Starting phenix.real_space_refine on Wed Jul 1 21:57:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ug0_26482/07_2026/7ug0_26482.cif" } resolution = 2.55 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= 0.001 sd= 0.033 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: 6 Type Number sf(0) Gaussians S 17 5.16 5 Na 2 4.78 5 C 2050 2.51 5 N 507 2.21 5 O 549 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3126 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3103 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 18, 'TRANS': 399} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 23 Unusual residues: {' NA': 2, 'TB1': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Time building chain proxies: 1.09, per 1000 atoms: 0.35 Number of scatterers: 3126 At special positions: 0 Unit cell: (67.308, 78.384, 70.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 Na 2 11.00 F 1 9.00 O 549 8.00 N 507 7.00 C 2050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 113.5 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.637A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.625A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 57 removed outlier: 4.088A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.542A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.637A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 107 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.590A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.514A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 224 through 246 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.198A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.521A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.501A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.993A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.581A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 349 removed outlier: 3.516A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.252A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 4.108A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 418 removed outlier: 4.182A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 750 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: 0.51 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 987 1.37 - 1.55: 2162 1.55 - 1.73: 0 1.73 - 1.92: 32 1.92 - 2.10: 1 Bond restraints: 3182 Sorted by residual: bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C1 TB1 A 501 " pdb=" C4 TB1 A 501 " ideal model delta sigma weight residual 1.503 1.529 -0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.365 0.023 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C10 TB1 A 501 " pdb=" C7 TB1 A 501 " ideal model delta sigma weight residual 1.548 1.526 0.022 2.00e-02 2.50e+03 1.20e+00 ... (remaining 3177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4287 1.45 - 2.90: 34 2.90 - 4.35: 5 4.35 - 5.80: 8 5.80 - 7.25: 3 Bond angle restraints: 4337 Sorted by residual: angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 108.90 -7.25 3.00e+00 1.11e-01 5.83e+00 angle pdb=" O1 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 126.71 119.70 7.01 3.00e+00 1.11e-01 5.47e+00 angle pdb=" O3 TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" O4 TB1 A 501 " ideal model delta sigma weight residual 126.45 120.01 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 109.54 -5.56 3.00e+00 1.11e-01 3.44e+00 angle pdb=" C11 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 115.01 120.10 -5.09 3.00e+00 1.11e-01 2.88e+00 ... (remaining 4332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.67: 1681 12.67 - 25.35: 124 25.35 - 38.02: 38 38.02 - 50.69: 8 50.69 - 63.36: 4 Dihedral angle restraints: 1855 sinusoidal: 671 harmonic: 1184 Sorted by residual: dihedral pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " pdb=" CE MET A 194 " ideal model delta sinusoidal sigma weight residual 180.00 122.68 57.32 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CB MET A 292 " pdb=" CG MET A 292 " pdb=" SD MET A 292 " pdb=" CE MET A 292 " ideal model delta sinusoidal sigma weight residual -60.00 -113.78 53.78 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CG ARG A 80 " pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " ideal model delta sinusoidal sigma weight residual -90.00 -129.22 39.22 2 1.50e+01 4.44e-03 8.53e+00 ... (remaining 1852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 387 0.033 - 0.066: 120 0.066 - 0.098: 26 0.098 - 0.131: 8 0.131 - 0.164: 1 Chirality restraints: 542 Sorted by residual: chirality pdb=" C7 TB1 A 501 " pdb=" N TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" C11 TB1 A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA VAL A 355 " pdb=" N VAL A 355 " pdb=" C VAL A 355 " pdb=" CB VAL A 355 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.96e-01 ... (remaining 539 not shown) Planarity restraints: 534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 45 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " -0.015 5.00e-02 4.00e+02 2.27e-02 8.26e-01 pdb=" N PRO A 153 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.48e-01 pdb=" N PRO A 377 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.012 5.00e-02 4.00e+02 ... (remaining 531 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 851 2.81 - 3.33: 3175 3.33 - 3.85: 4814 3.85 - 4.38: 5623 4.38 - 4.90: 9868 Nonbonded interactions: 24331 Sorted by model distance: nonbonded pdb=" OG SER A 278 " pdb=" O3 TB1 A 501 " model vdw 2.287 3.040 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 604 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 247 " pdb=" OD2 ASP A 312 " model vdw 2.341 3.040 nonbonded pdb=" OD2 ASP A 405 " pdb=" O HOH A 601 " model vdw 2.359 3.040 nonbonded pdb=" N TB1 A 501 " pdb=" O1 TB1 A 501 " model vdw 2.361 3.120 ... (remaining 24326 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: 7.500 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.500 Find NCS groups from input model: 0.020 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:8.