Starting phenix.real_space_refine on Thu Sep 10 20:53:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23if_68990/09_2026/23if_68990.cif Found real_map, /net/cci-nas-00/data/ceres_data/23if_68990/09_2026/23if_68990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/23if_68990/09_2026/23if_68990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23if_68990/09_2026/23if_68990.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/23if_68990/09_2026/23if_68990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23if_68990/09_2026/23if_68990.map" } resolution = 3.3 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 19 5.16 5 C 2152 2.51 5 N 514 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3241 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 15, 'TRANS': 411} Chain breaks: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.91, per 1000 atoms: 0.28 Number of scatterers: 3246 At special positions: 0 Unit cell: (68, 70.55, 79.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 1 15.00 O 560 8.00 N 514 7.00 C 2152 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: 0.26 Conformation dependent library (CDL) restraints added in 141.3 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 1 sheets defined 83.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 27 through 57 removed outlier: 4.277A pdb=" N VAL A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Proline residue: A 49 - end of helix removed outlier: 3.581A pdb=" N LYS A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.824A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 71 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 72' Processing helix chain 'A' and resid 90 through 116 removed outlier: 3.569A pdb=" N HIS A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 116 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 removed outlier: 4.265A pdb=" N GLY A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 147 through 163 removed outlier: 3.693A pdb=" N GLN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.856A pdb=" N SER A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 Processing helix chain 'A' and resid 191 through 207 Processing helix chain 'A' and resid 208 through 211 Processing helix chain 'A' and resid 216 through 233 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.634A pdb=" N TRP A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 311 removed outlier: 3.623A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 4.004A pdb=" N HIS A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 326 through 350 Processing helix chain 'A' and resid 351 through 374 removed outlier: 3.893A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE A 364 " --> pdb=" O MET A 360 " (cutoff:3.500A) Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 377 through 401 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 414 removed outlier: 6.232A pdb=" N SER A 412 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 446 removed outlier: 3.590A pdb=" N THR A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 468 through 476 Processing sheet with id=AA1, first strand: chain 'A' and resid 271 through 272 removed outlier: 7.543A pdb=" N ASN A 271 " --> pdb=" O ARG A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 232 hydrogen bonds defined for protein. 687 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: 0.41 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 961 1.34 - 1.46: 761 1.46 - 1.58: 1580 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 3335 Sorted by residual: bond pdb=" C ILE A 48 " pdb=" N PRO A 49 " ideal model delta sigma weight residual 1.336 1.349 -0.013 1.25e-02 6.40e+03 1.13e+00 bond pdb=" C ILE A 281 " pdb=" N PRO A 282 " ideal model delta sigma weight residual 1.332 1.343 -0.011 1.12e-02 7.97e+03 9.86e-01 bond pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.77e-01 bond pdb=" CA ILE A 48 " pdb=" C ILE A 48 " ideal model delta sigma weight residual 1.520 1.527 -0.008 8.80e-03 1.29e+04 7.34e-01 bond pdb=" C LEU A 305 " pdb=" N PRO A 306 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.52e-01 ... (remaining 3330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 4403 1.35 - 2.70: 107 2.70 - 4.06: 20 4.06 - 5.41: 10 5.41 - 6.76: 4 Bond angle restraints: 4544 Sorted by residual: angle pdb=" C LEU A 113 " pdb=" N GLY A 114 " pdb=" CA GLY A 114 " ideal model delta sigma weight residual 120.03 123.75 -3.72 1.12e+00 7.97e-01 1.11e+01 angle pdb=" C GLY A 138 " pdb=" N ALA A 139 " pdb=" CA ALA A 139 " ideal model delta sigma weight residual 120.38 124.72 -4.34 1.37e+00 5.33e-01 1.00e+01 angle pdb=" N PRO A 282 " pdb=" CA PRO A 282 " pdb=" C PRO A 282 " ideal model delta sigma weight residual 110.95 114.62 -3.67 1.62e+00 3.81e-01 5.14e+00 angle pdb=" CB ARG A 116 " pdb=" CG ARG A 116 " pdb=" CD ARG A 116 " ideal model delta sigma weight residual 111.30 116.29 -4.99 2.30e+00 1.89e-01 4.72e+00 angle pdb=" CG ARG A 69 " pdb=" CD ARG A 69 " pdb=" NE ARG A 69 " ideal model delta sigma weight residual 112.00 116.75 -4.75 