Starting phenix.real_space_refine on Thu Jul 2 00:37:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l1a_62739/07_2026/9l1a_62739_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l1a_62739/07_2026/9l1a_62739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l1a_62739/07_2026/9l1a_62739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l1a_62739/07_2026/9l1a_62739.map" model { file = "/net/cci-nas-00/data/ceres_data/9l1a_62739/07_2026/9l1a_62739_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l1a_62739/07_2026/9l1a_62739_trim.cif" } resolution = 2.75 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= -0.003 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 32 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 2981 2.51 5 N 662 2.21 5 O 745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4422 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4319 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 28, 'TRANS': 513} Chain breaks: 1 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 101 Ad-hoc single atom residues: {' NA': 1, ' CL': 1} Unusual residues: {'CLR': 1, 'Y01': 2} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Chain breaks: 2 Time building chain proxies: 1.04, per 1000 atoms: 0.24 Number of scatterers: 4422 At special positions: 0 Unit cell: (76.824, 67.221, 92.829, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 32 16.00 Na 1 11.00 O 745 8.00 N 662 7.00 C 2981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 162.0 milliseconds 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 79.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.041A pdb=" N GLY A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.636A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.731A pdb=" N GLU A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.893A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.504A pdb=" N ARG A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 238 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 250 through 267 removed outlier: 4.488A pdb=" N PHE A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.629A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 removed outlier: 3.688A pdb=" N GLU A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 302 removed outlier: 4.295A pdb=" N TRP A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.766A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 356 removed outlier: 4.398A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.704A pdb=" N TYR A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.550A pdb=" N THR A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.673A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.979A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.817A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 4.410A pdb=" N LYS A 505 " --> pdb=" O GLY A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.185A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 568 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 586 through 593 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 284 hydrogen bonds defined for protein. 834 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: 0.65 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 652 1.32 - 1.44: 1367 1.44 - 1.56: 2503 1.56 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 4568 Sorted by residual: bond pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.33e+01 bond pdb=" N ARG A 177 " pdb=" CA ARG A 177 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta sigma weight residual 1.461 1.498 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.30e-02 5.92e+03 9.44e+00 bond pdb=" N TRP A 166 " pdb=" CA TRP A 166 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.26e-02 6.30e+03 8.87e+00 ... (remaining 4563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 5734 1.20 - 2.41: 330 2.41 - 3.61: 133 3.61 - 4.82: 41 4.82 - 6.02: 9 Bond angle restraints: 6247 Sorted by residual: angle pdb=" N CYS A 305 " pdb=" CA CYS A 305 " pdb=" C CYS A 305 " ideal model delta sigma weight residual 113.23 107.63 5.60 1.22e+00 6.72e-01 2.11e+01 angle pdb=" C HIS A 212 " pdb=" N PRO A 213 " pdb=" CA PRO A 213 " ideal model delta sigma weight residual 119.05 123.44 -4.39 1.11e+00 8.12e-01 1.57e+01 angle pdb=" CA ASN A 167 " pdb=" C ASN A 167 " pdb=" O ASN A 167 " ideal model delta sigma weight residual 120.38 116.21 4.17 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CA VAL A 239 " pdb=" C VAL A 239 " pdb=" O VAL A 239 " ideal model delta sigma weight residual 120.95 117.04 3.91 1.04e+00 9.25e-01 1.41e+01 angle pdb=" C MET A 176 " pdb=" N ARG A 177 " pdb=" CA ARG A 177 " ideal model delta sigma weight residual 120.60 126.57 -5.97 1.60e+00 3.91e-01 1.39e+01 ... (remaining 6242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 2368 16.31 - 32.62: 255 32.62 - 48.93: 78 48.93 - 65.24: 22 65.24 - 81.55: 4 Dihedral angle restraints: 2727 sinusoidal: 1167 harmonic: 1560 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -117.91 31.91 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CA