ( 8) hydrogen bonds : bond 0.18017 / 12.94 ( 165) hydrogen bonds : angle 8.26333 / 5.66 ( 438) metal coordination : bond 0.18789 / 9.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 117 time to evaluate : 0.165 Fit side-chains REVERT: H 69 ILE cc_start: 0.8494 (mt) cc_final: 0.8241 (mt) REVERT: H 204 ASN cc_start: 0.8041 (m-40) cc_final: 0.7797 (m-40) outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 0.0892 time to fit residues: 12.7087 Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 27 GLN L 152 ASN L 158 ASN H 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.084571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.065099 restraints weight = 9457.096| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.29 r_work: 0.2701 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4179 Z= 0.175 Angle : 0.712 14.425 5674 Z= 0.374 Chirality : 0.049 0.161 639 Planarity : 0.006 0.040 730 Dihedral : 5.594 39.440 576 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.64 % Allowed : 7.71 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 2.79 (0.37), residues: 526 helix: 0.03 (0.99), residues: 24 sheet: 2.34 (0.33), residues: 227 loop : 1.78 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.017 0.002 TYR H 145 PHE 0.016 0.002 PHE L 83 TRP 0.010 0.002 TRP H 36 HIS 0.006 0.002 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 4172) covalent geometry : angle 0.71018 / 0.37 ( 5666) SS BOND : bond 0.00873 / 0.43 ( 4) SS BOND : angle 1.45504 / 1.11 ( 8) hydrogen bonds : bond 0.03868 / 2.83 ( 165) hydrogen bonds : angle 6.15353 / 4.37 ( 438) metal coordination : bond 0.00762 / 0.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: H 204 ASN cc_start: 0.8611 (m-40) cc_final: 0.8400 (m110) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.0937 time to fit residues: 9.4917 Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 206 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS H 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.062711 restraints weight = 9454.365| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.08 r_work: 0.2601 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.029 1.838 4179 Z= 0.960 Angle : 0.639 13.510 5674 Z= 0.339 Chirality : 0.047 0.139 639 Planarity : 0.005 0.041 730 Dihedral : 5.136 23.150 576 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.86 % Allowed : 10.13 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 2.15 (0.36), residues: 526 helix: 0.83 (1.14), residues: 22 sheet: 2.10 (0.33), residues: 224 loop : 1.03 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 61 TYR 0.014 0.002 TYR H 145 PHE 0.015 0.002 PHE H 91 TRP 0.011 0.002 TRP H 36 HIS 0.003 0.001 HIS H 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 4172) covalent geometry : angle 0.63714 / 0.34 ( 5666) SS BOND : bond 0.00662 / 0.33 ( 4) SS BOND : angle 1.46184 / 1.05 ( 8) hydrogen bonds : bond 0.03919 / 2.87 ( 165) hydrogen bonds : angle 5.76550 / 4.08 ( 438) metal coordination : bond 1.06094 / 50.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: L 126 LYS cc_start: 0.9138 (mmmm) cc_final: 0.8870 (ttmt) REVERT: L 209 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7343 (t80) outliers start: 13 outliers final: 6 residues processed: 75 average time/residue: 0.1008 time to fit residues: 9.0387 Evaluate side-chains 65 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 209 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 206 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 137 ASN H 171 GLN H 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.061326 restraints weight = 9226.694| |-----------------------------------------------------------------------------| r_work (start): 0.2662 rms_B_bonded: 2.18 r_work: 0.2577 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2471 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 4179 Z= 0.174 Angle : 0.644 12.756 5674 Z= 0.332 Chirality : 0.047 0.148 639 Planarity : 0.005 0.044 730 Dihedral : 5.053 21.170 574 Min Nonbonded Distance : 1.368 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.64 % Allowed : 13.22 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 1.76 (0.36), residues: 526 helix: 0.94 (1.12), residues: 22 sheet: 2.02 (0.33), residues: 219 loop : 0.56 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 83 TYR 0.014 0.002 TYR H 145 PHE 0.013 0.002 PHE H 91 TRP 0.009 0.002 TRP H 36 HIS 0.010 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 ( 4172) covalent geometry : angle 0.64226 / 0.33 ( 5666) SS BOND : bond 0.00558 / 0.27 ( 4) SS BOND : angle 1.24565 / 0.97 ( 8) hydrogen bonds : bond 0.03591 / 2.64 ( 165) hydrogen bonds : angle 5.65300 / 4.02 ( 438) metal coordination : bond 0.08868 / 4.