2.20e+00 2.07e-01 4.66e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.70: 1543 9.70 - 19.40: 197 19.40 - 29.10: 80 29.10 - 38.80: 35 38.80 - 48.50: 10 Dihedral angle restraints: 1865 sinusoidal: 665 harmonic: 1200 Sorted by residual: dihedral pdb=" C ILE A 48 " pdb=" N ILE A 48 " pdb=" CA ILE A 48 " pdb=" CB ILE A 48 " ideal model delta harmonic sigma weight residual -122.00 -129.37 7.37 0 2.50e+00 1.60e-01 8.68e+00 dihedral pdb=" CB MET A 456 " pdb=" CG MET A 456 " pdb=" SD MET A 456 " pdb=" CE MET A 456 " ideal model delta sinusoidal sigma weight residual 60.00 108.50 -48.50 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CB MET A 223 " pdb=" CG MET A 223 " pdb=" SD MET A 223 " pdb=" CE MET A 223 " ideal model delta sinusoidal sigma weight residual 60.00 106.26 -46.26 3 1.50e+01 4.44e-03 8.31e+00 ... (remaining 1862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 327 0.032 - 0.063: 138 0.063 - 0.094: 41 0.094 - 0.126: 21 0.126 - 0.157: 1 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA TRP A 166 " pdb=" N TRP A 166 " pdb=" C TRP A 166 " pdb=" CB TRP A 166 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 525 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 233 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C PHE A 233 " 0.037 2.00e-02 2.50e+03 pdb=" O PHE A 233 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU A 234 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 57 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 58 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 438 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO A 439 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " 0.024 5.00e-02 4.00e+02 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 799 2.80 - 3.32: 3283 3.32 - 3.85: 5537 3.85 - 4.37: 6184 4.37 - 4.90: 10992 Nonbonded interactions: 26795 Sorted by model distance: nonbonded pdb=" CD LYS A 269 " pdb=" CB ARG A 418 " model vdw 2.274 3.840 nonbonded pdb=" N TYR A 27 " pdb=" O TYR A 27 " model vdw 2.576 2.496 nonbonded pdb=" O ASP A 87 " pdb=" OD1 ASP A 87 " model vdw 2.604 3.040 nonbonded pdb=" O VAL A 230 " pdb=" O PHE A 233 " model vdw 2.639 3.040 nonbonded pdb=" N TRP A 80 " pdb=" O TRP A 80 " model vdw 2.644 2.496 ... (remaining 26790 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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.590 Find NCS groups from input model: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3335 Z= 0.130 Angle : 0.574 6.759 4544 Z= 0.304 Chirality : 0.041 0.157 528 Planarity : 0.005 0.047 550 Dihedral : 12.009 48.500 1103 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.97 (0.42), residues: 419 helix: 1.18 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -0.68 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 69 TYR 0.014 0.001 TYR A 150 PHE 0.016 0.001 PHE A 122 TRP 0.012 0.001 TRP A 80 HIS 0.007 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 3335) covalent geometry : angle 0.57365 / 0.30 ( 4544) hydrogen bonds : bond 0.11921 / 7.87 ( 232) hydrogen bonds : angle 5.76201 / 4.11 ( 687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.106 Fit side-chains REVERT: A 44 MET cc_start: 0.8710 (ttm) cc_final: 0.8442 (ttm) REVERT: A 294 SER cc_start: 0.8754 (t) cc_final: 0.8534 (t) REVERT: A 345 ILE cc_start: 0.8474 (mt) cc_final: 0.8257 (mp) REVERT: A 360 MET cc_start: 0.8805 (mmm) cc_final: 0.8437 (mmm) REVERT: A 376 MET cc_start: 0.6245 (tpt) cc_final: 0.5886 (tpt) REVERT: A 385 MET cc_start: 0.8680 (tpt) cc_final: 0.8316 (tpt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0601 time to fit residues: 8.8819 Evaluate side-chains 92 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144691 restraints weight = 5623.567| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.39 r_work: 0.3689 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3335 Z= 0.172 Angle : 0.597 7.551 4544 Z= 0.301 Chirality : 0.043 0.194 528 Planarity : 0.005 0.046 550 Dihedral : 3.813 17.495 447 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.96 % Allowed : 14.50 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.42), residues: 419 helix: 1.39 (0.29), residues: 311 sheet: None (None), residues: 0 loop : -0.39 (0.67), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 418 TYR 0.021 0.002 TYR A 103 PHE 0.018 0.002 PHE A 133 TRP 0.026 0.002 TRP A 450 HIS 0.005 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 3335) covalent geometry : angle 0.59679 / 0.30 ( 4544) hydrogen bonds : bond 0.04418 / 2.89 ( 232) hydrogen bonds : angle 4.66919 / 3.27 ( 687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 35 THR cc_start: 0.8483 (p) cc_final: 0.8255 (p) REVERT: A 294 SER cc_start: 0.8944 (t) cc_final: 0.8742 (t) REVERT: A 332 ASP cc_start: 0.7252 (m-30) cc_final: 0.7011 (m-30) REVERT: A 345 ILE cc_start: 0.8482 (mt) cc_final: 0.8268 (mt) REVERT: A 360 MET cc_start: 0.8965 (mmm) cc_final: 0.8740 (mmm) REVERT: A 385 MET cc_start: 0.8641 (tpt) cc_final: 0.8290 (tpt) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.0430 time to