Starting phenix.real_space_refine on Wed Jul 1 21:05:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5c_36901/07_2026/8k5c_36901.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5c_36901/07_2026/8k5c_36901.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5c_36901/07_2026/8k5c_36901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5c_36901/07_2026/8k5c_36901.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5c_36901/07_2026/8k5c_36901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5c_36901/07_2026/8k5c_36901.cif" } 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= -0.002 sd= 0.041 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 1588 2.51 5 N 397 2.21 5 O 374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2369 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.56, per 1000 atoms: 0.24 Number of scatterers: 2380 At special positions: 0 Unit cell: (61.005, 70.965, 73.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 374 8.00 N 397 7.00 C 1588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 51.9 milliseconds 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 78.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 29 through 54 Processing helix chain 'A' and resid 61 through 89 removed outlier: 3.527A pdb=" N PHE A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.904A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.773A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.559A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.913A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.043A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 removed outlier: 4.076A pdb=" N ILE A 182 " --> pdb=" O CYS A 19 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 483 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: 0.21 Time building geometry restraints manager: 0.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 344 1.32 - 1.45: 730 1.45 - 1.57: 1343 1.57 - 1.70: 0 1.70 - 1.83: 31 Bond restraints: 2448 Sorted by residual: bond pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.16e-02 7.43e+03 1.55e+01 bond pdb=" C06 OJX A 401 " pdb=" N04 OJX A 401 " ideal model delta sigma weight residual 1.382 1.317 0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C07 OJX A 401 " pdb=" N04 OJX A 401 " ideal model delta sigma weight residual 1.370 1.318 0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C06 OJX A 401 " pdb=" C10 OJX A 401 " ideal model delta sigma weight residual 1.477 1.522 -0.045 2.00e-02 2.50e+03 5.06e+00 bond pdb=" C06 OJX A 401 " pdb=" C09 OJX A 401 " ideal model delta sigma weight residual 1.424 1.382 0.042 2.00e-02 2.50e+03 4.31e+00 ... (remaining 2443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 3194 1.52 - 3.04: 95 3.04 - 4.55: 22 4.55 - 6.07: 7 6.07 - 7.59: 3 Bond angle restraints: 3321 Sorted by residual: angle pdb=" C PRO A 99 " pdb=" CA PRO A 99 " pdb=" CB PRO A 99 " ideal model delta sigma weight residual 112.11 116.62 -4.51 1.46e+00 4.69e-01 9.53e+00 angle pdb=" CA MET A 103 " pdb=" CB MET A 103 " pdb=" CG MET A 103 " ideal model delta sigma weight residual 114.10 108.41 5.69 2.00e+00 2.50e-01 8.10e+00 angle pdb=" N PRO A 99 " pdb=" CA PRO A 99 " pdb=" C PRO A 99 " ideal model delta sigma weight residual 113.57 109.93 3.64 1.31e+00 5.83e-01 7.73e+00 angle pdb=" CA PRO A 99 " pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 119.34 115.72 3.62 1.47e+00 4.63e-01 6.06e+00 angle pdb=" CA MET A 167 " pdb=" CB MET A 167 " pdb=" CG MET A 167 " ideal model delta sigma weight residual 114.10 118.61 -4.51 2.00e+00 2.50e-01 5.08e+00 ... (remaining 3316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.50: 1119 12.50 - 25.01: 166 25.01 - 37.51: 99 37.51 - 50.01: 32 50.01 - 62.51: 8 Dihedral angle restraints: 1424 sinusoidal: 570 harmonic: 854 Sorted by residual: dihedral pdb=" CA MET A 167 " pdb=" C MET A 167 " pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE A 197 " pdb=" C PHE A 197 " pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 266 " pdb=" CB CYS A 266 " ideal model delta sinusoidal sigma weight residual -86.00 -54.87 -31.13 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 1421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 213 0.028 - 0.056: 107 0.056 - 0.084: 37 0.084 - 0.111: 18 0.111 - 0.139: 4 Chirality restraints: 379 Sorted by residual: chirality pdb=" CA LEU A 30 " pdb=" N LEU A 30 " pdb=" C LEU A 30 " pdb=" CB LEU A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CB THR A 279 " pdb=" CA THR A 279 " pdb=" OG1 THR A 279 " pdb=" CG2 THR A 279 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO A 200 " pdb=" N PRO A 200 " pdb=" C PRO A 200 " pdb=" CB PRO A 200 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 376 not shown) Planarity restraints: 402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 31 