GLU A 114 " pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " pdb=" CD GLU A 114 " ideal model delta sinusoidal sigma weight residual -180.00 -121.38 -58.62 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB MET A 327 " pdb=" CG MET A 327 " pdb=" SD MET A 327 " pdb=" CE MET A 327 " ideal model delta sinusoidal sigma weight residual 180.00 124.54 55.46 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 2724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 507 0.043 - 0.086: 131 0.086 - 0.129: 39 0.129 - 0.172: 7 0.172 - 0.214: 7 Chirality restraints: 691 Sorted by residual: chirality pdb=" CA ILE A 210 " pdb=" N ILE A 210 " pdb=" C ILE A 210 " pdb=" CB ILE A 210 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA HIS A 212 " pdb=" N HIS A 212 " pdb=" C HIS A 212 " pdb=" CB HIS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS A 178 " pdb=" N LYS A 178 " pdb=" C LYS A 178 " pdb=" CB LYS A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 688 not shown) Planarity restraints: 749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 165 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C SER A 165 " -0.038 2.00e-02 2.50e+03 pdb=" O SER A 165 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP A 166 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 581 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 582 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 582 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 582 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 58 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C PHE A 58 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE A 58 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 59 " 0.011 2.00e-02 2.50e+03 ... (remaining 746 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 702 2.75 - 3.29: 4458 3.29 - 3.83: 7627 3.83 - 4.36: 9479 4.36 - 4.90: 16174 Nonbonded interactions: 38440 Sorted by model distance: nonbonded pdb=" O GLY A 56 " pdb="NA NA A 701 " model vdw 2.218 3.210 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 325 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP A 494 " pdb=" OG1 THR A 596 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 489 " pdb=" O GLY A 501 " model vdw 2.303 3.040 nonbonded pdb=" O PHE A 86 " pdb=" N GLY A 91 " model vdw 2.303 3.120 ... (remaining 38435 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: 1.580 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: 0.020 Set scattering table: 0.010 Process input model: 5.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.005 0.047 4569 Z= 0.344 Angle : 0.784 6.024 6249 Z= 0.504 Chirality : 0.047 0.214 691 Planarity : 0.005 0.048 749 Dihedral : 15.251 81.553 1738 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 20.13 % Favored : 79.87 % 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: 0.06 (0.35), residues: 538 helix: 0.56 (0.25), residues: 379 sheet: None (None), residues: 0 loop : -1.05 (0.49), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.011 0.001 TYR A 69 PHE 0.013 0.001 PHE A 58 TRP 0.016 0.001 TRP A 166 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.34 ( 4568) covalent geometry : angle 0.78369 / 0.50 ( 6247) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 1.60703 / 0.86 ( 2) hydrogen bonds : bond 0.21228 / 13.57 ( 284) hydrogen bonds : angle 7.82140 / 5.50 ( 834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 237 LYS cc_start: 0.6801 (mtpp) cc_final: 0.6040 (mmtt) REVERT: A 293 ASP cc_start: 0.8137 (m-30) cc_final: 0.7758 (m-30) REVERT: A 324 ARG cc_start: 0.7485 (mmt-90) cc_final: 0.7270 (mmt180) REVERT: A 364 GLU cc_start: 0.8490 (tt0) cc_final: 0.8137 (tt0) REVERT: A 378 VAL cc_start: 0.8679 (t) cc_final: 0.8097 (p) REVERT: A 383 LEU cc_start: 0.7989 (tp) cc_final: 0.7708 (mt) REVERT: A 495 MET cc_start: 0.8599 (mtp) cc_final: 0.8394 (mtp) REVERT: A 588 TRP cc_start: 0.7120 (m100) cc_final: 0.6826 (m100) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3466 time to fit residues: 43.5944 Evaluate side-chains 77 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 50 optimal weight: 0.1980 chunk 53 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.138018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118827 restraints weight = 5074.321| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.19 r_work: 0.3218 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4569 Z= 0.142 Angle : 0.598 6.956 6249 Z= 0.299 Chirality : 0.042 0.261 691 Planarity : 0.004 0.035 749 Dihedral : 8.513 57.870 798 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.33 % Allowed : 18.40 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.37), residues: 538 helix: 1.40 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.88 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 564 TYR 0.012 0.001 TYR A 578 PHE 0.013 0.002 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4568) covalent geometry : angle 0.59807 / 0.30 ( 6247) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.61225 / 0.33 ( 2) hydrogen bonds : bond 0.04806 / 3.13 ( 284) hydrogen bonds : angle 