fit residues: 5.1561 Evaluate side-chains 91 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 380 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135962 restraints weight = 5740.346| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.40 r_work: 0.3594 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3335 Z= 0.219 Angle : 0.614 5.600 4544 Z= 0.316 Chirality : 0.044 0.132 528 Planarity : 0.005 0.043 550 Dihedral : 4.079 17.680 447 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.44 % Allowed : 18.64 % Favored : 76.92 % 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: 0.95 (0.41), residues: 419 helix: 1.07 (0.28), residues: 312 sheet: None (None), residues: 0 loop : -0.46 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 418 TYR 0.014 0.002 TYR A 103 PHE 0.018 0.002 PHE A 133 TRP 0.030 0.002 TRP A 450 HIS 0.005 0.002 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.22 ( 3335) covalent geometry : angle 0.61430 / 0.32 ( 4544) hydrogen bonds : bond 0.04746 / 3.09 ( 232) hydrogen bonds : angle 4.79147 / 3.39 ( 687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.117 Fit side-chains REVERT: A 35 THR cc_start: 0.8574 (p) cc_final: 0.8294 (p) REVERT: A 43 HIS cc_start: 0.9046 (OUTLIER) cc_final: 0.8647 (m170) REVERT: A 223 MET cc_start: 0.8658 (tpp) cc_final: 0.8394 (tpp) REVERT: A 332 ASP cc_start: 0.7439 (m-30) cc_final: 0.7112 (m-30) REVERT: A 341 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 347 ASP cc_start: 0.8085 (m-30) cc_final: 0.7821 (m-30) REVERT: A 385 MET cc_start: 0.8656 (tpt) cc_final: 0.8354 (tpt) outliers start: 15 outliers final: 10 residues processed: 102 average time/residue: 0.0435 time to fit residues: 5.8925 Evaluate side-chains 96 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 380 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 5 optimal weight: 0.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141175 restraints weight = 5607.880| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.22 r_work: 0.3662 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3335 Z= 0.146 Angle : 0.554 5.494 4544 Z= 0.283 Chirality : 0.041 0.161 528 Planarity : 0.005 0.039 550 Dihedral : 3.963 17.616 447 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.25 % Allowed : 22.49 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.42), residues: 419 helix: 1.25 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.36 (0.69), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 69 TYR 0.014 0.001 TYR A 103 PHE 0.025 0.002 PHE A 386 TRP 0.029 0.001 TRP A 450 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 3335) covalent geometry : angle 0.55429 / 0.28 ( 4544) hydrogen bonds : bond 0.04213 / 2.74 ( 232) hydrogen bonds : angle 4.56852 / 3.22 ( 687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.120 Fit side-chains REVERT: A 35 THR cc_start: 0.8612 (p) cc_final: 0.8361 (p) REVERT: A 43 HIS cc_start: 0.8952 (OUTLIER) cc_final: 0.8429 (m170) REVERT: A 332 ASP cc_start: 0.7397 (m-30) cc_final: 0.7096 (m-30) REVERT: A 341 LEU cc_start: 0.8690 (mm) cc_final: 0.8270 (mm) REVERT: A 345 ILE cc_start: 0.8473 (mt) cc_final: 0.8206 (mt) REVERT: A 385 MET cc_start: 0.8607 (tpt) cc_final: 0.8349 (tpt) outliers start: 11 outliers final: 8 residues processed: 97 average time/residue: 0.0391 time to fit residues: 5.0864 Evaluate side-chains 94 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 380 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139638 restraints weight = 5655.346| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.35 r_work: 0.3638 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3335 Z= 0.159 Angle : 0.561 5.567 4544 Z= 0.288 Chirality : 0.041 0.140 528 Planarity : 0.004 0.042 550 Dihedral : 3.998 17.203 447 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.73 % Allowed : 20.12 % Favored : 75.15 % 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: 1.27 (0.42), residues: 419 helix: 1.29 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.36 (0.70), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.013 0.001 TYR A 103 PHE 0.017 0.001 PHE A 133 TRP 0.032 0.002 TRP A 450 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 3335) covalent geometry : angle 0.56080 / 0.29 ( 4544) hydrogen bonds : bond 0.04231 / 2.75 ( 232) hydrogen bonds : angle 4.50143 / 3.17 ( 687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.090 Fit side-chains REVERT: A 35 THR cc_start: 0.8612 (p) cc_final: 0.8355 (p) REVERT: A 43 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8467 (m170) REVERT: A 223 MET cc_start: 0.8567 (tpp) cc_final: 0.8349 (tpp) REVERT: A 233 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6268 (t80) REVERT: A 332 ASP cc_start: 0.7463 (m-30) cc_final: 0.7135 (m-30) REVERT: A 364 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 385 MET cc_start: 0.8636 (tpt) cc_final: 0.8370 (tpt) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.0401 time to fit residues: 5.3153 Evaluate side-chains 99 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 380 