Starting phenix.real_space_refine on Wed Sep 17 03:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoa_38524/09_2025/8xoa_38524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoa_38524/09_2025/8xoa_38524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xoa_38524/09_2025/8xoa_38524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoa_38524/09_2025/8xoa_38524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xoa_38524/09_2025/8xoa_38524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoa_38524/09_2025/8xoa_38524.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 1807 2.51 5 N 419 2.21 5 O 461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2713 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2700 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 23, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 3, 'GLU:plan': 3, 'PHE:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'WRF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.90, per 1000 atoms: 0.33 Number of scatterers: 2713 At special positions: 0 Unit cell: (52.7, 63.75, 69.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 461 8.00 N 419 7.00 C 1807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 69.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 93.1% 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 19 through 49 removed outlier: 3.903A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 132 through 157 removed outlier: 4.323A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.913A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.674A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.556A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix removed outlier: 3.773A pdb=" N GLU A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.760A pdb=" N GLY A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.092A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.574A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix removed outlier: 3.897A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 435 removed outlier: 3.686A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.769A pdb=" N ARG A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) 243 hydrogen bonds defined for protein. 720 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: 0.43 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 446 1.33 - 1.45: 682 1.45 - 1.57: 1605 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 2777 Sorted by residual: bond pdb=" N GLN A 271 " pdb=" CA GLN A 271 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.10e-03 1.98e+04 1.69e+01 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ILE A 174 " pdb=" CA ILE A 174 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 9.95e+00 bond pdb=" N VAL A 269 " pdb=" CA VAL A 269 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.28e-02 6.10e+03 9.54e+00 ... (remaining 2772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 3581 2.04 - 4.07: 182 4.07 - 6.11: 24 6.11 - 8.15: 5 8.15 - 10.19: 3 Bond angle restraints: 3795 Sorted by residual: angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 111.28 105.93 5.35 1.09e+00 8.42e-01 2.41e+01 angle pdb=" CA GLN A 271 " pdb=" C GLN A 271 " pdb=" N PRO A 272 " ideal model delta sigma weight residual 118.09 122.14 -4.05 8.30e-01 1.45e+00 2.38e+01 angle pdb=" N LEU A 255 " pdb=" CA LEU A 255 " pdb=" C LEU A 255 " ideal model delta sigma weight residual 111.28 106.44 4.84 1.09e+00 8.42e-01 1.97e+01 angle pdb=" N PRO A 45 " pdb=" CA PRO A 45 " pdb=" C PRO A 45 " ideal model delta sigma weight residual 113.78 106.62 7.16 1.62e+00 3.81e-01 1.95e+01 angle pdb=" N LYS A 290 " pdb=" CA LYS A 290 " pdb=" C LYS A 290 " ideal model delta sigma weight residual 113.28 108.13 5.15 1.22e+00 6.72e-01 1.78e+01 ... (remaining 3790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.11: 1380 11.11 - 22.22: 159 22.22 - 33.32: 52 33.32 - 44.43: 13 44.43 - 55.54: 5 Dihedral angle restraints: 1609 sinusoidal: 549 harmonic: 1060 Sorted by residual: dihedral pdb=" C LYS A 290 " pdb=" N LYS A 290 " pdb=" CA LYS A 290 " pdb=" CB LYS A 290 " ideal model delta harmonic sigma weight residual -122.60 -110.21 -12.39 0 2.50e+00 1.60e-01 2.46e+01 dihedral pdb=" CA VAL A 417 " pdb=" C VAL A 417 " pdb=" N TYR A 418 " pdb=" CA TYR A 418 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE A 350 " pdb=" C ILE A 350 " pdb=" N LEU A 351 " pdb=" CA LEU A 351 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 1606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 397 0.075 - 0.150: 55 0.150 - 0.225: 11 0.225 - 0.300: 2 0.300 - 0.374: 2 Chirality restraints: 467 Sorted by residual: chirality pdb=" CA LYS A 290 " pdb=" N LYS A 290 " pdb=" C LYS A 290 " pdb=" CB LYS A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CA ASP A 262 " pdb=" N ASP A 262 " pdb=" C ASP A 262 " pdb=" CB ASP A 262 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA LEU A 255 " pdb=" N LEU A 255 " pdb=" C LEU A 255 " pdb=" CB LEU A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 464 not shown) Planarity restraints: 468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 473 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 474 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 474 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 474 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 280 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C GLN A 280 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 280 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 281 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 44 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ILE A 44 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 44 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO A 45 " 0.011 2.00e-02 2.50e+03 ... (remaining 465 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 903 2.86 - 3.37: 2902 3.37 - 3.88: 4311 3.88 - 4.39: 5042 4.39 - 4.90: 8872 Nonbonded interactions: 22030 Sorted by model distance: nonbonded pdb=" NE2 GLN A 142 " pdb=" OD2 ASP A 426 " model vdw 2.346 3.120 nonbonded pdb=" O LEU A 30 " pdb=" ND2 ASN A 34 " model vdw 2.393 3.120 nonbonded pdb=" O SER A 180 " pdb=" OG SER A 180 " model vdw 2.452 3.040 nonbonded pdb=" O PRO A 473 " pdb=" CA PRO A 474 " model vdw 2.594 2.776 nonbonded pdb=" O ILE A 43 " pdb=" N