Starting phenix.real_space_refine on Thu Sep 10 19:48:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23wo_69323/09_2026/23wo_69323.cif Found real_map, /net/cci-nas-00/data/ceres_data/23wo_69323/09_2026/23wo_69323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23wo_69323/09_2026/23wo_69323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23wo_69323/09_2026/23wo_69323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23wo_69323/09_2026/23wo_69323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23wo_69323/09_2026/23wo_69323.map" } resolution = 3.5 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= 0.004 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 6 5.16 5 C 1053 2.51 5 N 297 2.21 5 O 309 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 1666 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1598 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 67 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} 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: 0.50, per 1000 atoms: 0.30 Number of scatterers: 1666 At special positions: 0 Unit cell: (59.85, 53.01, 65.55, 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 6 16.00 O 309 8.00 N 297 7.00 C 1053 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: 0.22 Conformation dependent library (CDL) restraints added in 98.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 93 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 89 " 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 1 sheets defined 62.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.787A pdb=" N ILE A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 79 through 102 Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.534A pdb=" N GLU A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.566A pdb=" N ALA A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 163 through 183 removed outlier: 4.147A pdb=" N ARG A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 183 " --> pdb=" O TYR A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 215 removed outlier: 3.560A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 5.934A pdb=" N LEU A 10 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLU A 73 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA A 12 " --> pdb=" O GLU A 73 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 303 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: 0.12 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 297 1.32 - 1.44: 381 1.44 - 1.56: 998 1.56 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 1688 Sorted by residual: bond pdb=" C HIS A 89 " pdb=" N GLN A 90 " ideal model delta sigma weight residual 1.335 1.277 0.058 1.30e-02 5.92e+03 2.01e+01 bond pdb=" N HIS A 89 " pdb=" CA HIS A 89 " ideal model delta sigma weight residual 1.457 1.412 0.045 1.29e-02 6.01e+03 1.22e+01 bond pdb=" CA HIS A 89 " pdb=" CB HIS A 89 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.69e-02 3.50e+03 1.21e+01 bond pdb=" C GLN A 90 " pdb=" O GLN A 90 " ideal model delta sigma weight residual 1.236 1.199 0.038 1.18e-02 7.18e+03 1.02e+01 bond pdb=" C HIS A 89 " pdb=" O HIS A 89 " ideal model delta sigma weight residual 1.235 1.197 0.038 1.26e-02 6.30e+03 9.02e+00 ... (remaining 1683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 2230 2.33 - 4.67: 46 4.67 - 7.00: 11 7.00 - 9.34: 4 9.34 - 11.67: 2 Bond angle restraints: 2293 Sorted by residual: angle pdb=" N ASP A 64 " pdb=" CA ASP A 64 " pdb=" C ASP A 64 " ideal model delta sigma weight residual 113.72 106.18 7.54 1.52e+00 4.33e-01 2.46e+01 angle pdb=" C ILE A 18 " pdb=" N PRO A 19 " pdb=" CA PRO A 19 " ideal model delta sigma weight residual 119.47 114.28 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" N GLU A 73 " pdb=" CA GLU A 73 " pdb=" C GLU A 73 " ideal model delta sigma weight residual 109.41 115.48 -6.07 1.52e+00 4.33e-01 1.60e+01 angle pdb=" CA GLN A 90 " pdb=" C GLN A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 117.22 121.73 -4.51 1.17e+00 7.31e-01 1.49e+01 angle pdb=" C SER A 13 " pdb=" N SER A 14 " pdb=" CA SER A 14 " ideal model delta sigma weight residual 121.80 131.09 -9.29 2.44e+00 1.68e-01 1.45e+01 ... (remaining 2288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 857 15.75 - 31.50: 115 31.50 - 47.25: 41 47.25 - 63.00: 11 63.00 - 78.76: 4 Dihedral angle restraints: 1028 sinusoidal: 400 harmonic: 628 Sorted by residual: dihedral pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N GLU A 33 " pdb=" CA GLU A 33 " ideal model delta harmonic sigma weight residual -180.00 -150.17 -29.83 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" N LEU A 28 " pdb=" CA LEU A 28 " pdb=" CB LEU A 28 " pdb=" CG LEU A 28 " ideal model delta sinusoidal sigma weight residual -60.00 -118.86 58.86 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA SER A 14 " pdb=" C SER A 14 " pdb=" N PRO A 15 " pdb=" CA PRO A 15 " ideal model delta harmonic sigma weight residual 