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 474 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.151448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140492 restraints weight = 5738.740| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.36 r_work: 0.3641 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3335 Z= 0.144 Angle : 0.545 5.616 4544 Z= 0.280 Chirality : 0.041 0.137 528 Planarity : 0.004 0.041 550 Dihedral : 3.983 16.980 447 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.44 % Allowed : 21.60 % Favored : 73.96 % 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: 1.34 (0.43), residues: 419 helix: 1.35 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.34 (0.71), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 418 TYR 0.013 0.001 TYR A 103 PHE 0.025 0.002 PHE A 386 TRP 0.036 0.001 TRP A 450 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3335) covalent geometry : angle 0.54512 / 0.28 ( 4544) hydrogen bonds : bond 0.04093 / 2.67 ( 232) hydrogen bonds : angle 4.43361 / 3.12 ( 687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.112 Fit side-chains REVERT: A 35 THR cc_start: 0.8576 (p) cc_final: 0.8314 (p) REVERT: A 43 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.8610 (m170) REVERT: A 233 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6406 (t80) REVERT: A 332 ASP cc_start: 0.7477 (m-30) cc_final: 0.7115 (m-30) REVERT: A 364 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 385 MET cc_start: 0.8657 (tpt) cc_final: 0.8427 (tpt) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.0388 time to fit residues: 5.0480 Evaluate side-chains 97 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 380 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 474 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.149450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138706 restraints weight = 5842.290| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.38 r_work: 0.3618 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3335 Z= 0.184 Angle : 0.593 5.839 4544 Z= 0.303 Chirality : 0.042 0.137 528 Planarity : 0.004 0.042 550 Dihedral : 4.092 16.785 447 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.33 % Allowed : 21.89 % Favored : 72.78 % 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: 1.10 (0.42), residues: 419 helix: 1.17 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.40 (0.70), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.012 0.001 TYR A 103 PHE 0.018 0.002 PHE A 133 TRP 0.043 0.002 TRP A 450 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 3335) covalent geometry : angle 0.59325 / 0.30 ( 4544) hydrogen bonds : bond 0.04476 / 2.95 ( 232) hydrogen bonds : angle 4.52653 / 3.19 ( 687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 35 THR cc_start: 0.8634 (p) cc_final: 0.8382 (p) REVERT: A 43 HIS cc_start: 0.9021 (OUTLIER) cc_final: 0.8650 (m170) REVERT: A 210 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5123 (m-80) REVERT: A 233 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.6433 (t80) REVERT: A 332 ASP cc_start: 0.7581 (m-30) cc_final: 0.7198 (m-30) REVERT: A 364 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 385 MET cc_start: 0.8636 (tpt) cc_final: 0.8413 (tpt) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.0379 time to fit residues: 4.8947 Evaluate side-chains 96 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 380 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 474 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140775 restraints weight = 5899.134| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.39 r_work: 0.3632 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3335 Z= 0.140 Angle : 0.558 6.350 4544 Z= 0.283 Chirality : 0.041 0.140 528 Planarity : 0.004 0.043 550 Dihedral : 4.021 16.996 447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.03 % Allowed : 22.78 % Favored : 72.19 % 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: 1.16 (0.42), residues: 419 helix: 1.25 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -0.54 (0.69), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.013 0.001 TYR A 103 PHE 0.027 0.001 PHE A 386 TRP 0.033 0.001 TRP A 450 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 3335) covalent geometry : angle 0.55764 / 0.28 ( 4544) hydrogen bonds : bond 0.04145 / 2.75 ( 232) hydrogen bonds : angle 4.41237 / 3.12 ( 687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 35 THR cc_start: 0.8547 (p) cc_final: 0.8292 (p) REVERT: A 43 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.8661 (m170) REVERT: A 116 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6198 (mpp80) REVERT: A 210 PHE cc_start: 0.6077 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: A 233 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.6396 (t80) REVERT: A 332 ASP cc_start: 0.7572 (m-30) cc_final: 0.7181 (m-30) REVERT: A 364 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 385 MET cc_start: 0.8623 (tpt) cc_final: 0.8399 (tpt) outliers start: 17 outliers final: 11 residues