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 126 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8883 (ttmt) REVERT: L 209 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7329 (t80) REVERT: H 56 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8736 (p) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.0843 time to fit residues: 6.7909 Evaluate side-chains 67 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 209 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 199 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.0040 overall best weight: 0.1870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 137 ASN L 158 ASN H 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.083418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.063949 restraints weight = 8909.787| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.24 r_work: 0.2677 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 4179 Z= 0.111 Angle : 0.542 11.652 5674 Z= 0.281 Chirality : 0.044 0.132 639 Planarity : 0.005 0.037 730 Dihedral : 4.329 17.903 574 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.98 % Allowed : 14.10 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 1.81 (0.37), residues: 526 helix: 0.85 (1.12), residues: 23 sheet: 1.96 (0.34), residues: 220 loop : 0.70 (0.38), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.013 0.001 TYR L 49 PHE 0.008 0.001 PHE L 139 TRP 0.007 0.001 TRP H 36 HIS 0.014 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 4172) covalent geometry : angle 0.54112 / 0.28 ( 5666) SS BOND : bond 0.00405 / 0.20 ( 4) SS BOND : angle 0.83523 / 0.59 ( 8) hydrogen bonds : bond 0.02716 / 2.01 ( 165) hydrogen bonds : angle 5.08426 / 3.64 ( 438) metal coordination : bond 0.06825 / 3.38 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 126 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8857 (ttmt) outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.1141 time to fit residues: 9.4283 Evaluate side-chains 68 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain H residue 47 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.078171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.059145 restraints weight = 9369.483| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.21 r_work: 0.2516 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 4179 Z= 0.226 Angle : 0.733 12.893 5674 Z= 0.377 Chirality : 0.049 0.160 639 Planarity : 0.005 0.050 730 Dihedral : 5.318 21.281 574 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.08 % Allowed : 13.44 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 1.35 (0.36), residues: 526 helix: 0.92 (1.12), residues: 22 sheet: 1.81 (0.34), residues: 217 loop : 0.21 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 61 TYR 0.019 0.002 TYR H 145 PHE 0.016 0.003 PHE H 91 TRP 0.010 0.003 TRP H 36 HIS 0.013 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 ( 4172) covalent geometry : angle 0.71394 / 0.37 ( 5666) SS BOND : bond 0.01023 / 0.51 ( 4) SS BOND : angle 4.43932 / 2.53 ( 8) hydrogen bonds : bond 0.04141 / 3.02 ( 165) hydrogen bonds : angle 5.86016 / 4.13 ( 438) metal coordination : bond 0.07701 / 3.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.8888 (mmm-85) cc_final: 0.8613 (tpt-90) REVERT: L 126 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8930 (ttmt) REVERT: L 209 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7575 (t80) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.1289 time to fit residues: 10.9686 Evaluate side-chains 77 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 209 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.0010 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 158 ASN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.080112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.061190 restraints weight = 9243.900| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.17 r_work: 0.2564 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 4179 Z= 0.151 Angle : 0.632 12.309 5674 Z= 0.325 Chirality : 0.046 0.137 639 Planarity : 0.005 0.045 730 Dihedral : 4.919 20.466 574 Min Nonbonded Distance : 1.345 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.64 % Allowed : 14.10 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 1.40 (0.36), residues: 526 helix: 1.01 (1.14), residues: 22 sheet: 1.77 (0.34), residues: 217 loop : 0.30 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.013 0.002 TYR H 145 PHE 0.010 0.002 PHE H 91 TRP 0.009 0.001 TRP H 36 HIS 0.013 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 4172) covalent geometry : angle 0.62160 / 0.32 ( 5666) SS BOND : bond 0.00748 / 0.37 ( 4) SS BOND : angle 3.05731 / 1.78 ( 8) hydrogen bonds : bond 0.03349 / 2.45 ( 165) hydrogen bonds : angle 5.49968 / 3.89 ( 438) metal coordination : bond 0.07054 / 3.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8517 (tpt-90) REVERT: L 126 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8917 (ttmt) REVERT: L 209 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7278 (t80) outliers start: 12 outliers final: 9 residues processed: 70 average time/residue: 0.1226 time to fit residues: 9.8880 Evaluate side-chains 72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain L residue 209 PHE Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 17 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 158 ASN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.081239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.062527 restraints weight = 9033.420| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.13 r_work: 0.2606 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.7727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 4179 Z= 0.125 Angle : 0.583 11.933 5674 Z= 0.300 Chirality : 0.045 0.134 639 Planarity : 0.005 0.040 730 Dihedral : 4.586 18.384 574 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.98 % Allowed : 14.98 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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 (0.37), residues: 526 helix: 1.05 (1.16), residues: 22 sheet: 1.82 (0.34), residues: 217 loop : 0.47 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.013 0.001 TYR L 49 PHE 0.008 0.001 PHE L 98 TRP 0.010 0.001 TRP H 36 HIS 0.014 0.001 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 4172) covalent geometry : angle 0.57745 / 0.30 ( 5666) SS BOND : bond 0.00583 / 0.29 ( 4) SS BOND : angle 2.27574 / 1.36 ( 8) hydrogen bonds : bond 0.02960 / 2.18 ( 165) hydrogen bonds : angle 5.31670 / 3.78 ( 438) metal coordination : bond 0.06649 / 3.