TYR A 47 " model vdw 2.595 3.120 ... (remaining 22025 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: 1.060 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.520 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.007 0.060 2777 Z= 0.431 Angle : 1.002 10.186 3795 Z= 0.662 Chirality : 0.061 0.374 467 Planarity : 0.007 0.056 468 Dihedral : 11.516 55.540 933 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.30 % 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 aren not related in a simple way. whole: 0.90 (0.43), residues: 372 helix: 0.99 (0.30), residues: 304 sheet: None (None), residues: 0 loop : -0.93 (0.77), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.012 0.002 TYR A 408 PHE 0.017 0.002 PHE A 238 TRP 0.015 0.002 TRP A 318 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 2777) covalent geometry : angle 1.00220 ( 3795) hydrogen bonds : bond 0.14609 ( 243) hydrogen bonds : angle 6.45375 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0417 time to fit residues: 2.4245 Evaluate side-chains 39 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.182569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168637 restraints weight = 3292.501| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.28 r_work: 0.3784 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2777 Z= 0.161 Angle : 0.690 9.427 3795 Z= 0.331 Chirality : 0.041 0.126 467 Planarity : 0.006 0.051 468 Dihedral : 4.534 17.802 390 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.73 % Allowed : 9.09 % Favored : 90.18 % 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 aren not related in a simple way. whole: 1.24 (0.43), residues: 372 helix: 1.15 (0.29), residues: 314 sheet: None (None), residues: 0 loop : -0.65 (0.83), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 217 TYR 0.015 0.002 TYR A 422 PHE 0.015 0.002 PHE A 238 TRP 0.007 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 2777) covalent geometry : angle 0.69025 ( 3795) hydrogen bonds : bond 0.04644 ( 243) hydrogen bonds : angle 5.13960 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.059 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.0459 time to fit residues: 2.5458 Evaluate side-chains 40 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.4980 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 4 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.188256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.174874 restraints weight = 3323.681| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.24 r_work: 0.3725 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2777 Z= 0.126 Angle : 0.613 9.369 3795 Z= 0.291 Chirality : 0.040 0.201 467 Planarity : 0.006 0.046 468 Dihedral : 4.125 15.546 390 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.82 % Allowed : 10.91 % Favored : 87.27 % 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 aren not related in a simple way. whole: 1.99 (0.44), residues: 372 helix: 1.70 (0.29), residues: 315 sheet: None (None), residues: 0 loop : -0.69 (0.85), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 217 TYR 0.012 0.001 TYR A 422 PHE 0.014 0.001 PHE A 348 TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2777) covalent geometry : angle 0.61346 ( 3795) hydrogen bonds : bond 0.03936 ( 243) hydrogen bonds : angle 4.67132 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.104 Fit side-chains REVERT: A 347 ILE cc_start: 0.8213 (mm) cc_final: 0.7978 (pt) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.0448 time to fit residues: 2.9629 Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.185246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.171277 restraints weight = 3254.498| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 1.28 r_work: 0.3781 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2777 Z= 0.139 Angle : 0.633 9.356 3795 Z= 0.299 Chirality : 0.041 0.205 467 Planarity : 0.006 0.044 468 Dihedral : 4.122 16.044 390 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.09 % Allowed : 12.36 % Favored : 86.55 % 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 aren not related in a simple way. whole: 1.95 (0.44), residues: 372 helix: 1.68 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.87 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 217 TYR 0.014 0.001 TYR A 422 PHE 0.020 0.002 PHE A 238 TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2777) covalent geometry : angle 0.63338 ( 3795) hydrogen bonds : bond 0.04015 ( 243) hydrogen bonds : angle 4.67691 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.106 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.0419 time to fit residues: 2.6706 Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.185002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171114 restraints weight = 3227.101| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.27 r_work: 0.3801 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2777 Z= 0.135 Angle : 0.619 9.377 3795 Z= 0.293 Chirality : 0.040 0.135 467 Planarity : 0.006 0.044 468 Dihedral : 4.090 15.883 390 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.55 % Allowed : 12.00 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.43), residues: 372 helix: 1.69 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.94 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 217 TYR 0.014 0.001 TYR A 422 PHE 0.019 0.002 PHE A 238 TRP 0.003 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2777) covalent geometry : angle 0.61947 ( 3795) hydrogen bonds : bond 0.03903 ( 243) hydrogen bonds : angle 4.63084 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.060 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.0355 time to fit residues: 2.5676 Evaluate side-chains 48 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.183942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170016 restraints weight = 3275.137| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.28 r_work: 0.3795 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2777 Z= 0.137 Angle : 0.627 9.390 3795 Z= 0.298 Chirality : 0.040 0.123 467 Planarity : 0.006 0.043 468 Dihedral : 4.100 15.950 390 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.82 % Allowed : 12.73 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.43), residues: 372 helix: 1.68 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.98 