Starting phenix.real_space_refine on Thu Sep 10 19:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23wm_69321/09_2026/23wm_69321.cif Found real_map, /net/cci-nas-00/data/ceres_data/23wm_69321/09_2026/23wm_69321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23wm_69321/09_2026/23wm_69321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23wm_69321/09_2026/23wm_69321.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23wm_69321/09_2026/23wm_69321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23wm_69321/09_2026/23wm_69321.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 4 5.16 5 C 1364 2.51 5 N 351 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2046 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 69 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} 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: 0.82, per 1000 atoms: 0.39 Number of scatterers: 2116 At special positions: 0 Unit cell: (67.26, 62.7, 55.29, 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 4 16.00 O 396 8.00 N 351 7.00 C 1364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 82.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 114 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 118 " 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 494 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 1 sheets defined 68.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 6 through 14 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 40 through 49 Processing helix chain 'A' and resid 58 through 66 removed outlier: 3.735A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 106 through 124 removed outlier: 4.081A pdb=" N LEU A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.629A pdb=" N LEU A 130 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 150 removed outlier: 3.640A pdb=" N TYR A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 169 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.502A pdb=" N VAL A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 201 through 219 removed outlier: 3.675A pdb=" N ALA A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 240 through 259 removed outlier: 3.804A pdb=" N LYS A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.548A pdb=" N LEU A 56 " --> pdb=" O VAL A 18 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 354 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: 0.30 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 695 1.34 - 1.46: 322 1.46 - 1.57: 1122 1.57 - 1.69: 0 1.69 - 1.80: 8 Bond restraints: 2147 Sorted by residual: bond pdb=" C ILE A 101 " pdb=" O ILE A 101 " ideal model delta sigma weight residual 1.231 1.240 -0.009 1.02e-02 9.61e+03 7.40e-01 bond pdb=" CA LYS A 95 " pdb=" C LYS A 95 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 7.13e-01 bond pdb=" N ILE A 190 " pdb=" CA ILE A 190 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.25e-02 6.40e+03 4.96e-01 bond pdb=" CB ARG A 184 " pdb=" CG ARG A 184 " ideal model delta sigma weight residual 1.520 1.537 -0.017 3.00e-02 1.11e+03 3.12e-01 bond pdb=" CG PRO A 176 " pdb=" CD PRO A 176 " ideal model delta sigma weight residual 1.503 1.484 0.019 3.40e-02 8.65e+02 3.12e-01 ... (remaining 2142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 2828 1.72 - 3.44: 57 3.44 - 5.16: 6 5.16 - 6.87: 1 6.87 - 8.59: 1 Bond angle restraints: 2893 Sorted by residual: angle pdb=" C ASN A 189 " pdb=" N ILE A 190 " pdb=" CA ILE A 190 " ideal model delta sigma weight residual 121.97 126.74 -4.77 1.80e+00 3.09e-01 7.04e+00 angle pdb=" CA LEU A 146 " pdb=" CB LEU A 146 " pdb=" CG LEU A 146 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.03e+00 angle pdb=" CA LYS A 95 " pdb=" C LYS A 95 " pdb=" N ARG A 96 " ideal model delta sigma weight residual 114.17 117.37 -3.20 1.45e+00 4.76e-01 4.87e+00 angle pdb=" CB MET A 252 " pdb=" CG MET A 252 " pdb=" SD MET A 252 " ideal model delta sigma weight residual 112.70 106.22 6.48 3.00e+00 1.11e-01 4.67e+00 angle pdb=" C ASP A 122 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta sigma weight residual 122.63 120.30 2.33 1.19e+00 7.06e-01 3.84e+00 ... (remaining 2888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 1097 17.22 - 34.45: 145 34.45 - 51.67: 59 51.67 - 68.89: 13 68.89 - 86.12: 3 Dihedral angle restraints: 1317 sinusoidal: 548 harmonic: 769 Sorted