Starting phenix.real_space_refine on Thu Oct 22 17:13:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22wp_68735/10_2026/22wp_68735_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/22wp_68735/10_2026/22wp_68735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22wp_68735/10_2026/22wp_68735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22wp_68735/10_2026/22wp_68735.map" model { file = "/net/cci-nas-00/data/ceres_data/22wp_68735/10_2026/22wp_68735_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22wp_68735/10_2026/22wp_68735_neut.cif" } resolution = 3.33 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= 0.026 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 9 5.16 5 C 1160 2.51 5 N 284 2.21 5 O 296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1749 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1734 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain breaks: 2 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 374 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'91Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.52, per 1000 atoms: 0.30 Number of scatterers: 1749 At special positions: 0 Unit cell: (56.42, 60.06, 69.16, 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 9 16.00 O 296 8.00 N 284 7.00 C 1160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " 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: 0.14 Conformation dependent library (CDL) restraints added in 125.3 milliseconds 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 494 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 92.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 81 through 102 removed outlier: 4.027A pdb=" N ASN A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 179 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 188 through 208 Processing helix chain 'A' and resid 208 through 216 removed outlier: 3.982A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLN A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.666A pdb=" N VAL A 221 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 3.969A pdb=" N SER A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 263 Processing helix chain 'A' and resid 317 through 348 removed outlier: 3.815A pdb=" N MET A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 355 through 382 removed outlier: 4.243A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 392 170 hydrogen bonds defined for protein. 507 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: 0.24 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: 1.23 - 1.35: 540 1.35 - 1.46: 451 1.46 - 1.58: 789 1.58 - 1.70: 0 1.70 - 1.81: 11 Bond restraints: 1791 Sorted by residual: bond pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.77e+01 bond pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.19e+01 bond pdb=" N MET A 208 " pdb=" CA MET A 208 " ideal model delta sigma weight residual 1.462 1.491 -0.030 9.50e-03 1.11e+04 9.68e+00 bond pdb=" N VAL A 221 " pdb=" CA VAL A 221 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.75e+00 bond pdb=" N ILE A 245 " pdb=" CA ILE A 245 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.23e-02 6.61e+03 8.73e+00 ... (remaining 1786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 2283 1.34 - 2.67: 147 2.67 - 4.01: 35 4.01 - 5.34: 8 5.34 - 6.68: 2 Bond angle restraints: 2475 Sorted by residual: angle pdb=" C LEU A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta sigma weight residual 123.16 118.10 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA ALA A 90 " pdb=" C ALA A 90 " pdb=" O ALA A 90 " ideal model delta sigma weight residual 120.90 116.16 4.74 1.03e+00 9.43e-01 2.12e+01 angle pdb=" C PHE A 244 " pdb=" CA PHE A 244 " pdb=" CB PHE A 244 " ideal model delta sigma weight residual 110.90 117.58 -6.68 1.58e+00 4.01e-01 1.79e+01 angle pdb=" N VAL A 84 " pdb=" CA VAL A 84 " pdb=" C VAL A 84 " ideal model delta sigma weight residual 110.53 106.90 3.63 9.40e-01 1.13e+00 1.49e+01 angle pdb=" N PHE A 125 " pdb=" CA PHE A 125 " pdb=" C PHE A 125 " ideal model delta sigma weight residual 113.88 109.37 4.51 1.23e+00 6.61e-01 1.35e+01 ... (remaining 2470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.23: 932 13.23 - 26.45: 54 26.45 - 39.68: 18 39.68 - 52.90: 4 52.90 - 66.13: 3 Dihedral angle restraints: 1011 sinusoidal: 256 harmonic: 755 Sorted by residual: dihedral pdb=" CB CYS A 148 " pdb=" SG CYS A 148 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual -86.00 -142.85 56.85 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" N ASN A 343 " pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " pdb=" CG ASN A 343 " ideal model delta sinusoidal sigma weight residual 180.00 -129.35 -50.65 3 1.50e+01 4.44e-03 8.92e+00 dihedral pdb=" CA MET A 335 " pdb=" CB MET A 335 " pdb=" CG MET A 335 " pdb=" SD MET A 335 " ideal model delta sinusoidal sigma weight residual -60.00 -110.44 50.44 3 1.50e+01 4.44e-03 8.90e+00 ... (remaining 1008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 228 0.047 - 0.094: 63 0.094 - 0.141: 13 0.141 - 0.188: 9 0.188 - 0.235: 1 Chirality restraints: 314 Sorted by residual: chirality pdb=" CA VAL A 84 " pdb=" N VAL A 84 " pdb=" C VAL A 84 " pdb=" CB VAL A 84 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB VAL A 84 " pdb=" CA VAL A 84 " pdb=" CG1 VAL A 84 " pdb=" CG2 VAL A 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CA VAL A 130 " pdb=" N VAL A 130 " pdb=" C VAL A 130 " pdb=" CB VAL A 130 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 