Starting phenix.real_space_refine on Tue Feb 3 15:32:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg5_61451/02_2026/9jg5_61451.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg5_61451/02_2026/9jg5_61451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jg5_61451/02_2026/9jg5_61451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg5_61451/02_2026/9jg5_61451.map" model { file = "/net/cci-nas-00/data/ceres_data/9jg5_61451/02_2026/9jg5_61451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg5_61451/02_2026/9jg5_61451.cif" } resolution = 3.2 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 31 5.16 5 Cl 1 4.86 5 C 2891 2.51 5 N 657 2.21 5 O 747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4327 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4320 Classifications: {'peptide': 544} Link IDs: {'PTRANS': 28, 'TRANS': 515} Chain breaks: 2 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1, 'water': 6} Link IDs: {None: 6} Time building chain proxies: 0.77, per 1000 atoms: 0.18 Number of scatterers: 4327 At special positions: 0 Unit cell: (70.81, 71.54, 91.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 31 16.00 O 747 8.00 N 657 7.00 C 2891 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: 0.21 Conformation dependent library (CDL) restraints added in 177.4 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: 990 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 80.9% alpha, 0.4% 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 46 through 55 removed outlier: 3.551A pdb=" N ALA A 55 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.558A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 removed outlier: 3.716A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 removed outlier: 3.608A pdb=" N LEU A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 90 through 106 Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 151 removed outlier: 3.694A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.883A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 217 through 237 removed outlier: 3.539A pdb=" N ILE A 235 " --> pdb=" O CYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.963A pdb=" N VAL A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 4.516A pdb=" N PHE A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 321 through 356 removed outlier: 3.887A pdb=" N ASP A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.586A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.530A pdb=" N ILE A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Proline residue: A 375 - end of helix removed outlier: 3.623A pdb=" N MET A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 418 removed outlier: 3.691A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 447 removed outlier: 4.221A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 4.444A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 481 removed outlier: 3.785A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 removed outlier: 3.614A 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: 3.556A pdb=" N ILE A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.743A 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 removed outlier: 3.738A pdb=" N LEU A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 4.093A pdb=" N TYR A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 281 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: 0.40 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1261 1.35 - 1.46: 1274 1.46 - 1.58: 1882 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 4461 Sorted by residual: bond pdb=" C GLU A 584 " pdb=" N PRO A 585 " ideal model delta sigma weight residual 1.340 1.365 -0.025 2.76e-02 1.31e+03 8.17e-01 bond pdb=" N GLY A 484 " pdb=" CA GLY A 484 " ideal model delta sigma weight residual 1.463 1.449 0.014 2.07e-02 2.33e+03 4.46e-01 bond pdb=" C CYS A 556 " pdb=" N VAL A 557 " ideal model delta sigma weight residual 1.329 1.337 -0.007 1.13e-02 7.83e+03 4.19e-01 bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.244 1.237 0.006 9.80e-03 1.04e+04 4.08e-01 bond pdb=" C LEU A 80 " pdb=" N ILE A 81 " ideal model delta sigma weight residual 1.329 1.336 -0.007 1.13e-02 7.83e+03 4.00e-01 ... (remaining 4456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 6014 1.80 - 3.60: 60 3.60 - 5.41: 11 5.41 - 7.21: 0 7.21 - 9.01: 1 Bond angle restraints: 6086 Sorted by residual: angle pdb=" N VAL A 203 " pdb=" CA VAL A 203 " pdb=" C VAL A 203 " ideal model delta sigma weight residual 111.67 109.22 2.45 9.50e-01 