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 245 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO A 246 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 98 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C ILE A 98 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 98 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 99 " 0.010 2.00e-02 2.50e+03 ... (remaining 399 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 825 2.85 - 3.36: 2333 3.36 - 3.88: 3932 3.88 - 4.39: 4380 4.39 - 4.90: 7700 Nonbonded interactions: 19170 Sorted by model distance: nonbonded pdb=" OG SER A 62 " pdb=" OD2 ASP A 124 " model vdw 2.341 3.040 nonbonded pdb=" O GLY A 41 " pdb=" ND2 ASN A 45 " model vdw 2.365 3.120 nonbonded pdb=" O HIS A 131 " pdb=" ND2 ASN A 137 " model vdw 2.416 3.120 nonbonded pdb=" OG SER A 179 " pdb=" NE2 HIS A 189 " model vdw 2.416 3.120 nonbonded pdb=" OH TYR A 284 " pdb=" N05 OJX A 401 " model vdw 2.486 3.120 ... (remaining 19165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.020 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.004 0.065 2451 Z= 0.216 Angle : 0.678 7.587 3327 Z= 0.354 Chirality : 0.041 0.139 379 Planarity : 0.006 0.048 402 Dihedral : 16.996 62.514 857 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.78 % Allowed : 25.97 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.50), residues: 289 helix: 1.44 (0.36), residues: 198 sheet: None (None), residues: 0 loop : -2.05 (0.64), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.003 0.001 TYR A 126 PHE 0.009 0.001 PHE A 82 TRP 0.024 0.002 TRP A 256 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 ( 2448) covalent geometry : angle 0.67818 / 0.35 ( 3321) SS BOND : bond 0.00214 / 0.11 ( 3) SS BOND : angle 0.74835 / 0.41 ( 6) hydrogen bonds : bond 0.12994 / 8.72 ( 165) hydrogen bonds : angle 5.45702 / 3.99 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.052 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.0651 time to fit residues: 2.3664 Evaluate side-chains 32 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.0040 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.155084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139745 restraints weight = 3025.178| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.45 r_work: 0.3437 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2451 Z= 0.145 Angle : 0.576 7.151 3327 Z= 0.305 Chirality : 0.041 0.130 379 Planarity : 0.006 0.050 402 Dihedral : 5.636 41.175 319 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.49 % Allowed : 25.19 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.51), residues: 289 helix: 1.51 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -1.45 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.003 0.001 TYR A 295 PHE 0.016 0.001 PHE A 232 TRP 0.013 0.001 TRP A 256 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 2448) covalent geometry : angle 0.57416 / 0.30 ( 3321) SS BOND : bond 0.00155 / 0.08 ( 3) SS BOND : angle 1.10138 / 0.61 ( 6) hydrogen bonds : bond 0.04337 / 2.69 ( 165) hydrogen bonds : angle 4.33362 / 3.01 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.116 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 0.0548 time to fit residues: 2.4865 Evaluate side-chains 37 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.154126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.138558 restraints weight = 3070.445| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.47 r_work: 0.3416 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2451 Z= 0.154 Angle : 0.578 7.048 3327 Z= 0.308 Chirality : 0.042 0.187 379 Planarity : 0.006 0.052 402 Dihedral : 5.064 24.939 317 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.04 % Allowed : 24.42 % Favored : 70.54 % 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: 1.05 (0.51), residues: 289 helix: 1.57 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.54 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.015 0.001 PHE A 232 TRP 0.013 0.002 TRP A 50 HIS 0.001 0.001 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 2448) covalent geometry : angle 0.57738 / 0.31 ( 3321) SS BOND : bond 0.00166 / 0.09 ( 3) SS BOND : angle 0.95074 / 0.52 ( 6) hydrogen bonds : bond 0.04388 / 2.72 ( 165) hydrogen bonds : angle 4.27963 / 2.96 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.051 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 41 average time/residue: 0.0689 time to fit residues: 3.2713 Evaluate side-chains 40 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.154671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138928 restraints weight = 3077.687| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.47 r_work: 0.3420 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2451 Z= 0.159 Angle : 0.588 6.746 3327 Z= 0.311 Chirality : 0.042 0.127 379 Planarity : 0.005 0.051 