by residual: dihedral pdb=" CB GLU A 240 " pdb=" CG GLU A 240 " pdb=" CD GLU A 240 " pdb=" OE1 GLU A 240 " ideal model delta sinusoidal sigma weight residual 0.00 -86.12 86.12 1 3.00e+01 1.11e-03 9.94e+00 dihedral pdb=" CG ARG A 229 " pdb=" CD ARG A 229 " pdb=" NE ARG A 229 " pdb=" CZ ARG A 229 " ideal model delta sinusoidal sigma weight residual -90.00 -132.82 42.82 2 1.50e+01 4.44e-03 9.85e+00 dihedral pdb=" CG ARG A 109 " pdb=" CD ARG A 109 " pdb=" NE ARG A 109 " pdb=" CZ ARG A 109 " ideal model delta sinusoidal sigma weight residual 180.00 137.97 42.03 2 1.50e+01 4.44e-03 9.56e+00 ... (remaining 1314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 198 0.026 - 0.052: 86 0.052 - 0.078: 28 0.078 - 0.104: 12 0.104 - 0.130: 5 Chirality restraints: 329 Sorted by residual: chirality pdb=" CA ILE A 39 " pdb=" N ILE A 39 " pdb=" C ILE A 39 " pdb=" CB ILE A 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ASP A 122 " pdb=" N ASP A 122 " pdb=" C ASP A 122 " pdb=" CB ASP A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 chirality pdb=" CA ILE A 54 " pdb=" N ILE A 54 " pdb=" C ILE A 54 " pdb=" CB ILE A 54 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 326 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 14 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" CG ASP A 14 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 14 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 14 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 69 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO A 70 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 39 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A 40 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 40 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 40 " -0.017 5.00e-02 4.00e+02 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 14 2.57 - 3.15: 1563 3.15 - 3.73: 3038 3.73 - 4.32: 4059 4.32 - 4.90: 7097 Nonbonded interactions: 15771 Sorted by model distance: nonbonded pdb=" OE2 GLU A 204 " pdb="ZN ZN A1601 " model vdw 1.985 2.230 nonbonded pdb=" OE1 GLU A 204 " pdb="ZN ZN A1601 " model vdw 2.195 2.230 nonbonded pdb=" CD GLU A 204 " pdb="ZN ZN A1601 " model vdw 2.308 2.460 nonbonded pdb=" O ASN A 189 " pdb=" N VAL A 191 " model vdw 2.357 3.120 nonbonded pdb=" CG1 VAL B 18 " pdb="ZN ZN A1601 " model vdw 2.381 2.650 ... (remaining 15766 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: 6.930 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.680 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.003 0.019 2149 Z= 0.138 Angle : 0.583 8.594 2893 Z= 0.309 Chirality : 0.038 0.130 329 Planarity : 0.004 0.035 369 Dihedral : 18.722 86.117 823 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.05 % Favored : 91.19 % Rotamer: Outliers : 0.45 % Allowed : 29.28 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.53), residues: 261 helix: 1.15 (0.42), residues: 168 sheet: 1.65 (1.22), residues: 12 loop : -2.93 (0.58), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.004 0.001 TYR A 213 PHE 0.009 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.004 0.002 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 2147) covalent geometry : angle 0.58300 / 0.31 ( 2893) hydrogen bonds : bond 0.14054 / 9.46 ( 119) hydrogen bonds : angle 4.63335 / 3.46 ( 354) metal coordination : bond 0.00374 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.086 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.0628 time to fit residues: 1.7858 Evaluate side-chains 22 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.173895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136470 restraints weight = 2147.223| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.21 r_work: 0.3371 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2149 Z= 0.114 Angle : 0.501 5.319 2893 Z= 0.265 Chirality : 0.037 0.126 329 Planarity : 0.004 0.042 369 Dihedral : 3.711 14.801 290 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.28 % Favored : 91.95 % Rotamer: Outliers : 3.15 % Allowed : 28.38 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.53), residues: 261 helix: 1.22 (0.41), residues: 175 sheet: 1.74 (1.22), residues: 12 loop : -3.19 (0.60), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.008 0.001 TYR A 69 PHE 0.008 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 2147) covalent