1.11e+00 6.63e+00 angle pdb=" CA LEU A 216 " pdb=" CB LEU A 216 " pdb=" CG LEU A 216 " ideal model delta sigma weight residual 116.30 125.31 -9.01 3.50e+00 8.16e-02 6.63e+00 angle pdb=" N VAL A 447 " pdb=" CA VAL A 447 " pdb=" C VAL A 447 " ideal model delta sigma weight residual 111.91 109.63 2.28 8.90e-01 1.26e+00 6.57e+00 angle pdb=" C GLY A 91 " pdb=" N LEU A 92 " pdb=" CA LEU A 92 " ideal model delta sigma weight residual 120.09 122.89 -2.80 1.25e+00 6.40e-01 5.02e+00 angle pdb=" N GLY A 451 " pdb=" CA GLY A 451 " pdb=" C GLY A 451 " ideal model delta sigma weight residual 115.66 112.63 3.03 1.56e+00 4.11e-01 3.77e+00 ... (remaining 6081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.89: 2328 12.89 - 25.79: 125 25.79 - 38.68: 32 38.68 - 51.58: 19 51.58 - 64.47: 13 Dihedral angle restraints: 2517 sinusoidal: 952 harmonic: 1565 Sorted by residual: dihedral pdb=" CA MET A 446 " pdb=" CB MET A 446 " pdb=" CG MET A 446 " pdb=" SD MET A 446 " ideal model delta sinusoidal sigma weight residual 60.00 119.67 -59.67 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE A 58 " pdb=" CA PHE A 58 " pdb=" CB PHE A 58 " pdb=" CG PHE A 58 " ideal model delta sinusoidal sigma weight residual 60.00 0.76 59.24 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE A 520 " pdb=" CA PHE A 520 " pdb=" CB PHE A 520 " pdb=" CG PHE A 520 " ideal model delta sinusoidal sigma weight residual 60.00 118.68 -58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 456 0.027 - 0.053: 114 0.053 - 0.080: 71 0.080 - 0.106: 27 0.106 - 0.133: 2 Chirality restraints: 670 Sorted by residual: chirality pdb=" CG LEU A 216 " pdb=" CB LEU A 216 " pdb=" CD1 LEU A 216 " pdb=" CD2 LEU A 216 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA VAL A 528 " pdb=" N VAL A 528 " pdb=" C VAL A 528 " pdb=" CB VAL A 528 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CA VAL A 590 " pdb=" N VAL A 590 " pdb=" C VAL A 590 " pdb=" CB VAL A 590 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.70e-01 ... (remaining 667 not shown) Planarity restraints: 744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 92 " -0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 93 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 207 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 208 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 135 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C ASN A 135 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN A 135 " 0.007 2.00e-02 2.50e+03 pdb=" N VAL A 136 " 0.006 2.00e-02 2.50e+03 ... (remaining 741 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 73 2.70 - 3.25: 4522 3.25 - 3.80: 7101 3.80 - 4.35: 8890 4.35 - 4.90: 14728 Nonbonded interactions: 35314 Sorted by model distance: nonbonded pdb=" OD2 ASP A 281 " pdb=" OG1 THR A 283 " model vdw 2.152 3.040 nonbonded pdb=" O ASP A 459 " pdb=" OG SER A 464 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 461 " pdb=" OH TYR A 527 " model vdw 2.243 3.040 nonbonded pdb=" O VAL A 262 " pdb=" OG1 THR A 266 " model vdw 2.309 3.040 nonbonded pdb=" O LEU A 329 " pdb=" ND2 ASN A 333 " model vdw 2.309 3.120 ... (remaining 35309 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: 1.390 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.820 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4462 Z= 0.111 Angle : 0.503 9.012 6088 Z= 0.291 Chirality : 0.034 0.133 670 Planarity : 0.004 0.032 744 Dihedral : 10.930 64.471 1524 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.60 % Allowed : 5.17 % Favored : 89.22 % 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: -0.92 (0.34), residues: 538 helix: -0.08 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -1.64 (0.43), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 284 TYR 0.009 0.001 TYR A 69 PHE 0.010 0.001 PHE A 520 TRP 0.007 0.001 TRP A 113 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 4461) covalent geometry : angle 0.50273 ( 6086) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.77147 ( 2) hydrogen bonds : bond 0.15710 ( 281) hydrogen bonds : angle 6.65986 ( 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 118 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7221 (tp) REVERT: A 69 TYR cc_start: 0.5568 (OUTLIER) cc_final: 0.5018 (p90) REVERT: A 154 GLN cc_start: 0.7708 (mt0) cc_final: 0.7085 (mt0) REVERT: A 172 MET cc_start: 0.5502 (ttm) cc_final: 0.5194 (mtm) REVERT: A 200 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6580 (tt0) REVERT: A 316 ASN cc_start: 0.6587 (m-40) cc_final: 0.6165 (m110) REVERT: A 