5.17679 / 3.60 ( 834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: A 383 LEU cc_start: 0.8288 (tp) cc_final: 0.8042 (mt) REVERT: A 587 ARG cc_start: 0.6912 (ptm-80) cc_final: 0.6309 (ptm-80) outliers start: 20 outliers final: 9 residues processed: 87 average time/residue: 0.3003 time to fit residues: 27.6652 Evaluate side-chains 74 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 593 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN A 487 ASN A 567 GLN A 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114139 restraints weight = 5072.883| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.25 r_work: 0.3161 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4569 Z= 0.154 Angle : 0.575 6.699 6249 Z= 0.288 Chirality : 0.042 0.232 691 Planarity : 0.004 0.035 749 Dihedral : 8.165 59.555 798 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.41 % Allowed : 17.75 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.36), residues: 538 helix: 1.36 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -1.01 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.013 0.001 TYR A 578 PHE 0.014 0.002 PHE A 392 TRP 0.023 0.001 TRP A 588 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 4568) covalent geometry : angle 0.57459 / 0.29 ( 6247) SS BOND : bond 0.00057 / 0.03 ( 1) SS BOND : angle 1.20815 / 0.64 ( 2) hydrogen bonds : bond 0.04428 / 2.88 ( 284) hydrogen bonds : angle 4.95138 / 3.46 ( 834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7841 (mmt) REVERT: A 380 MET cc_start: 0.8515 (mmm) cc_final: 0.8164 (mmp) REVERT: A 383 LEU cc_start: 0.8235 (tp) cc_final: 0.8009 (mt) REVERT: A 402 SER cc_start: 0.8943 (t) cc_final: 0.8676 (m) REVERT: A 520 PHE cc_start: 0.7800 (t80) cc_final: 0.7581 (t80) REVERT: A 586 ASN cc_start: 0.7479 (OUTLIER) cc_final: 0.7238 (t0) REVERT: A 587 ARG cc_start: 0.7016 (ptm-80) cc_final: 0.6358 (ptm-80) REVERT: A 588 TRP cc_start: 0.7431 (m100) cc_final: 0.7049 (m100) outliers start: 25 outliers final: 12 residues processed: 86 average time/residue: 0.3313 time to fit residues: 29.9988 Evaluate side-chains 82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115192 restraints weight = 4989.002| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.22 r_work: 0.3159 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4569 Z= 0.144 Angle : 0.566 6.582 6249 Z= 0.282 Chirality : 0.042 0.224 691 Planarity : 0.004 0.036 749 Dihedral : 8.011 58.911 798 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.19 % Allowed : 17.10 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.36), residues: 538 helix: 1.39 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.08 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 499 TYR 0.014 0.001 TYR A 578 PHE 0.014 0.002 PHE A 392 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 4568) covalent geometry : angle 0.56538 / 0.28 ( 6247) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 1.18220 / 0.63 ( 2) hydrogen bonds : bond 0.04178 / 2.70 ( 284) hydrogen bonds : angle 4.90222 / 3.44 ( 834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7867 (mmt) REVERT: A 380 MET cc_start: 0.8523 (mmm) cc_final: 0.8159 (mmp) REVERT: A 383 LEU cc_start: 0.8222 (tp) cc_final: 0.8005 (mt) REVERT: A 402 SER cc_start: 0.8910 (t) cc_final: 0.8682 (m) REVERT: A 587 ARG cc_start: 0.6997 (ptm-80) cc_final: 0.6479 (ptm-80) REVERT: A 596 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8057 (t) outliers start: 24 outliers final: 13 residues processed: 89 average time/residue: 0.3820 time to fit residues: 35.7653 Evaluate side-chains 73 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 202 ASN A 410 GLN A 567 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.137802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118769 restraints weight = 5057.168| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.27 r_work: 0.3211 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4569 Z= 0.148 Angle : 0.569 7.938 6249 Z= 0.282 Chirality : 0.042 0.219 691 Planarity : 0.004 0.036 749 Dihedral : 8.021 59.207 798 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.19 % Allowed : 16.67 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.36), residues: 538 helix: 1.43 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 324 TYR 0.016 0.001 TYR A 578 PHE 0.014 0.002 PHE A 392 TRP 0.015 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 4568) covalent geometry : angle 0.56828 / 0.28 ( 6247) SS BOND : bond 0.00043 / 0.02 ( 1) SS BOND : angle 1.34076 / 0.71 ( 2) hydrogen bonds : bond 0.04100 / 2.64 ( 284) hydrogen bonds : angle 4.78465 / 3.38 ( 834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7914 (mmt) REVERT: A 237 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.5864 (mmmt) REVERT: A 324 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6766 (mpt90) REVERT: A 380 MET cc_start: 0.8514 (mmm) cc_final: 0.8133 (mmp) REVERT: A 383 LEU cc_start: 0.8227 (tp) cc_final: 0.8020 (mt) REVERT: A 402 SER cc_start: 0.8828 (t) cc_final: 0.8621 (m) REVERT: A 596 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8118 (t) outliers