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 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 : 0.002 0.047 3182 Z= 0.112 Angle : 0.451 7.246 4337 Z= 0.208 Chirality : 0.036 0.164 542 Planarity : 0.003 0.031 534 Dihedral : 10.597 63.364 1105 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.00 (0.39), residues: 413 helix: 1.50 (0.26), residues: 336 sheet: None (None), residues: 0 loop : 0.91 (0.78), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.013 0.001 TYR A 299 PHE 0.005 0.001 PHE A 210 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 3182) covalent geometry : angle 0.45145 / 0.21 ( 4337) hydrogen bonds : bond 0.28026 / 18.32 ( 250) hydrogen bonds : angle 6.14949 / 4.48 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.119 Fit side-chains REVERT: A 174 GLU cc_start: 0.7990 (tp30) cc_final: 0.7645 (tp30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.6779 time to fit residues: 27.7041 Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070661 restraints weight = 5621.962| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.42 r_work: 0.2788 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.148 Angle : 0.472 4.596 4337 Z= 0.260 Chirality : 0.038 0.128 542 Planarity : 0.004 0.029 534 Dihedral : 4.003 41.375 446 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.23 % Allowed : 3.70 % Favored : 95.06 % 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: 3.53 (0.40), residues: 413 helix: 2.66 (0.27), residues: 343 sheet: None (None), residues: 0 loop : 0.69 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 177 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 323 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 3182) covalent geometry : angle 0.47179 / 0.26 ( 4337) hydrogen bonds : bond 0.06962 / 4.52 ( 250) hydrogen bonds : angle 3.80312 / 2.71 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.077 Fit side-chains REVERT: A 296 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 311 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7903 (mtp) REVERT: A 390 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7731 (m-30) outliers start: 4 outliers final: 0 residues processed: 37 average time/residue: 0.5874 time to fit residues: 22.2584 Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 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 = 0.3324 r_free = 0.3324 target = 0.093030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.069843 restraints weight = 5616.576| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.36 r_work: 0.2779 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.147 Angle : 0.456 4.682 4337 Z= 0.246 Chirality : 0.037 0.129 542 Planarity : 0.004 0.029 534 Dihedral : 3.656 30.668 446 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.54 % Allowed : 4.94 % Favored : 93.52 % 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: 3.87 (0.41), residues: 413 helix: 2.93 (0.28), residues: 343 sheet: None (None), residues: 0 loop : 0.60 (0.72), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 80 TYR 0.023 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 3182) covalent geometry : angle 0.45632 / 0.25 ( 4337) hydrogen bonds : bond 0.06784 / 4.41 ( 250) hydrogen bonds : angle 3.63066 / 2.62 ( 750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.081 Fit side-chains REVERT: A 296 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7478 (tm-30) outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.8357 time to fit residues: 31.5681 Evaluate side-chains 34 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.093409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070366 restraints weight = 5540.066| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.34 r_work: 0.2817 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.139 Angle : 0.458 4.654 4337 Z= 0.246 Chirality : 0.037 0.129 542 Planarity : 0.004 0.029 534 Dihedral : 3.611 28.573 446 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.23 % Allowed : 6.48 % Favored : 92.28 % 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: 3.94 (0.41), residues: 413 helix: 3.05 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.36 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 287 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 3182) covalent geometry : angle 0.45796 / 0.25 ( 4337) hydrogen bonds : bond 0.06258 / 4.07 ( 250) hydrogen bonds : angle 3.52083 / 2.54 ( 750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.114 Fit side-chains REVERT: A 9 GLU cc_start: 0.8582 (mp0) cc_final: 0.8253 (mp0) REVERT: A 291 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 296 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7438 (tm-30) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.6544 time to fit residues: 24.1054 Evaluate side-chains 33 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.092385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069221 restraints weight = 5613.263| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.39 r_work: 0.2769 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3182 Z= 0.146 Angle : 0.464 4.664 4337 Z= 0.249 Chirality : 0.037 0.129 542 Planarity : 0.004 0.029 534 Dihedral : 3.604 27.721 446 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.62 % Allowed : 8.33 % Favored : 91.05 % 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: 3.91 (0.41), residues: 413 helix: 3.03 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.34 (0.69), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 287 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 3182) covalent geometry : angle 0.46407 / 0.25 ( 4337) hydrogen bonds : bond 0.06537 / 4.24 ( 250) hydrogen bonds : angle 3.53512 / 2.56 ( 750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.116 Fit side-chains REVERT: A 9 GLU cc_start: 0.8648 (mp0) cc_final: 0.8222 (mp0) REVERT: A 291 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 296 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7491 (tm-30) outliers start: 2 outliers final: 2 residues processed: 35 average time/residue: 0.8084 time to fit residues: 29.0284 Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.097602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074455 restraints weight = 5533.456| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.40 r_work: 0.2881 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3182 Z= 0.113 Angle : 0.419 4.669 4337 Z= 0.223 Chirality : 0.036 0.124 542 Planarity : 0.004 0.030 534 Dihedral : 3.424 25.129 446 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.54 % Allowed : 8.64 % Favored : 89.81 % 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: 4.20 (0.41), residues: 413 helix: 3.21 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.50 (0.71), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.007 0.001 PHE A 210 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 3182) covalent geometry : angle 0.41920 / 0.22 ( 4337) hydrogen bonds : bond 0.04837 / 3.16 ( 250) hydrogen bonds : angle 3.27534 / 2.38 ( 750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.118 Fit side-chains REVERT: A 9 GLU cc_start: 0.8683 (mp0) cc_final: 0.8157 (mp0) REVERT: A 291 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 296 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7347 (tm-30) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.7091 time to fit residues: 26.1682 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.070877 restraints weight = 5588.687| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.40 r_work: 0.2810 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3182 Z= 0.132 Angle : 0.442 4.639 4337 Z= 0.235 Chirality : 0.036 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 3.449 25.025 446 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.93 % Allowed : 9.57 % Favored : 89.51 % 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: 4.11 (0.41), residues: 413 helix: 3.16 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.37 (0.72), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 3182) covalent geometry : angle 0.44212 / 0.24 ( 4337) hydrogen bonds : bond 0.05919 / 3.84 ( 250) hydrogen bonds : angle 3.37631 / 2.45 ( 750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.070 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 296 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7453 (tm-30) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.5020 time to fit residues: 17.9673 Evaluate side-chains 36 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.091420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.068158 restraints weight = 5758.489| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.43 r_work: 0.2747 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3182 Z= 0.157 Angle : 0.480 5.668 4337 Z= 0.257 Chirality : 0.037 0.130 542 Planarity : 0.004 0.030 534 Dihedral : 3.575 26.702 446 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.23 % Allowed : 10.19 % Favored : 88.58 % 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: 4.05 (0.41), residues: 413 helix: 3.16 (0.28), residues: 339 sheet: None (None), residues: 0 loop : 0.22 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 287 TYR 0.022 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 3182) covalent geometry : angle 0.48020 / 0.26 ( 4337) hydrogen bonds : bond 0.06723 / 4.36 ( 250) hydrogen bonds : angle 3.49969 / 2.54 ( 750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 296 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7500 (tm-30) outliers start: 4 outliers final: 1 residues processed: 36 average time/residue: 0.7879 time to fit residues: 28.9954 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.093427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070285 restraints weight = 5656.714| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.40 r_work: 0.2809 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3182 Z= 0.136 Angle : 0.456 5.658 4337 Z= 0.244 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 3.537 26.657 446 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.93 % Allowed : 11.11 % Favored : 87.96 % 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: 4.05 (0.41), residues: 413 helix: 3.15 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.19 (0.70), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.021 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 3182) covalent geometry : angle 0.45623 / 0.24 ( 4337) hydrogen bonds : bond 0.06007 / 3.90 ( 250) hydrogen bonds : angle 3.40808 / 2.48 ( 750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 296 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7433 (tm-30) outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.7352 time to fit residues: 27.1176 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.070180 restraints weight = 5603.102| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.38 r_work: 0.2808 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3182 Z= 0.137 Angle : 0.466 6.933 4337 Z= 0.249 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 3.531 26.868 446 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.31 % Allowed : 11.42 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.41), residues: 413 helix: 3.16 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.14 (0.70), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 3182) covalent geometry : angle 0.46633 / 0.25 ( 4337) hydrogen bonds : bond 0.05985 / 3.89 ( 250) hydrogen bonds : angle 3.39657 / 2.46 ( 750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.118 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 296 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.7514 time to fit residues: 26.9220 Evaluate side-chains 35 residues out of total 324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.093546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070414 restraints weight = 5639.903| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.40 r_work: 0.2789 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3182 Z= 0.134 Angle : 0.458 6.233 4337 Z= 0.244 Chirality : 0.037 0.127 542 Planarity : 0.004 0.030 534 Dihedral : 3.521 26.710 446 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.31 % Allowed : 11.73 % Favored : 87.96 % 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: 4.09 (0.41), residues: 413 helix: 3.18 (0.28), residues: 341 sheet: None (None), residues: 0 loop : 0.15 (0.70), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.020 0.001 TYR A 299 PHE 0.008 0.001 PHE A 156 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3182) covalent geometry : angle 0.45826 / 0.24 ( 4337) hydrogen bonds : bond 0.05903 / 3.83 ( 250) hydrogen bonds : angle 3.37701 / 2.45 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.99 seconds wall clock time: 23 minutes 42.63 seconds (1422.63 seconds total)