394 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6620 (ppp) REVERT: A 482 ILE cc_start: 0.3895 (mm) cc_final: 0.3446 (mm) REVERT: A 587 ARG cc_start: 0.4186 (OUTLIER) cc_final: 0.3152 (mtm-85) outliers start: 26 outliers final: 8 residues processed: 110 average time/residue: 0.0357 time to fit residues: 5.4177 Evaluate side-chains 80 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN A 355 GLN A 586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.213000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196374 restraints weight = 4962.128| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.64 r_work: 0.4181 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4462 Z= 0.118 Angle : 0.507 8.628 6088 Z= 0.249 Chirality : 0.039 0.134 670 Planarity : 0.004 0.033 744 Dihedral : 8.047 58.640 617 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.53 % Allowed : 9.91 % Favored : 85.56 % 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: 1.23 (0.36), residues: 538 helix: 1.63 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -1.18 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.017 0.001 TYR A 137 PHE 0.016 0.001 PHE A 520 TRP 0.013 0.001 TRP A 113 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4461) covalent geometry : angle 0.50694 ( 6086) SS BOND : bond 0.00256 ( 1) SS BOND : angle 1.39928 ( 2) hydrogen bonds : bond 0.04117 ( 281) hydrogen bonds : angle 4.27466 ( 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 101 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5595 (p90) REVERT: A 120 PHE cc_start: 0.6249 (m-80) cc_final: 0.5917 (m-80) REVERT: A 154 GLN cc_start: 0.8033 (mt0) cc_final: 0.7558 (mt0) REVERT: A 172 MET cc_start: 0.5647 (ttm) cc_final: 0.5349 (mtm) REVERT: A 200 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7335 (tt0) REVERT: A 316 ASN cc_start: 0.7455 (m-40) cc_final: 0.7005 (m110) REVERT: A 394 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7357 (ppp) REVERT: A 482 ILE cc_start: 0.5715 (mm) cc_final: 0.5165 (mm) REVERT: A 559 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6778 (mm) REVERT: A 577 LYS cc_start: 0.5782 (tppt) cc_final: 0.5497 (ptmt) REVERT: A 587 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.3348 (mtm-85) outliers start: 21 outliers final: 11 residues processed: 93 average time/residue: 0.0533 time to fit residues: 6.7776 Evaluate side-chains 86 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.207967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.191123 restraints weight = 4980.490| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.71 r_work: 0.4109 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4462 Z= 0.122 Angle : 0.509 8.169 6088 Z= 0.250 Chirality : 0.039 0.153 670 Planarity : 0.004 0.032 744 Dihedral : 7.838 58.968 613 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.17 % Allowed : 11.64 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.37), residues: 538 helix: 1.81 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.39 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.016 0.001 TYR A 69 PHE 0.029 0.002 PHE A 386 TRP 0.012 0.001 TRP A 228 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4461) covalent geometry : angle 0.50892 ( 6086) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.41270 ( 2) hydrogen bonds : bond 0.04018 ( 281) hydrogen bonds : angle 4.14777 ( 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 93 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.6219 (p90) REVERT: A 172 MET cc_start: 0.5889 (ttm) cc_final: 0.5525 (mtm) REVERT: A 200 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7421 (tt0) REVERT: A 482 ILE cc_start: 0.5899 (mm) cc_final: 0.5245 (mm) REVERT: A 559 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.6810 (mm) REVERT: A 563 ILE cc_start: 0.5099 (mt) cc_final: 0.4467 (mt) REVERT: A 587 ARG cc_start: 0.4930 (OUTLIER) cc_final: 0.3384 (mtm-85) outliers start: 24 outliers final: 12 residues processed: 86 average time/residue: 0.0440 time to fit residues: 5.4308 Evaluate side-chains 79 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.202787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.185464 restraints weight = 4945.592| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.75 r_work: 0.4051 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3930 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 4462 Z= 0.134 Angle : 0.525 8.160 6088 Z= 0.257 Chirality : 0.040 0.120 670 Planarity : 0.004 0.036 744 Dihedral : 7.169 59.795 608 