start: 24 outliers final: 13 residues processed: 74 average time/residue: 0.4032 time to fit residues: 31.4130 Evaluate side-chains 75 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.0020 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121421 restraints weight = 5149.902| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.29 r_work: 0.3246 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4569 Z= 0.116 Angle : 0.541 8.370 6249 Z= 0.267 Chirality : 0.040 0.209 691 Planarity : 0.004 0.034 749 Dihedral : 7.682 59.886 798 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.41 % Allowed : 17.10 % Favored : 77.49 % 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 (0.37), residues: 538 helix: 1.61 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.06 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 587 TYR 0.018 0.001 TYR A 578 PHE 0.011 0.001 PHE A 474 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4568) covalent geometry : angle 0.54051 / 0.27 ( 6247) SS BOND : bond 0.00057 / 0.03 ( 1) SS BOND : angle 1.10558 / 0.60 ( 2) hydrogen bonds : bond 0.03772 / 2.41 ( 284) hydrogen bonds : angle 4.67541 / 3.30 ( 834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7862 (mmt) REVERT: A 237 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.5831 (mmmt) REVERT: A 324 ARG cc_start: 0.7478 (mpt90) cc_final: 0.7104 (mmm160) REVERT: A 364 GLU cc_start: 0.8653 (tt0) cc_final: 0.8269 (tt0) REVERT: A 380 MET cc_start: 0.8455 (mmm) cc_final: 0.8140 (mmp) REVERT: A 514 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8413 (t) REVERT: A 587 ARG cc_start: 0.6912 (ttp-110) cc_final: 0.6518 (ptm-80) REVERT: A 596 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (t) outliers start: 25 outliers final: 10 residues processed: 78 average time/residue: 0.3838 time to fit residues: 31.5575 Evaluate side-chains 72 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 593 GLU Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 30 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.141328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121640 restraints weight = 5097.490| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.37 r_work: 0.3242 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4569 Z= 0.115 Angle : 0.537 9.013 6249 Z= 0.263 Chirality : 0.040 0.207 691 Planarity : 0.004 0.033 749 Dihedral : 7.479 58.443 798 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.55 % Allowed : 17.75 % Favored : 77.71 % 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: 1.39 (0.37), residues: 538 helix: 1.70 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.05 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.019 0.001 TYR A 578 PHE 0.011 0.001 PHE A 474 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 4568) covalent geometry : angle 0.53638 / 0.26 ( 6247) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 1.08925 / 0.58 ( 2) hydrogen bonds : bond 0.03651 / 2.34 ( 284) hydrogen bonds : angle 4.56999 / 3.22 ( 834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7879 (mmt) REVERT: A 237 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6139 (mmtt) REVERT: A 324 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7121 (mmm160) REVERT: A 364 GLU cc_start: 0.8649 (tt0) cc_final: 0.8248 (tt0) REVERT: A 380 MET cc_start: 0.8449 (mmm) cc_final: 0.8128 (mmp) REVERT: A 514 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8366 (t) REVERT: A 554 MET cc_start: 0.9027 (mtp) cc_final: 0.8790 (mtp) REVERT: A 587 ARG cc_start: 0.6927 (ttp-110) cc_final: 0.6539 (ptm-80) REVERT: A 596 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8012 (t) outliers start: 21 outliers final: 12 residues processed: 75 average time/residue: 0.3976 time to fit residues: 31.3837 Evaluate side-chains 78 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119314 restraints weight = 5139.013| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.31 r_work: 0.3239 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4569 Z= 0.132 Angle : 0.554 9.187 6249 Z= 0.273 Chirality : 0.041 0.209 691 Planarity : 0.004 0.034 749 Dihedral : 7.445 59.275 798 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.33 % Allowed : 19.05 % Favored : 76.62 % 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: 1.35 (0.37), residues: 538 helix: 1.64 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.98 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 587 TYR 0.021 0.001 TYR A 578 PHE 0.014 0.001 PHE A 434 TRP 0.014 0.001 TRP A 218 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 4568) covalent geometry : angle 0.55326 / 0.27 ( 6247) SS BOND : bond 0.00020 / 0.01 ( 1) SS BOND : angle 1.31408 / 0.70 ( 2) hydrogen bonds : bond 0.03851 / 2.46 ( 284) hydrogen bonds : angle 4.62869 / 3.27 ( 834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7878 (mmt) REVERT: A 237 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6165 (mmtt) REVERT: A 324 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7109 (mmm160) REVERT: A 364 GLU cc_start: 0.8662 (tt0) cc_final: 0.8284 (tt0) REVERT: A 380 MET cc_start: 0.8522 (mmm) cc_final: 0.8170 (mmp) REVERT: A 514 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8378 (t) REVERT: A 587 ARG cc_start: 0.6937 (ttp-110) cc_final: 0.6560 (ptm-80) REVERT: A 596 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8076 (t) outliers start: 20 outliers final: 12 residues processed: 73 average time/residue: 0.3973 time to fit residues: 30.5716 Evaluate side-chains 78 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121035 restraints weight = 5133.810| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.30 r_work: 0.3264 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4569 Z= 0.118 Angle : 0.541 9.743 6249 Z= 0.265 Chirality : 0.040 0.203 691 Planarity : 0.004 0.033 749 Dihedral : 7.315 59.342 798 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.55 % Allowed : 18.83 % Favored : 76.62 % 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: 1.40 (0.37), residues: 538 helix: 1.66 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 587 TYR 0.021 0.001 TYR A 578 PHE 0.011 0.001 PHE A 392 TRP 0.016 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 4568) covalent geometry : angle 0.54060 / 0.27 ( 6247) SS BOND : bond 0.00060 / 0.03 ( 1) SS BOND : angle 1.23997 / 0.66 ( 2) hydrogen bonds : bond 0.03681 / 2.35 ( 284) hydrogen bonds : angle 4.55601 / 3.22 ( 834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7914 (mmt) REVERT: A 219 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7827 (p0) REVERT: A 237 LYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6143 (mmtt) REVERT: A 324 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7213 (mmm160) REVERT: A 364 GLU cc_start: 0.8648 (tt0) cc_final: 0.8245 (tt0) REVERT: A 380 MET cc_start: 0.8457 (mmm) cc_final: 0.8133 (mmp) REVERT: A 514 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8383 (t) REVERT: A 587 ARG cc_start: 0.6925 (ttp-110) cc_final: 0.6548 (ptm-80) REVERT: A 596 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8061 (t) outliers start: 21 outliers final: 11 residues processed: 73 average time/residue: 0.3927 time to fit residues: 30.2364 Evaluate side-chains 77 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119089 restraints weight = 5141.727| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.30 r_work: 0.3254 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4569 Z= 0.130 Angle : 0.552 9.269 6249 Z= 0.271 Chirality : 0.041 0.206 691 Planarity : 0.004 0.033 749 Dihedral : 7.330 59.720 798 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.90 % Allowed : 20.35 % Favored : 75.76 % 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: 1.40 (0.37), residues: 538 helix: 1.66 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.93 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 587 TYR 0.023 0.001 TYR A 578 PHE 0.013 0.001 PHE A 392 TRP 0.014 0.001 TRP A 218 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4568) covalent geometry : angle 0.55139 / 0.27 ( 6247) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 1.29972 / 0.69 ( 2) hydrogen bonds : bond 0.03784 / 2.42 ( 284) hydrogen bonds : angle 4.58982 / 3.25 ( 834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1076 Ramachandran restraints generated. 538 Oldfield, 0 Emsley, 538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7929 (mmt) REVERT: A 237 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6159 (mmtt) REVERT: A 324 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7222 (mmm160) REVERT: A 364 GLU cc_start: 0.8664 (tt0) cc_final: 0.8246 (tt0) REVERT: A 380 MET cc_start: 0.8486 (mmm) cc_final: 0.8164 (mmp) REVERT: A 514 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8391 (t) REVERT: A 596 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8151 (t) outliers start: 18 outliers final: 12 residues processed: 72 average time/residue: 0.4060 time to fit residues: 30.7672 Evaluate side-chains 78 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 596 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 HIS A 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118954 restraints weight = 5129.090| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.35 r_work: 0.3197 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4569 Z= 0.134 Angle : 0.564 9.071 6249 Z= 0.277 Chirality : 0.041 0.206 691 Planarity : 0.004 0.045 749 Dihedral : 7.345 59.796 798 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.55 % Allowed : 19.48 % Favored : 75.97 % 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: 1.37 (0.37), residues: 538 helix: 1.64 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -0.94 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 587 TYR 0.024 0.001 TYR A 578 PHE 0.014 0.001 PHE A 392 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 4568) covalent geometry : angle 0.56310 / 0.28 ( 6247) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 1.31891 / 0.70 ( 2) hydrogen bonds : bond 0.03809 / 2.43 ( 284) hydrogen bonds : angle 4.60081 / 3.25 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1466.11 seconds wall clock time: 25 minutes 45.80 seconds (1545.80 seconds total)