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 357 TYR 0.014 0.001 TYR A 422 PHE 0.032 0.002 PHE A 238 TRP 0.002 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 2777) covalent geometry : angle 0.62724 ( 3795) hydrogen bonds : bond 0.03859 ( 243) hydrogen bonds : angle 4.62013 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.099 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.0511 time to fit residues: 3.2079 Evaluate side-chains 45 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.182499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.168558 restraints weight = 3267.637| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.28 r_work: 0.3732 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2777 Z= 0.144 Angle : 0.638 9.423 3795 Z= 0.305 Chirality : 0.041 0.131 467 Planarity : 0.006 0.044 468 Dihedral : 4.165 16.433 390 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.45 % Allowed : 12.36 % Favored : 86.18 % 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 aren not related in a simple way. whole: 1.77 (0.43), residues: 372 helix: 1.56 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.94 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.015 0.002 TYR A 422 PHE 0.014 0.002 PHE A 166 TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 2777) covalent geometry : angle 0.63769 ( 3795) hydrogen bonds : bond 0.03947 ( 243) hydrogen bonds : angle 4.68438 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.100 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.0420 time to fit residues: 2.7265 Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.0040 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.184263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.170332 restraints weight = 3330.325| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.29 r_work: 0.3638 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2777 Z= 0.139 Angle : 0.628 9.434 3795 Z= 0.299 Chirality : 0.040 0.137 467 Planarity : 0.006 0.043 468 Dihedral : 4.134 16.532 390 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.45 % Allowed : 13.82 % Favored : 84.73 % 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 aren not related in a simple way. whole: 1.80 (0.43), residues: 372 helix: 1.60 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.01 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.014 0.002 TYR A 422 PHE 0.031 0.002 PHE A 238 TRP 0.004 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2777) covalent geometry : angle 0.62801 ( 3795) hydrogen bonds : bond 0.03861 ( 243) hydrogen bonds : angle 4.66210 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.059 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.0402 time to fit residues: 2.5387 Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.179668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.165009 restraints weight = 3397.071| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.36 r_work: 0.3719 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2777 Z= 0.139 Angle : 0.632 9.419 3795 Z= 0.302 Chirality : 0.041 0.145 467 Planarity : 0.006 0.043 468 Dihedral : 4.126 16.348 390 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.45 % Allowed : 14.18 % Favored : 84.36 % 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 aren not related in a simple way. whole: 1.84 (0.43), residues: 372 helix: 1.61 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.89 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 217 TYR 0.015 0.002 TYR A 422 PHE 0.015 0.001 PHE A 166 TRP 0.005 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2777) covalent geometry : angle 0.63160 ( 3795) hydrogen bonds : bond 0.03846 ( 243) hydrogen bonds : angle 4.66135 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.112 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.0419 time to fit residues: 2.7184 Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 350 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.183485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.169572 restraints weight = 3328.002| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.29 r_work: 0.3632 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2777 Z= 0.153 Angle : 0.648 9.456 3795 Z= 0.311 Chirality : 0.041 0.163 467 Planarity : 0.006 0.044 468 Dihedral : 4.232 16.928 390 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.73 % Allowed : 15.27 % Favored : 84.00 % 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 aren not related in a simple way. whole: 1.73 (0.43), residues: 372 helix: 1.52 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.80 (0.81), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.015 0.002 TYR A 422 PHE 0.016 0.002 PHE A 468 TRP 0.006 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2777) covalent geometry : angle 0.64839 ( 3795) hydrogen bonds : bond 0.04017 ( 243) hydrogen bonds : angle 4.78165 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.100 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.0511 time to fit residues: 3.0069 Evaluate side-chains 45 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.0050 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 36 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.192766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.180615 restraints weight = 3213.933| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.12 r_work: 0.3766 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2777 Z= 0.122 Angle : 0.615 9.376 3795 Z= 0.293 Chirality : 0.039 0.162 467 Planarity : 0.006 0.041 468 Dihedral : 3.967 15.227 390 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.73 % Allowed : 15.27 % Favored : 84.00 % 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 aren not related in a simple way. whole: 2.28 (0.44), residues: 372 helix: 1.91 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.77 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 189 TYR 0.013 0.001 TYR A 422 PHE 0.014 0.001 PHE A 166 TRP 0.006 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 2777) covalent geometry : angle 0.61547 ( 3795) hydrogen bonds : bond 0.03549 ( 243) hydrogen bonds : angle 4.47489 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 851.01 seconds wall clock time: 15 minutes 16.12 seconds (916.12 seconds total)