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.09 % Allowed : 13.36 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.37), residues: 538 helix: 1.74 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -1.43 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 564 TYR 0.017 0.001 TYR A 69 PHE 0.022 0.001 PHE A 572 TRP 0.012 0.001 TRP A 228 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4461) covalent geometry : angle 0.52473 ( 6086) SS BOND : bond 0.00221 ( 1) SS BOND : angle 1.14948 ( 2) hydrogen bonds : bond 0.04059 ( 281) hydrogen bonds : angle 4.12711 ( 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 91 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6733 (p90) REVERT: A 172 MET cc_start: 0.5923 (ttm) cc_final: 0.5573 (mtm) REVERT: A 200 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7432 (tt0) REVERT: A 446 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7833 (mtm) REVERT: A 482 ILE cc_start: 0.5934 (mm) cc_final: 0.5208 (mm) REVERT: A 559 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6862 (mm) REVERT: A 563 ILE cc_start: 0.5258 (mt) cc_final: 0.4754 (mt) REVERT: A 587 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.3464 (mtm-85) outliers start: 19 outliers final: 9 residues processed: 86 average time/residue: 0.0387 time to fit residues: 4.8360 Evaluate side-chains 82 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.231473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.214768 restraints weight = 5245.816| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 1.55 r_work: 0.4382 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4255 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4462 Z= 0.136 Angle : 0.534 8.106 6088 Z= 0.262 Chirality : 0.040 0.119 670 Planarity : 0.004 0.036 744 Dihedral : 7.130 58.584 608 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.45 % Allowed : 16.16 % Favored : 80.39 % 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: 1.26 (0.37), residues: 538 helix: 1.65 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -1.33 (0.49), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 201 TYR 0.018 0.002 TYR A 69 PHE 0.026 0.002 PHE A 520 TRP 0.012 0.001 TRP A 228 HIS 0.002 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 4461) covalent geometry : angle 0.53377 ( 6086) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.42294 ( 2) hydrogen bonds : bond 0.04034 ( 281) hydrogen bonds : angle 4.14156 ( 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 86 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.7235 (p90) REVERT: A 172 MET cc_start: 0.6100 (ttm) cc_final: 0.5896 (mtm) REVERT: A 200 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7668 (tt0) REVERT: A 482 ILE cc_start: 0.6463 (mm) cc_final: 0.5710 (mm) REVERT: A 559 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7023 (mm) REVERT: A 563 ILE cc_start: 0.5316 (mt) cc_final: 0.4905 (mt) REVERT: A 587 ARG cc_start: 0.5224 (OUTLIER) cc_final: 0.3536 (mtm-85) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.0322 time to fit residues: 3.8156 Evaluate side-chains 81 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 42 optimal weight: 0.0470 chunk 36 optimal weight: 0.4980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.187635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.164339 restraints weight = 5195.966| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.25 r_work: 0.3715 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4462 Z= 0.114 Angle : 0.505 8.124 6088 Z= 0.247 Chirality : 0.039 0.115 670 Planarity : 0.004 0.037 744 Dihedral : 6.280 57.206 604 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.66 % Allowed : 16.59 % Favored : 79.74 % 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: 1.44 (0.37), residues: 538 helix: 1.82 (0.27), residues: 387 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.016 0.001 TYR A 69 PHE 0.020 0.001 PHE A 520 TRP 0.010 0.001 TRP A 228 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4461) covalent geometry : angle 0.50505 ( 6086) SS BOND : bond 0.00137 ( 1) SS BOND : angle 1.14434 ( 2) hydrogen bonds : bond 0.03772 ( 281) hydrogen bonds : angle 4.03414 ( 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 88 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6375 (p90) REVERT: A 172 MET cc_start: 0.5458 (ttm) cc_final: 0.5139 (mtm) REVERT: A 200 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6799 (tt0) REVERT: A 482 ILE cc_start: 0.5075 (mm) cc_final: 0.4356 (mm) REVERT: A 559 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6153 (mm) REVERT: A 563 ILE cc_start: 0.5121 (mt) cc_final: 0.4747 (mt) REVERT: A 565 LEU cc_start: 0.6903 (tt) cc_final: 0.6606 (tt) REVERT: A 586 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6954 (t0) REVERT: A 587 ARG cc_start: 0.4945 (OUTLIER) cc_final: 0.3309 (mtm-85) outliers start: 17 outliers final: 8 residues processed: 83 average time/residue: 0.0359 time to fit residues: 4.3612 Evaluate side-chains 80 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.199804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182103 restraints weight = 4921.725| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.73 r_work: 0.4032 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4462 Z= 0.120 Angle : 0.511 8.180 6088 Z= 0.253 Chirality : 0.039 0.123 670 Planarity : 0.004 0.037 744 Dihedral : 6.257 56.713 604 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.66 % Allowed : 17.46 % Favored : 78.88 % 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: 1.51 (0.37), residues: 538 helix: 1.90 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.32 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 592 TYR 0.017 0.001 TYR A 69 PHE 0.019 0.001 PHE A 572 TRP 0.010 0.001 TRP A 228 HIS 0.001 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4461) covalent geometry : angle 0.51014 ( 6086) SS BOND : bond 0.00070 ( 1) SS BOND : angle 1.38972 ( 2) hydrogen bonds : bond 0.03794 ( 281) hydrogen bonds : angle 4.03194 ( 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 85 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7364 (p90) REVERT: A 172 MET cc_start: 0.5922 (ttm) cc_final: 0.5576 (mtm) REVERT: A 200 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7564 (tt0) REVERT: A 482 ILE cc_start: 0.6313 (mm) cc_final: 0.5505 (mm) REVERT: A 559 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7031 (mm) REVERT: A 563 ILE cc_start: 0.5349 (mt) cc_final: 0.4911 (mt) REVERT: A 565 LEU cc_start: 0.7716 (tt) cc_final: 0.7380 (tt) REVERT: A 586 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6409 (t0) REVERT: A 587 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.3498 (mtm-85) outliers start: 17 outliers final: 11 residues processed: 81 average time/residue: 0.0471 time to fit residues: 5.4208 Evaluate side-chains 83 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.197365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.179005 restraints weight = 5047.680| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 1.68 r_work: 0.4029 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4462 Z= 0.117 Angle : 0.513 8.219 6088 Z= 0.253 Chirality : 0.039 0.115 670 Planarity : 0.004 0.037 744 Dihedral : 6.244 56.021 604 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.66 % Allowed : 17.46 % Favored : 78.88 % 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: 1.54 (0.37), residues: 538 helix: 1.93 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.34 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 592 TYR 0.017 0.001 TYR A 69 PHE 0.017 0.001 PHE A 520 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4461) covalent geometry : angle 0.51282 ( 6086) SS BOND : bond 0.00060 ( 1) SS BOND : angle 1.25924 ( 2) hydrogen bonds : bond 0.03784 ( 281) hydrogen bonds : angle 4.00770 ( 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 85 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7452 (OUTLIER) cc_final: 0.7225 (p90) REVERT: A 172 MET cc_start: 0.5831 (ttm) cc_final: 0.5463 (mtm) REVERT: A 200 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7405 (tt0) REVERT: A 380 MET cc_start: 0.7089 (tpt) cc_final: 0.6545 (tpt) REVERT: A 482 ILE cc_start: 0.6038 (mm) cc_final: 0.5244 (mm) REVERT: A 559 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7012 (mm) REVERT: A 563 ILE cc_start: 0.5346 (mt) cc_final: 0.4914 (mt) REVERT: A 565 LEU cc_start: 0.7528 (tt) cc_final: 0.7191 (tt) REVERT: A 586 ASN cc_start: 0.7403 (OUTLIER) cc_final: 0.6478 (t0) REVERT: A 587 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.3468 (mtm-85) outliers start: 17 outliers final: 9 residues processed: 81 average time/residue: 0.0398 time to fit residues: 4.6647 Evaluate side-chains 81 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.196446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178365 restraints weight = 5018.483| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.75 r_work: 0.3995 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4462 Z= 0.140 Angle : 0.539 8.242 6088 Z= 0.267 Chirality : 0.040 0.118 670 Planarity : 0.004 