402 Dihedral : 5.126 25.402 317 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.65 % Allowed : 24.03 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.50), residues: 289 helix: 1.60 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.58 (0.74), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.015 0.002 PHE A 232 TRP 0.012 0.001 TRP A 256 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 2448) covalent geometry : angle 0.58733 / 0.31 ( 3321) SS BOND : bond 0.00172 / 0.09 ( 3) SS BOND : angle 0.90004 / 0.48 ( 6) hydrogen bonds : bond 0.04411 / 2.75 ( 165) hydrogen bonds : angle 4.26180 / 2.94 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.094 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 42 average time/residue: 0.0969 time to fit residues: 4.6596 Evaluate side-chains 42 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 11 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 = 0.3667 r_free = 0.3667 target = 0.152722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137735 restraints weight = 3044.139| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.39 r_work: 0.3405 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2451 Z= 0.173 Angle : 0.592 6.879 3327 Z= 0.313 Chirality : 0.042 0.133 379 Planarity : 0.006 0.051 402 Dihedral : 5.184 25.879 317 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.43 % Allowed : 24.81 % Favored : 69.77 % 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: 0.99 (0.50), residues: 289 helix: 1.49 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -1.49 (0.75), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.002 PHE A 232 TRP 0.016 0.002 TRP A 93 HIS 0.001 0.000 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 2448) covalent geometry : angle 0.59109 / 0.31 ( 3321) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 1.12210 / 0.63 ( 6) hydrogen bonds : bond 0.04463 / 2.78 ( 165) hydrogen bonds : angle 4.29240 / 2.96 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.086 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 45 average time/residue: 0.0758 time to fit residues: 3.9617 Evaluate side-chains 45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 259 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.153609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138077 restraints weight = 2997.643| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.44 r_work: 0.3414 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2451 Z= 0.157 Angle : 0.587 6.748 3327 Z= 0.312 Chirality : 0.042 0.132 379 Planarity : 0.005 0.050 402 Dihedral : 5.139 25.232 317 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.04 % Allowed : 25.97 % Favored : 68.99 % 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: 1.07 (0.51), residues: 289 helix: 1.57 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.48 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.001 PHE A 232 TRP 0.014 0.001 TRP A 256 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 2448) covalent geometry : angle 0.58669 / 0.31 ( 3321) SS BOND : bond 0.00175 / 0.09 ( 3) SS BOND : angle 0.92476 / 0.50 ( 6) hydrogen bonds : bond 0.04381 / 2.74 ( 165) hydrogen bonds : angle 4.24850 / 2.93 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.102 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 43 average time/residue: 0.0896 time to fit residues: 4.4255 Evaluate side-chains 44 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.151794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.136257 restraints weight = 3046.689| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.45 r_work: 0.3392 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2451 Z= 0.176 Angle : 0.596 6.807 3327 Z= 0.317 Chirality : 0.042 0.131 379 Planarity : 0.006 0.050 402 Dihedral : 5.212 25.593 317 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.04 % Allowed : 25.19 % Favored : 69.77 % 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: 0.95 (0.50), residues: 289 helix: 1.44 (0.35), residues: 206 sheet: None (None), residues: 0 loop : -1.44 (0.76), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.002 PHE A 232 TRP 0.013 0.002 TRP A 50 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 2448) covalent geometry : angle 0.59423 / 0.32 ( 3321) SS BOND : bond 0.00197 / 0.10 ( 3) SS BOND : angle 1.13750 / 0.64 ( 6) hydrogen bonds : bond 0.04478 / 2.78 ( 165) hydrogen bonds : angle 4.31137 / 2.97 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.089 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 44 average time/residue: 0.0922 time to fit residues: 4.6235 Evaluate side-chains 46 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.0050 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139525 restraints weight = 3011.570| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.44 r_work: 0.3436 