geometry : angle 0.50094 / 0.26 ( 2893) hydrogen bonds : bond 0.04130 / 2.70 ( 119) hydrogen bonds : angle 3.71244 / 2.76 ( 354) metal coordination : bond 0.00291 / 0.18 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.112 Fit side-chains REVERT: A 61 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5417 (mt-10) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 0.0649 time to fit residues: 2.1424 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 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 = 0.3944 r_free = 0.3944 target = 0.171548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134475 restraints weight = 2132.897| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.21 r_work: 0.3343 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2149 Z= 0.153 Angle : 0.559 6.291 2893 Z= 0.289 Chirality : 0.039 0.127 329 Planarity : 0.004 0.045 369 Dihedral : 3.785 14.469 290 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.77 % Allowed : 8.05 % Favored : 91.19 % Rotamer: Outliers : 3.15 % Allowed : 28.83 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.52), residues: 261 helix: 1.12 (0.40), residues: 175 sheet: 1.44 (1.24), residues: 12 loop : -3.26 (0.59), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.006 0.001 TYR A 69 PHE 0.010 0.002 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 2147) covalent geometry : angle 0.55878 / 0.29 ( 2893) hydrogen bonds : bond 0.04977 / 3.24 ( 119) hydrogen bonds : angle 3.74883 / 2.74 ( 354) metal coordination : bond 0.00379 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.081 Fit side-chains REVERT: A 61 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5505 (mt-10) REVERT: A 186 MET cc_start: 0.3511 (pp-130) cc_final: 0.2811 (pp-130) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.0524 time to fit residues: 1.8357 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.170171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133081 restraints weight = 2123.393| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.21 r_work: 0.3333 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2149 Z= 0.172 Angle : 0.589 6.938 2893 Z= 0.301 Chirality : 0.040 0.131 329 Planarity : 0.004 0.046 369 Dihedral : 3.932 14.600 290 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.66 % Favored : 91.57 % Rotamer: Outliers : 2.70 % Allowed : 28.83 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.52), residues: 261 helix: 1.03 (0.40), residues: 174 sheet: 1.25 (1.28), residues: 12 loop : -3.34 (0.58), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.006 0.001 TYR A 69 PHE 0.011 0.002 PHE A 255 TRP 0.003 0.001 TRP A 38 HIS 0.003 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 2147) covalent geometry : angle 0.58906 / 0.30 ( 2893) hydrogen bonds : bond 0.05271 / 3.43 ( 119) hydrogen bonds : angle 3.80950 / 2.77 ( 354) metal coordination : bond 0.00410 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.090 Fit side-chains REVERT: A 61 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5497 (mt-10) REVERT: A 186 MET cc_start: 0.3514 (pp-130) cc_final: 0.2878 (pp-130) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.0574 time to fit residues: 1.7911 Evaluate side-chains 25 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.0270 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.175664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138939 restraints weight = 2124.575| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.15 r_work: 0.3407 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2149 Z= 0.101 Angle : 0.513 6.635 2893 Z= 0.265 Chirality : 0.037 0.129 329 Planarity : 0.004 0.044 369 Dihedral : 3.660 14.918 290 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.72 % Rotamer: Outliers : 2.70 % Allowed : 27.93 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.53), residues: 261 helix: 1.46 (0.40), residues: 174 sheet: 1.26 (1.30), residues: 12 loop : -3.07 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.005 0.001 TYR A 69 PHE 0.008 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 2147) covalent geometry : angle 0.51334 / 0.26 ( 2893) hydrogen bonds : bond 0.03479 / 2.27 ( 119) hydrogen bonds : angle 3.48832 / 2.56 ( 354) metal coordination : bond 0.00209 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.053 Fit side-chains