311 not shown) Planarity restraints: 307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 135 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.88e+00 pdb=" C ILE A 135 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE A 135 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 136 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 336 " 0.011 2.00e-02 2.50e+03 1.03e-02 2.68e+00 pdb=" CG TRP A 336 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 336 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 336 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 336 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 336 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 336 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 336 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 336 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 336 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 337 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C CYS A 337 " -0.025 2.00e-02 2.50e+03 pdb=" O CYS A 337 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO A 338 " 0.009 2.00e-02 2.50e+03 ... (remaining 304 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1268 3.07 - 3.53: 2116 3.53 - 3.99: 2631 3.99 - 4.44: 3370 4.44 - 4.90: 4915 Nonbonded interactions: 14300 Sorted by model distance: nonbonded pdb=" N SER A 188 " pdb=" O SER A 188 " model vdw 2.613 2.496 nonbonded pdb=" N LEU A 143 " pdb=" O LEU A 143 " model vdw 2.638 2.496 nonbonded pdb=" N LEU A 136 " pdb=" N TYR A 137 " model vdw 2.649 2.560 nonbonded pdb=" N VAL A 221 " pdb=" N PHE A 222 " model vdw 2.661 2.560 nonbonded pdb=" N SER A 226 " pdb=" O SER A 226 " model vdw 2.663 2.496 ... (remaining 14295 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.130 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 : 0.006 0.038 1792 Z= 0.442 Angle : 0.781 6.675 2477 Z= 0.550 Chirality : 0.053 0.235 314 Planarity : 0.004 0.024 307 Dihedral : 11.581 66.129 514 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: 0.82 (0.53), residues: 251 helix: 1.00 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.96 (1.12), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 388 TYR 0.008 0.001 TYR A 387 PHE 0.012 0.001 PHE A 244 TRP 0.028 0.003 TRP A 336 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.44 ( 1791) covalent geometry : angle 0.78081 / 0.55 ( 2475) SS BOND : bond 0.00209 / 0.11 ( 1) SS BOND : angle 0.41227 / 0.22 ( 2) hydrogen bonds : bond 0.12753 / 9.03 ( 170) hydrogen bonds : angle 6.58928 / 4.74 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0127 time to fit residues: 0.4243 Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [12, 24, 13, 1, 8, 16, 15, 9, 11, 18, 6] chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.156066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136293 restraints weight = 2143.159| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.78 r_work: 0.3531 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1792 Z= 0.130 Angle : 0.511 5.578 2477 Z= 0.264 Chirality : 0.039 0.106 314 Planarity : 0.004 0.030 307 Dihedral : 6.190 55.096 269 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.78 % Allowed : 9.30 % Favored : 89.92 % 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: 1.99 (0.54), residues: 251 helix: 1.78 (0.35), residues: 219 sheet: None (None), residues: 0 loop : -1.88 (1.16), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.009 0.001 TYR A 174 PHE 0.016 0.002 PHE A 234 TRP 0.010 0.002 TRP A 367 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 1791) covalent geometry : angle 0.51130 / 0.26 ( 2475) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.25049 / 0.14 ( 2) hydrogen bonds : bond 0.03247 / 2.27 ( 170) hydrogen bonds : angle 4.49054 / 3.39 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.034 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 0.0136 time to fit residues: 0.4129 Evaluate side-chains 19 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [0, 10, 19, 6, 1, 13, 20, 22, 9, 12, 24] chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.156266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136349 restraints weight = 2147.289| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.89 r_work: 0.3497 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1792 Z= 0.146 Angle : 0.509 5.367 2477 Z= 0.264 Chirality : 0.039 0.108 314 Planarity : 0.004 0.032 307 Dihedral : 5.781 49.088 269 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.78 % Allowed : 10.85 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.54), residues: 251 helix: 1.78 (0.35), residues: 219 sheet: None (None), residues: 0 loop : -1.74 (1.18), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.009 0.001 TYR A 174 PHE 0.015 0.002 PHE A 234 TRP 0.010 0.001 TRP A 367 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 1791) covalent geometry : angle 0.50912 / 0.26 ( 2475) SS BOND : bond 0.00038 / 0.02 ( 1) SS BOND : angle 0.41817 / 0.22 ( 2) hydrogen bonds : bond 0.03300 / 2.36 ( 170) hydrogen bonds : angle 4.37088 / 3.33 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.060 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.0172 time to fit residues: 0.5915 Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [17, 4, 24, 22, 18, 20, 1, 9, 19, 14, 16] chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.152408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132548 restraints weight = 