processed: 90 average time/residue: 0.0398 time to fit residues: 4.8321 Evaluate side-chains 96 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 380 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 474 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.151366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.140692 restraints weight = 5854.296| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.37 r_work: 0.3632 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3335 Z= 0.146 Angle : 0.566 6.674 4544 Z= 0.286 Chirality : 0.041 0.134 528 Planarity : 0.004 0.041 550 Dihedral : 4.021 16.687 447 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.03 % Allowed : 22.19 % Favored : 72.78 % 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: 1.17 (0.42), residues: 419 helix: 1.26 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.58 (0.70), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.012 0.001 TYR A 103 PHE 0.016 0.001 PHE A 133 TRP 0.032 0.001 TRP A 450 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3335) covalent geometry : angle 0.56588 / 0.29 ( 4544) hydrogen bonds : bond 0.04162 / 2.75 ( 232) hydrogen bonds : angle 4.38106 / 3.10 ( 687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.127 Fit side-chains REVERT: A 35 THR cc_start: 0.8532 (p) cc_final: 0.8278 (p) REVERT: A 43 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8727 (m170) REVERT: A 116 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6407 (mpp80) REVERT: A 210 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5039 (m-80) REVERT: A 233 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6438 (t80) REVERT: A 332 ASP cc_start: 0.7575 (m-30) cc_final: 0.7165 (m-30) REVERT: A 364 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 385 MET cc_start: 0.8627 (tpt) cc_final: 0.8401 (tpt) outliers start: 17 outliers final: 9 residues processed: 90 average time/residue: 0.0384 time to fit residues: 4.6560 Evaluate side-chains 94 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 380 TRP Chi-restraints excluded: chain A residue 474 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 16 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.9525 > 50:) chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139186 restraints weight = 5790.774| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.22 r_work: 0.3629 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3335 Z= 0.179 Angle : 0.614 8.098 4544 Z= 0.307 Chirality : 0.042 0.139 528 Planarity : 0.004 0.042 550 Dihedral : 4.125 16.734 447 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.62 % Allowed : 22.49 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.42), residues: 419 helix: 1.12 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.70 (0.69), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 116 TYR 0.012 0.001 TYR A 103 PHE 0.028 0.002 PHE A 386 TRP 0.032 0.002 TRP A 450 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 3335) covalent geometry : angle 0.61364 / 0.31 ( 4544) hydrogen bonds : bond 0.04386 / 2.87 ( 232) hydrogen bonds : angle 4.50153 / 3.17 ( 687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.113 Fit side-chains REVERT: A 35 THR cc_start: 0.8600 (p) cc_final: 0.8349 (p) REVERT: A 43 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8772 (m170) REVERT: A 116 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6504 (mpp80) REVERT: A 210 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5058 (m-80) REVERT: A 233 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6400 (t80) REVERT: A 332 ASP cc_start: 0.7632 (m-30) cc_final: 0.7197 (m-30) REVERT: A 364 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 385 MET cc_start: 0.8633 (tpt) cc_final: 0.8390 (tpt) outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.0493 time to fit residues: 5.9883 Evaluate side-chains 99 residues out of total 338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 380 TRP Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 474 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139438 restraints weight = 5809.510| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.20 r_work: 0.3640 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3335 Z= 0.172 Angle : 0.621 7.350 4544 Z= 0.312 Chirality : 0.042 0.139 528 Planarity : 0.005 0.067 550 Dihedral : 4.184 16.942 447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.03 % Allowed : 23.96 % Favored : 71.01 % 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: 0.88 (0.42), residues: 419 helix: 1.10 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.82 (0.68), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 69 TYR 0.012 0.001 TYR A 103 PHE 0.016 0.001 PHE A 133 TRP 0.031 0.001 TRP A 450 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 3335) covalent geometry : angle 0.62139 / 0.31 ( 4544) hydrogen bonds : bond 0.04280 / 2.81 ( 232) hydrogen bonds : angle 4.47597 / 3.15 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 896.90 seconds wall clock time: 16 minutes 4.62 seconds (964.62 seconds total)