180.00 164.63 15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 1025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 238 0.060 - 0.119: 29 0.119 - 0.178: 5 0.178 - 0.238: 0 0.238 - 0.297: 2 Chirality restraints: 274 Sorted by residual: chirality pdb=" CG LEU A 45 " pdb=" CB LEU A 45 " pdb=" CD1 LEU A 45 " pdb=" CD2 LEU A 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA GLN A 90 " pdb=" N GLN A 90 " pdb=" C GLN A 90 " pdb=" CB GLN A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL A 72 " pdb=" N VAL A 72 " pdb=" C VAL A 72 " pdb=" CB VAL A 72 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 271 not shown) Planarity restraints: 301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 76 " 0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 77 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 14 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO A 15 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 74 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 75 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " -0.028 5.00e-02 4.00e+02 ... (remaining 298 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 27 2.62 - 3.19: 1506 3.19 - 3.76: 2437 3.76 - 4.33: 3042 4.33 - 4.90: 5098 Nonbonded interactions: 12110 Sorted by model distance: nonbonded pdb=" OE2 GLU A 117 " pdb="ZN ZN A1501 " model vdw 2.056 2.230 nonbonded pdb=" N GLU A 80 " pdb=" OE1 GLU A 80 " model vdw 2.221 3.120 nonbonded pdb=" O ARG A 32 " pdb=" N VAL A 34 " model vdw 2.304 3.120 nonbonded pdb=" O ARG A 76 " pdb=" C PRO A 77 " model vdw 2.372 3.270 nonbonded pdb=" O ALA A 50 " pdb=" N MET A 52 " model vdw 2.395 3.120 ... (remaining 12105 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 5.150 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.950 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:0.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 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 : 0.008 0.189 1690 Z= 0.379 Angle : 0.931 11.672 2293 Z= 0.523 Chirality : 0.048 0.297 274 Planarity : 0.009 0.082 301 Dihedral : 17.496 78.756 622 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 3.69 % Allowed : 9.68 % Favored : 86.64 % Rotamer: Outliers : 1.21 % Allowed : 33.33 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.59), residues: 217 helix: 1.01 (0.46), residues: 133 sheet: -1.86 (1.00), residues: 17 loop : -4.56 (0.68), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.003 0.001 TYR A 179 PHE 0.009 0.002 PHE A 209 TRP 0.019 0.004 TRP A 46 HIS 0.009 0.003 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.32 ( 1688) covalent geometry : angle 0.93134 / 0.52 ( 2293) hydrogen bonds : bond 0.15940 / 11.12 ( 104) hydrogen bonds : angle 6.50496 / 4.52 ( 303) metal coordination : bond 0.17323 / 8.61 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.035 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.0408 time to fit residues: 1.4975 Evaluate side-chains 28 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.187687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.166487 restraints weight = 2213.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.168080 restraints weight = 1632.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.169321 restraints weight = 1338.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.170072 restraints weight = 1181.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.170076 restraints weight = 1073.306| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 1690 Z= 0.175 Angle : 0.722 7.377 2293 Z= 0.379 Chirality : 0.042 0.209 274 Planarity : 0.009 0.084 301 Dihedral : 5.570 34.927 244 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 2.30 % Allowed : 11.06 % Favored : 86.64 % Rotamer: Outliers : 6.67 % Allowed : 30.30 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -0.68 (0.59), residues: 217 helix: 1.24 (0.44), residues: 136 sheet: -0.93 (1.04), residues: 17 loop : -4.28 (0.72), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 47 TYR 0.005 0.001 TYR A 179 PHE 0.010 0.002 PHE A 209 TRP 0.009 0.003 TRP A 46 HIS 0.004 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 1688) covalent geometry : angle 0.72167 / 0.38 ( 2293) hydrogen bonds : bond 0.05622 / 3.80 ( 104) hydrogen bonds : angle 4.47959 / 3.24 ( 303) metal coordination : bond 0.00485 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.035 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 37 average time/residue: 0.0280 time to fit residues: 1.2468 Evaluate side-chains 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.190417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.169175 restraints weight = 2245.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170876 restraints weight = 1646.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.172321 restraints weight = 1337.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173016 restraints weight = 1159.