2189.385| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.87 r_work: 0.3478 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1792 Z= 0.153 Angle : 0.509 5.301 2477 Z= 0.265 Chirality : 0.039 0.112 314 Planarity : 0.004 0.033 307 Dihedral : 5.517 45.375 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.55 % Allowed : 12.40 % Favored : 86.05 % 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: 2.07 (0.53), residues: 251 helix: 1.86 (0.34), residues: 216 sheet: None (None), residues: 0 loop : -1.76 (1.10), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 173 TYR 0.007 0.001 TYR A 387 PHE 0.017 0.002 PHE A 234 TRP 0.010 0.001 TRP A 367 HIS 0.001 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 1791) covalent geometry : angle 0.50889 / 0.27 ( 2475) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 0.42625 / 0.23 ( 2) hydrogen bonds : bond 0.03259 / 2.31 ( 170) hydrogen bonds : angle 4.34528 / 3.30 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.061 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 19 average time/residue: 0.0173 time to fit residues: 0.5598 Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [24, 13, 1, 7, 18, 8, 6, 10, 21, 3, 22] chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.154449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134866 restraints weight = 2165.375| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.81 r_work: 0.3503 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1792 Z= 0.130 Angle : 0.482 5.274 2477 Z= 0.250 Chirality : 0.038 0.109 314 Planarity : 0.004 0.034 307 Dihedral : 5.094 39.969 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.78 % Allowed : 14.73 % Favored : 84.50 % 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: 2.38 (0.54), residues: 251 helix: 2.10 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -1.81 (1.10), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.006 0.001 TYR A 387 PHE 0.014 0.002 PHE A 234 TRP 0.011 0.001 TRP A 367 HIS 0.001 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 1791) covalent geometry : angle 0.48231 / 0.25 ( 2475) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 0.34609 / 0.18 ( 2) hydrogen bonds : bond 0.03087 / 2.19 ( 170) hydrogen bonds : angle 4.24191 / 3.22 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.060 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0180 time to fit residues: 0.5469 Evaluate side-chains 17 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [14, 6, 11, 19, 10, 22, 0, 13, 24, 20, 23] chunk 14 optimal weight: 7.9990 chunk 6 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.154226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135077 restraints weight = 2167.048| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.76 r_work: 0.3514 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1792 Z= 0.132 Angle : 0.480 5.285 2477 Z= 0.250 Chirality : 0.038 0.110 314 Planarity : 0.004 0.034 307 Dihedral : 4.921 37.646 269 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.78 % Allowed : 15.50 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.53), residues: 251 helix: 2.13 (0.34), residues: 217 sheet: None (None), residues: 0 loop : -1.67 (1.12), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.006 0.001 TYR A 387 PHE 0.015 0.002 PHE A 234 TRP 0.010 0.001 TRP A 367 HIS 0.001 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 1791) covalent geometry : angle 0.48056 / 0.25 ( 2475) SS BOND : bond 0.00058 / 0.03 ( 1) SS BOND : angle 0.36317 / 0.19 ( 2) hydrogen bonds : bond 0.03054 / 2.16 ( 170) hydrogen bonds : angle 4.23614 / 3.21 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.052 Fit side-chains REVERT: A 387 TYR cc_start: 0.8485 (m-80) cc_final: 0.7636 (m-80) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0159 time to fit residues: 0.5079 Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [12, 21, 14, 18, 19, 8, 3, 20, 5, 9, 17] chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 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 = 0.3791 r_free = 0.3791 target = 0.153616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134512 restraints weight = 2134.936| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.74 r_work: 0.3516 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1792 Z= 0.139 Angle : 0.487 5.297 2477 Z= 0.255 Chirality : 0.039 0.115 314 Planarity : 0.004 0.034 307 Dihedral : 4.982 38.370 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.78 % Allowed : 14.73 % Favored : 84.50 % 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: 2.44 (0.53), residues: 251 helix: 2.11 (0.34), residues: 217 sheet: None (None), residues: 0 loop : -1.69 (1.12), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.006 0.001 TYR A 387 PHE 0.015 0.002 PHE A 234 TRP 0.010 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 1791) covalent geometry : angle 0.48728 / 0.26 ( 2475) SS BOND : bond 0.00049 / 0.03 ( 1) SS BOND : angle 0.36019 / 0.19 ( 2) hydrogen bonds : bond 0.03097 / 2.19 ( 170) hydrogen bonds : angle 4.28085 / 3.24 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.059 Fit side-chains REVERT: A 387 TYR cc_start: 0.8499 (m-80) cc_final: 0.7636 (m-80) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0173 time to fit residues: 0.5188 Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [19, 21, 17, 15, 1, 0, 22, 23, 3, 7, 18] chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.154887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135728 restraints weight = 2154.778| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.75 r_work: 0.3522 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1792 Z= 0.124 Angle : 0.471 5.290 2477 Z= 0.246 Chirality : 0.038 0.112 314 Planarity : 0.004 0.034 307 Dihedral : 4.776 35.571 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.78 % Allowed : 14.73 % Favored : 84.50 % 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: 2.65 (0.54), residues: 251 helix: 2.25 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.60 (1.14), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.005 0.001 TYR A 387 PHE 0.014 0.002 PHE A 234 TRP 0.011 0.001 TRP A 367 HIS 0.001 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 1791) covalent geometry : angle 0.47153 / 0.25 ( 2475) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.29715 / 0.16 ( 2) hydrogen bonds : bond 0.02975 / 2.10 ( 170) hydrogen bonds : angle 4.22654 / 3.19 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.036 Fit side-chains REVERT: A 387 TYR cc_start: 0.8477 (m-80) cc_final: 0.7650 (m-80) outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0175 time to fit residues: 0.4900 Evaluate side-chains 17 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [24, 12, 3, 5, 8, 9, 17, 4, 18, 23, 14] chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.154059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134750 restraints weight = 2175.366| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.77 r_work: 0.3514 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1792 Z= 0.136 Angle : 0.484 5.304 2477 Z= 0.253 Chirality : 0.038 0.115 314 Planarity : 0.004 0.033 307 Dihedral : 4.876 37.049 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.78 % Allowed : 14.73 % Favored : 84.50 % 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: 2.53 (0.54), residues: 251 helix: 2.16 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.64 (1.14), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.006 0.001 TYR A 387 PHE 0.014 0.002 PHE A 234 TRP 0.010 0.001 TRP A 367 HIS 0.001 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 1791) covalent geometry : angle 0.48365 / 0.25 ( 2475) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.37060 / 0.20 ( 2) hydrogen bonds : bond 0.03059 / 2.17 ( 170) hydrogen bonds : angle 4.26709 / 3.23 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.063 Fit side-chains REVERT: A 387 TYR cc_start: 0.8500 (m-80) cc_final: 0.7631 (m-80) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0193 time to fit residues: 0.5980 Evaluate side-chains 18 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [19, 24, 0, 1, 7, 9, 20, 6, 3, 21, 13] chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.0070 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.155592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136422 restraints weight = 2112.760| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.75 r_work: 0.3533 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1792 Z= 0.118 Angle : 0.463 5.275 2477 Z= 0.241 Chirality : 0.038 0.111 314 Planarity : 0.004 0.034 307 Dihedral : 4.628 33.215 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.78 % Allowed : 14.73 % Favored : 84.50 % 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: 2.77 (0.54), residues: 251 helix: 2.33 (0.35), residues: 217 sheet: None (None), residues: 0 loop : -1.63 (1.14), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.005 0.001 TYR A 387 PHE 0.014 0.001 PHE A 234 TRP 0.011 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 1791) covalent geometry : angle 0.46297 / 0.24 ( 2475) SS BOND : bond 0.00051 / 0.03 ( 1) SS BOND : angle 0.31605 / 0.17 ( 2) hydrogen bonds : bond 0.02900 / 2.05 ( 170) hydrogen bonds : angle 4.18718 / 3.16 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 502 Ramachandran restraints generated. 251 Oldfield, 0 Emsley, 251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.035 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 0.0125 time to fit residues: 0.3576 Evaluate side-chains 17 residues out of total 229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: [18, 8, 6, 15, 11, 22, 19, 24, 21, 13, 5] chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.0030 chunk 5 optimal weight: 0.9980 overall best weight: 0.3728 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.157728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138308 restraints weight = 2173.749| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.77 r_work: 0.3552 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1792 Z= 0.108 Angle : 0.450 5.278 2477 Z= 0.233 Chirality : 0.038 0.109 314 Planarity : 0.004 0.034 307 Dihedral : 4.389 29.071 269 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.78 % Allowed : 14.73 % Favored : 84.50 % 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: 2.98 (0.54), residues: 251 helix: 2.37 (0.35), residues: 221 sheet: None (None), residues: 0 loop : -1.18 (1.28), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 388 TYR 0.005 0.001 TYR A 387 PHE 0.013 0.001 PHE A 234 TRP 0.012 0.001 TRP A 367 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 1791) covalent geometry : angle 0.44970 / 0.23 ( 2475) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 0.27281 / 0.15 ( 2) hydrogen bonds : bond 0.02753 / 1.94 ( 170) hydrogen bonds : angle 4.08430 / 3.08 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 586.56 seconds wall clock time: 10 minutes 49.23 seconds (649.23 seconds total)