REVERT: A 163 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7063 (ttpp) REVERT: A 186 MET cc_start: 0.3709 (pp-130) cc_final: 0.3169 (pp-130) outliers start: 6 outliers final: 4 residues processed: 26 average time/residue: 0.0636 time to fit residues: 2.0109 Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.171664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134888 restraints weight = 2077.124| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.13 r_work: 0.3360 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2149 Z= 0.150 Angle : 0.559 6.968 2893 Z= 0.285 Chirality : 0.039 0.130 329 Planarity : 0.004 0.045 369 Dihedral : 3.784 13.858 290 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.90 % Favored : 92.34 % Rotamer: Outliers : 3.15 % Allowed : 27.03 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.52), residues: 261 helix: 1.24 (0.39), residues: 174 sheet: 1.30 (1.32), residues: 12 loop : -3.12 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.005 0.001 TYR A 213 PHE 0.010 0.002 PHE A 255 TRP 0.003 0.001 TRP A 38 HIS 0.003 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 2147) covalent geometry : angle 0.55943 / 0.28 ( 2893) hydrogen bonds : bond 0.04809 / 3.13 ( 119) hydrogen bonds : angle 3.76233 / 2.76 ( 354) metal coordination : bond 0.00374 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.082 Fit side-chains REVERT: A 61 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5490 (mt-10) REVERT: A 163 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6922 (ttpp) REVERT: A 186 MET cc_start: 0.3544 (pp-130) cc_final: 0.3035 (pp-130) outliers start: 7 outliers final: 5 residues processed: 28 average time/residue: 0.0604 time to fit residues: 2.0354 Evaluate side-chains 29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.172441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135523 restraints weight = 2103.836| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.16 r_work: 0.3366 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2149 Z= 0.130 Angle : 0.535 7.206 2893 Z= 0.271 Chirality : 0.038 0.127 329 Planarity : 0.004 0.045 369 Dihedral : 3.722 13.965 290 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.90 % Favored : 92.34 % Rotamer: Outliers : 3.60 % Allowed : 26.58 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.52), residues: 261 helix: 1.30 (0.39), residues: 174 sheet: 1.31 (1.32), residues: 12 loop : -3.01 (0.64), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.004 0.001 TYR A 69 PHE 0.009 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 2147) covalent geometry : angle 0.53472 / 0.27 ( 2893) hydrogen bonds : bond 0.04357 / 2.84 ( 119) hydrogen bonds : angle 3.66087 / 2.67 ( 354) metal coordination : bond 0.00322 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.080 Fit side-chains REVERT: A 61 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5460 (mt-10) REVERT: A 163 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6916 (ttpp) REVERT: A 186 MET cc_start: 0.3580 (pp-130) cc_final: 0.3091 (pp-130) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.0670 time to fit residues: 2.2450 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.171574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.134892 restraints weight = 2095.414| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.13 r_work: 0.3367 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2149 Z= 0.135 Angle : 0.540 7.439 2893 Z= 0.274 Chirality : 0.039 0.127 329 Planarity : 0.004 0.045 369 Dihedral : 3.738 13.646 290 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.72 % Rotamer: Outliers : 3.15 % Allowed : 26.13 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.53), residues: 261 helix: 1.20 (0.39), residues: 176 sheet: 1.25 (1.34), residues: 12 loop : -2.92 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.004 0.001 TYR A 230 PHE 0.009 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 2147) covalent geometry : angle 0.54027 / 0.27 ( 2893) hydrogen bonds : bond 0.04493 / 2.93 ( 119) hydrogen bonds : angle 3.67348 / 2.68 ( 354) metal coordination : bond 0.00342 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.074 Fit side-chains REVERT: A 61 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5408 (mt-10) REVERT: A 163 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6935 (ttpp) REVERT: A 186 MET cc_start: 0.3593 (pp-130) cc_final: 0.3107 (pp-130) outliers start: 7 outliers final: 5 residues processed: 27 average time/residue: 0.0577 time to fit residues: 1.8790 Evaluate side-chains 28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.170237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133367 restraints weight = 2133.336| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.14 r_work: 0.3349 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2149 Z= 0.165 Angle : 0.570 7.552 2893 Z= 0.288 Chirality : 0.040 0.134 329 Planarity : 0.004 0.045 369 Dihedral : 3.830 13.595 290 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.28 % Favored : 91.95 % Rotamer: Outliers : 4.05 % Allowed : 25.23 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.52), residues: 261 helix: 1.06 (0.39), residues: 176 sheet: 1.23 (1.35), residues: 12 loop : -2.99 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.005 0.001 TYR A 213 PHE 0.011 0.002 PHE A 255 TRP 0.003 0.001 TRP A 38 HIS 0.003 0.002 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 ( 2147) covalent geometry : angle 0.56988 / 0.29 ( 2893) hydrogen bonds : bond 0.05064 / 3.30 ( 119) hydrogen bonds : angle 3.77345 / 2.74 ( 354) metal coordination : bond 0.00424 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.080 Fit side-chains REVERT: A 61 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5496 (mt-10) REVERT: A 163 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.6995 (ttpp) REVERT: A 186 MET cc_start: 0.3688 (pp-130) cc_final: 0.3146 (pp-130) outliers start: 9 outliers final: 6 residues processed: 27 average time/residue: 0.0575 time to fit residues: 1.8778 Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 234 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 17 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.169821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133806 restraints weight = 2116.619| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.11 r_work: 0.3379 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2149 Z= 0.120 Angle : 0.524 7.686 2893 Z= 0.265 Chirality : 0.038 0.128 329 Planarity : 0.004 0.045 369 Dihedral : 3.682 14.031 290 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.72 % Rotamer: Outliers : 2.70 % Allowed : 26.58 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.53), residues: 261 helix: 1.30 (0.39), residues: 175 sheet: 1.27 (1.36), residues: 12 loop : -2.96 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.004 0.001 TYR A 230 PHE 0.009 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 2147) covalent geometry : angle 0.52435 / 0.26 ( 2893) hydrogen bonds : bond 0.04115 / 2.69 ( 119) hydrogen bonds : angle 3.60064 / 2.63 ( 354) metal coordination : bond 0.00315 / 0.19 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.078 Fit side-chains REVERT: A 163 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6916 (ttpp) REVERT: A 186 MET cc_start: 0.3698 (pp-130) cc_final: 0.3258 (pp-130) outliers start: 6 outliers final: 5 residues processed: 25 average time/residue: 0.0624 time to fit residues: 1.9451 Evaluate side-chains 26 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.173686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.136767 restraints weight = 2146.212| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.16 r_work: 0.3380 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2149 Z= 0.112 Angle : 0.519 7.731 2893 Z= 0.261 Chirality : 0.038 0.137 329 Planarity : 0.004 0.044 369 Dihedral : 3.578 13.490 290 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.72 % Rotamer: Outliers : 2.70 % Allowed : 27.03 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.53), residues: 261 helix: 1.40 (0.40), residues: 175 sheet: 1.29 (1.37), residues: 12 loop : -2.89 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 96 TYR 0.004 0.001 TYR A 230 PHE 0.009 0.001 PHE A 255 TRP 0.002 0.001 TRP A 38 HIS 0.003 0.002 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 2147) covalent geometry : angle 0.51941 / 0.26 ( 2893) hydrogen bonds : bond 0.03875 / 2.54 ( 119) hydrogen bonds : angle 3.52671 / 2.58 ( 354) metal coordination : bond 0.00320 / 0.19 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 768.45 seconds wall clock time: 13 minutes 51.33 seconds (831.33 seconds total)