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.173765 restraints weight = 1056.671| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 1690 Z= 0.150 Angle : 0.669 7.146 2293 Z= 0.349 Chirality : 0.041 0.198 274 Planarity : 0.008 0.067 301 Dihedral : 5.424 34.719 243 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 2.30 % Allowed : 9.22 % Favored : 88.48 % Rotamer: Outliers : 7.27 % Allowed : 28.48 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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 (0.60), residues: 217 helix: 1.74 (0.45), residues: 135 sheet: -0.56 (1.10), residues: 17 loop : -4.26 (0.69), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 47 TYR 0.004 0.001 TYR A 179 PHE 0.010 0.002 PHE A 209 TRP 0.011 0.002 TRP A 46 HIS 0.005 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 1688) covalent geometry : angle 0.66927 / 0.35 ( 2293) hydrogen bonds : bond 0.04875 / 3.29 ( 104) hydrogen bonds : angle 3.93972 / 2.83 ( 303) metal coordination : bond 0.00099 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.095 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 37 average time/residue: 0.0494 time to fit residues: 2.2276 Evaluate side-chains 39 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.0570 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.205266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.186299 restraints weight = 2239.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.188048 restraints weight = 1560.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.189483 restraints weight = 1228.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190177 restraints weight = 1051.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190177 restraints weight = 954.982| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 1690 Z= 0.126 Angle : 0.633 6.846 2293 Z= 0.326 Chirality : 0.040 0.193 274 Planarity : 0.007 0.065 301 Dihedral : 5.129 33.089 243 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 1.84 % Allowed : 9.68 % Favored : 88.48 % Rotamer: Outliers : 7.27 % Allowed : 29.09 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: 0.32 (0.60), residues: 217 helix: 2.17 (0.45), residues: 135 sheet: -0.28 (1.10), residues: 17 loop : -4.23 (0.67), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.002 0.001 TYR A 179 PHE 0.009 0.001 PHE A 209 TRP 0.011 0.002 TRP A 46 HIS 0.004 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 1688) covalent geometry : angle 0.63321 / 0.33 ( 2293) hydrogen bonds : bond 0.03946 / 2.66 ( 104) hydrogen bonds : angle 3.67021 / 2.67 ( 303) metal coordination : bond 0.00165 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.062 Fit side-chains REVERT: A 65 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.4897 (t80) outliers start: 12 outliers final: 8 residues processed: 40 average time/residue: 0.0602 time to fit residues: 2.7904 Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 10 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.201122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.188045 restraints weight = 2289.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.188030 restraints weight = 3126.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.188580 restraints weight = 2549.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.188679 restraints weight = 2214.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.189487 restraints weight = 1734.344| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 1690 Z= 0.159 Angle : 0.688 8.237 2293 Z= 0.348 Chirality : 0.041 0.189 274 Planarity : 0.007 0.064 301 Dihedral : 5.239 33.880 243 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 1.84 % Allowed : 11.06 % Favored : 87.10 % Rotamer: Outliers : 9.70 % Allowed : 29.09 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: 0.31 (0.60), residues: 217 helix: 2.08 (0.44), residues: 136 sheet: 0.03 (1.12), residues: 17 loop : -4.25 (0.69), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 37 TYR 0.004 0.001 TYR A 179 PHE 0.008 0.001 PHE A 192 TRP 0.011 0.002 TRP A 46 HIS 0.007 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 1688) covalent geometry : angle 0.68804 / 0.35 ( 2293) hydrogen bonds : bond 0.04944 / 3.32 ( 104) hydrogen bonds : angle 3.77865 / 2.74 ( 303) metal coordination : bond 0.01617 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.061 Fit side-chains REVERT: A 65 TYR cc_start: 0.6722 (OUTLIER) cc_final: 0.5137 (t80) outliers start: 16 outliers final: 13 residues processed: 41 average time/residue: 0.0572 time to fit residues: 2.7380 Evaluate side-chains 42 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.193125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.171666 restraints weight = 2199.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.173559 restraints weight = 1617.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174745 restraints weight = 1309.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.175653 restraints weight = 1132.