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2451 Z= 0.142 Angle : 0.568 6.732 3327 Z= 0.303 Chirality : 0.041 0.132 379 Planarity : 0.005 0.051 402 Dihedral : 4.940 22.776 317 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.88 % Allowed : 26.36 % Favored : 69.77 % 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: 1.23 (0.51), residues: 289 helix: 1.68 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.38 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.001 PHE A 232 TRP 0.018 0.002 TRP A 256 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 2448) covalent geometry : angle 0.56768 / 0.30 ( 3321) SS BOND : bond 0.00136 / 0.07 ( 3) SS BOND : angle 0.77210 / 0.41 ( 6) hydrogen bonds : bond 0.04238 / 2.65 ( 165) hydrogen bonds : angle 4.20813 / 2.89 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.097 Fit side-chains REVERT: A 116 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8570 (mt) outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 0.0916 time to fit residues: 4.3787 Evaluate side-chains 43 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 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 = 0.3668 r_free = 0.3668 target = 0.152747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.136957 restraints weight = 3099.709| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.48 r_work: 0.3402 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2451 Z= 0.173 Angle : 0.595 6.909 3327 Z= 0.317 Chirality : 0.042 0.134 379 Planarity : 0.006 0.050 402 Dihedral : 5.179 24.802 317 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.04 % Allowed : 25.58 % Favored : 69.38 % 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: 1.02 (0.51), residues: 289 helix: 1.52 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.44 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.002 PHE A 232 TRP 0.023 0.002 TRP A 256 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 2448) covalent geometry : angle 0.59364 / 0.32 ( 3321) SS BOND : bond 0.00182 / 0.10 ( 3) SS BOND : angle 0.95953 / 0.54 ( 6) hydrogen bonds : bond 0.04449 / 2.77 ( 165) hydrogen bonds : angle 4.29717 / 2.96 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.053 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 44 average time/residue: 0.0614 time to fit residues: 3.0581 Evaluate side-chains 45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.153336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.138050 restraints weight = 3077.249| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.39 r_work: 0.3415 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.004 0.036 2451 Z= 0.162 Angle : 0.586 6.816 3327 Z= 0.312 Chirality : 0.042 0.131 379 Planarity : 0.005 0.050 402 Dihedral : 5.112 24.372 317 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.26 % Allowed : 26.36 % Favored : 69.38 % 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: 1.07 (0.51), residues: 289 helix: 1.55 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.44 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.001 PHE A 232 TRP 0.027 0.002 TRP A 256 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 2448) covalent geometry : angle 0.58543 / 0.31 ( 3321) SS BOND : bond 0.00160 / 0.08 ( 3) SS BOND : angle 0.85146 / 0.47 ( 6) hydrogen bonds : bond 0.04398 / 2.75 ( 165) hydrogen bonds : angle 4.25198 / 2.91 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.054 Fit side-chains REVERT: A 116 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8621 (mt) outliers start: 11 outliers final: 10 residues processed: 43 average time/residue: 0.0637 time to fit residues: 3.1353 Evaluate side-chains 46 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.152306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136723 restraints weight = 3068.411| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.44 r_work: 0.3399 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2451 Z= 0.172 Angle : 0.600 6.879 3327 Z= 0.319 Chirality : 0.042 0.134 379 Planarity : 0.006 0.050 402 Dihedral : 5.154 24.451 317 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.04 % Allowed : 25.58 % Favored : 69.38 % 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: 1.00 (0.50), residues: 289 helix: 1.51 (0.35), residues: 205 sheet: None (None), residues: 0 loop : -1.47 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 89 TYR 0.004 0.001 TYR A 269 PHE 0.014 0.002 PHE A 232 TRP 0.032 0.002 TRP A 256 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 2448) covalent geometry : angle 0.59906 / 0.32 ( 3321) SS BOND : bond 0.00187 / 0.10 ( 3) SS BOND : angle 0.89689 / 0.50 ( 6) hydrogen bonds : bond 0.04468 / 2.80 ( 165) hydrogen bonds : angle 4.28973 / 2.94 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 768.93 seconds wall clock time: 13 minutes 50.21 seconds (830.21 seconds total)