0.037 744 Dihedral : 6.292 55.477 604 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.88 % Allowed : 17.46 % Favored : 78.66 % 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: 1.30 (0.37), residues: 538 helix: 1.73 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.019 0.001 TYR A 69 PHE 0.020 0.001 PHE A 572 TRP 0.018 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4461) covalent geometry : angle 0.53851 ( 6086) SS BOND : bond 0.00062 ( 1) SS BOND : angle 1.41769 ( 2) hydrogen bonds : bond 0.04062 ( 281) hydrogen bonds : angle 4.11225 ( 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 89 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 172 MET cc_start: 0.5943 (ttm) cc_final: 0.5610 (mtm) REVERT: A 200 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7533 (tt0) REVERT: A 394 MET cc_start: 0.7783 (tmm) cc_final: 0.7273 (ptt) REVERT: A 482 ILE cc_start: 0.6274 (mm) cc_final: 0.5452 (mm) REVERT: A 559 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 586 ASN cc_start: 0.7619 (OUTLIER) cc_final: 0.6660 (t0) REVERT: A 587 ARG cc_start: 0.5277 (OUTLIER) cc_final: 0.3498 (mtm-85) outliers start: 18 outliers final: 11 residues processed: 85 average time/residue: 0.0362 time to fit residues: 4.4002 Evaluate side-chains 85 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 51 optimal weight: 0.0170 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.0060 overall best weight: 0.3634 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.200154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182327 restraints weight = 5022.384| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 1.73 r_work: 0.4031 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4462 Z= 0.110 Angle : 0.509 8.217 6088 Z= 0.252 Chirality : 0.039 0.130 670 Planarity : 0.004 0.038 744 Dihedral : 6.189 55.142 604 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.45 % Allowed : 19.83 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.37), residues: 538 helix: 1.95 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -1.37 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 592 TYR 0.016 0.001 TYR A 69 PHE 0.017 0.001 PHE A 520 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4461) covalent geometry : angle 0.50842 ( 6086) SS BOND : bond 0.00105 ( 1) SS BOND : angle 1.16331 ( 2) hydrogen bonds : bond 0.03720 ( 281) hydrogen bonds : angle 4.03575 ( 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 84 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 138 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 172 MET cc_start: 0.5926 (ttm) cc_final: 0.5576 (mtm) REVERT: A 200 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7530 (tt0) REVERT: A 394 MET cc_start: 0.7787 (tmm) cc_final: 0.7308 (ptt) REVERT: A 482 ILE cc_start: 0.6366 (mm) cc_final: 0.5598 (mm) REVERT: A 559 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 565 LEU cc_start: 0.7608 (tt) cc_final: 0.7360 (tp) REVERT: A 586 ASN cc_start: 0.7489 (OUTLIER) cc_final: 0.6606 (t0) REVERT: A 587 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.3524 (mtm-85) outliers start: 16 outliers final: 9 residues processed: 80 average time/residue: 0.0405 time to fit residues: 4.7022 Evaluate side-chains 79 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 CYS Chi-restraints excluded: chain A residue 236 TRP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 587 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4600 r_free = 0.4600 target = 0.230021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.214220 restraints weight = 5357.694| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 1.43 r_work: 0.4325 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4462 Z= 0.138 Angle : 0.558 8.197 6088 Z= 0.280 Chirality : 0.041 0.180 670 Planarity : 0.004 0.037 744 Dihedral : 5.970 54.773 602 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.23 % Allowed : 20.04 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.37), residues: 538 helix: 1.82 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.46 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.020 0.002 TYR A 374 PHE 0.015 0.001 PHE A 520 TRP 0.017 0.001 TRP A 470 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4461) covalent geometry : angle 0.55783 ( 6086) SS BOND : bond 0.00071 ( 1) SS BOND : angle 1.35509 ( 2) hydrogen bonds : bond 0.04049 ( 281) hydrogen bonds : angle 4.17716 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1074.74 seconds wall clock time: 19 minutes 2.15 seconds (1142.15 seconds total)