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175755 restraints weight = 1023.152| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 1690 Z= 0.146 Angle : 0.676 7.619 2293 Z= 0.341 Chirality : 0.040 0.189 274 Planarity : 0.007 0.062 301 Dihedral : 5.070 33.114 243 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 1.84 % Allowed : 11.06 % Favored : 87.10 % Rotamer: Outliers : 9.09 % Allowed : 30.91 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.43 (0.60), residues: 217 helix: 2.17 (0.44), residues: 136 sheet: 0.24 (1.12), residues: 17 loop : -4.24 (0.67), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 47 TYR 0.003 0.001 TYR A 65 PHE 0.008 0.001 PHE A 209 TRP 0.013 0.002 TRP A 46 HIS 0.006 0.003 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 1688) covalent geometry : angle 0.67553 / 0.34 ( 2293) hydrogen bonds : bond 0.04407 / 2.96 ( 104) hydrogen bonds : angle 3.71995 / 2.71 ( 303) metal coordination : bond 0.00396 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.064 Fit side-chains REVERT: A 65 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.4982 (t80) outliers start: 15 outliers final: 11 residues processed: 39 average time/residue: 0.0418 time to fit residues: 1.9571 Evaluate side-chains 40 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0370 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.192577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.171815 restraints weight = 2128.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.172961 restraints weight = 1584.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.174494 restraints weight = 1321.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175427 restraints weight = 1133.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.175741 restraints weight = 1023.664| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 1690 Z= 0.148 Angle : 0.666 7.159 2293 Z= 0.338 Chirality : 0.040 0.191 274 Planarity : 0.007 0.061 301 Dihedral : 5.075 33.261 243 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 1.84 % Allowed : 11.06 % Favored : 87.10 % Rotamer: Outliers : 7.27 % Allowed : 30.91 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.45 (0.59), residues: 217 helix: 2.17 (0.44), residues: 136 sheet: 0.46 (1.13), residues: 17 loop : -4.23 (0.66), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.004 0.001 TYR A 179 PHE 0.007 0.001 PHE A 209 TRP 0.014 0.003 TRP A 46 HIS 0.006 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 1688) covalent geometry : angle 0.66624 / 0.34 ( 2293) hydrogen bonds : bond 0.04576 / 3.08 ( 104) hydrogen bonds : angle 3.64889 / 2.65 ( 303) metal coordination : bond 0.00304 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.059 Fit side-chains REVERT: A 65 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.4924 (t80) outliers start: 12 outliers final: 9 residues processed: 38 average time/residue: 0.0586 time to fit residues: 2.5752 Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.187754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167127 restraints weight = 2175.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.168733 restraints weight = 1598.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.169924 restraints weight = 1303.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170854 restraints weight = 1129.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170854 restraints weight = 1034.183| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 1690 Z= 0.189 Angle : 0.716 7.051 2293 Z= 0.365 Chirality : 0.042 0.187 274 Planarity : 0.007 0.059 301 Dihedral : 5.427 35.311 243 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 1.84 % Allowed : 10.60 % Favored : 87.56 % Rotamer: Outliers : 7.27 % Allowed : 30.30 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.26 (0.59), residues: 217 helix: 1.95 (0.43), residues: 136 sheet: 0.57 (1.19), residues: 17 loop : -4.22 (0.66), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 47 TYR 0.006 0.002 TYR A 179 PHE 0.010 0.002 PHE A 192 TRP 0.019 0.003 TRP A 46 HIS 0.006 0.002 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 1688) covalent geometry : angle 0.71558 / 0.37 ( 2293) hydrogen bonds : bond 0.05664 / 3.81 ( 104) hydrogen bonds : angle 3.88673 / 2.80 ( 303) metal coordination : bond 0.00401 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.059 Fit side-chains REVERT: A 65 TYR cc_start: 0.6593 (OUTLIER) cc_final: 0.5079 (t80) outliers start: 12 outliers final: 9 residues processed: 35 average time/residue: 0.0435 time to fit residues: 1.8334 Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.188390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.167610 restraints weight = 2220.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169354 restraints weight = 1585.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.170875 restraints weight = 1264.