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.9144 (mptt) cc_final: 0.8911 (mptt) REVERT: A 139 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8206 (mmtt) REVERT: L 24 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8510 (tpt-90) REVERT: L 126 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8899 (ttmt) outliers start: 9 outliers final: 8 residues processed: 69 average time/residue: 0.1196 time to fit residues: 9.5225 Evaluate side-chains 72 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 55 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 158 ASN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.081062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.062160 restraints weight = 9290.152| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 2.14 r_work: 0.2594 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2492 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.7780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 4179 Z= 0.129 Angle : 0.584 11.949 5674 Z= 0.302 Chirality : 0.045 0.134 639 Planarity : 0.005 0.042 730 Dihedral : 4.598 19.167 574 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.98 % Allowed : 14.54 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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 (0.37), residues: 526 helix: 0.92 (1.16), residues: 22 sheet: 1.79 (0.34), residues: 218 loop : 0.50 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.012 0.001 TYR L 49 PHE 0.010 0.001 PHE H 91 TRP 0.010 0.001 TRP H 36 HIS 0.014 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 4172) covalent geometry : angle 0.57802 / 0.30 ( 5666) SS BOND : bond 0.00617 / 0.30 ( 4) SS BOND : angle 2.28500 / 1.38 ( 8) hydrogen bonds : bond 0.03075 / 2.26 ( 165) hydrogen bonds : angle 5.31676 / 3.78 ( 438) metal coordination : bond 0.06656 / 3.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8211 (mmtt) REVERT: L 24 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8451 (tpt-90) outliers start: 9 outliers final: 9 residues processed: 68 average time/residue: 0.1131 time to fit residues: 8.8300 Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 158 ASN H 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.060533 restraints weight = 9086.333| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.16 r_work: 0.2556 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2453 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.7827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 4179 Z= 0.157 Angle : 0.628 12.120 5674 Z= 0.324 Chirality : 0.046 0.137 639 Planarity : 0.005 0.044 730 Dihedral : 4.874 19.914 574 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.20 % Allowed : 14.54 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 1.34 (0.37), residues: 526 helix: 0.84 (1.16), residues: 22 sheet: 1.69 (0.34), residues: 218 loop : 0.31 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.014 0.002 TYR H 145 PHE 0.013 0.002 PHE H 91 TRP 0.008 0.002 TRP H 36 HIS 0.014 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 ( 4172) covalent geometry : angle 0.62011 / 0.32 ( 5666) SS BOND : bond 0.00703 / 0.35 ( 4) SS BOND : angle 2.63488 / 1.62 ( 8) hydrogen bonds : bond 0.03477 / 2.55 ( 165) hydrogen bonds : angle 5.52676 / 3.91 ( 438) metal coordination : bond 0.06833 / 3.39 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8232 (mmtt) REVERT: L 24 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8505 (tpt-90) outliers start: 10 outliers final: 10 residues processed: 67 average time/residue: 0.0984 time to fit residues: 7.6751 Evaluate side-chains 73 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 86 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 151 ASP Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 158 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.079833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.060754 restraints weight = 9218.002| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.19 r_work: 0.2558 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.7879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 4179 Z= 0.151 Angle : 0.619 12.261 5674 Z= 0.320 Chirality : 0.046 0.137 639 Planarity : 0.005 0.043 730 Dihedral : 4.812 20.074 574 Min Nonbonded Distance : 1.352 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.76 % Allowed : 14.98 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % 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: 1.31 (0.37), residues: 526 helix: 0.75 (1.14), residues: 22 sheet: 1.68 (0.34), residues: 218 loop : 0.29 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.013 0.002 TYR H 145 PHE 0.012 0.002 PHE H 91 TRP 0.009 0.002 TRP H 36 HIS 0.014 0.002 HIS A 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4172) covalent geometry : angle 0.61218 / 0.32 ( 5666) SS BOND : bond 0.00668 / 0.33 ( 4) SS BOND : angle 2.47362 / 1.52 ( 8) hydrogen bonds : bond 0.03349 / 2.45 ( 165) hydrogen bonds : angle 5.46436 / 3.87 ( 438) metal coordination : bond 0.06730 / 3.33 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.91 seconds wall clock time: 21 minutes 30.14 seconds (1290.14 seconds total)