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171463 restraints weight = 1092.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.171480 restraints weight = 1002.655| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 1690 Z= 0.192 Angle : 0.716 6.974 2293 Z= 0.368 Chirality : 0.042 0.182 274 Planarity : 0.007 0.058 301 Dihedral : 5.506 35.786 243 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 1.84 % Allowed : 11.06 % Favored : 87.10 % Rotamer: Outliers : 6.06 % Allowed : 31.52 % Favored : 62.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.05 (0.58), residues: 217 helix: 1.78 (0.43), residues: 136 sheet: 0.49 (1.19), residues: 17 loop : -4.27 (0.66), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 101 TYR 0.005 0.002 TYR A 179 PHE 0.009 0.002 PHE A 192 TRP 0.019 0.003 TRP A 46 HIS 0.007 0.003 HIS A 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 1688) covalent geometry : angle 0.71647 / 0.37 ( 2293) hydrogen bonds : bond 0.05544 / 3.72 ( 104) hydrogen bonds : angle 4.00343 / 2.89 ( 303) metal coordination : bond 0.02919 / 1.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.065 Fit side-chains REVERT: A 65 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.5070 (t80) outliers start: 10 outliers final: 9 residues processed: 35 average time/residue: 0.0628 time to fit residues: 2.5329 Evaluate side-chains 37 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.191578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.170893 restraints weight = 2176.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172526 restraints weight = 1592.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.173936 restraints weight = 1287.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.174198 restraints weight = 1114.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.174526 restraints weight = 1057.308| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 1690 Z= 0.160 Angle : 0.694 6.868 2293 Z= 0.357 Chirality : 0.040 0.129 274 Planarity : 0.007 0.059 301 Dihedral : 5.719 34.672 243 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 1.38 % Allowed : 11.06 % Favored : 87.56 % Rotamer: Outliers : 5.45 % Allowed : 32.73 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.09 (0.59), residues: 217 helix: 1.86 (0.43), residues: 136 sheet: -0.09 (1.13), residues: 19 loop : -4.32 (0.67), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 47 TYR 0.004 0.001 TYR A 65 PHE 0.008 0.001 PHE A 209 TRP 0.019 0.003 TRP A 46 HIS 0.016 0.005 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 1688) covalent geometry : angle 0.69353 / 0.36 ( 2293) hydrogen bonds : bond 0.04767 / 3.20 ( 104) hydrogen bonds : angle 3.88862 / 2.79 ( 303) metal coordination : bond 0.03180 / 1.61 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 434 Ramachandran restraints generated. 217 Oldfield, 0 Emsley, 217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.5148 (t0) cc_final: 0.4925 (t0) REVERT: A 65 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.5024 (t80) outliers start: 9 outliers final: 8 residues processed: 34 average time/residue: 0.0447 time to fit residues: 1.8288 Evaluate side-chains 36 residues out of total 165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 0.0030 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 13 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.2188 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.202272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.184788 restraints weight = 2162.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.186163 restraints weight = 1620.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.187160 restraints weight = 1325.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188174 restraints weight = 1151.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188175 restraints weight = 1046.709| |-----------------------------------------------------------------------------| r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 1690 Z= 0.133 Angle : 0.661 6.926 2293 Z= 0.334 Chirality : 0.040 0.201 274 Planarity : 0.007 0.061 301 Dihedral : 5.246 31.434 243 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.22 % Favored : 89.86 % Rotamer: Outliers : 5.45 % Allowed : 33.33 % Favored : 61.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.42 (0.59), residues: 217 helix: 2.11 (0.43), residues: 136 sheet: -0.01 (1.14), residues: 19 loop : -4.14 (0.67), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 47 TYR 0.003 0.001 TYR A 145 PHE 0.008 0.001 PHE A 209 TRP 0.020 0.003 TRP A 46 HIS 0.012 0.004 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 1688) covalent geometry : angle 0.66115 / 0.33 ( 2293) hydrogen bonds : bond 0.03634 / 2.46 ( 104) hydrogen bonds : angle 3.52877 / 2.55 ( 303) metal coordination : bond 0.02656 / 1.34 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 634.55 seconds wall clock time: 11 minutes 35.45 seconds (695.45 seconds total)