Starting phenix.real_space_refine on Thu Jul 2 00:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jg5_61451/07_2026/9jg5_61451.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jg5_61451/07_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_61451/07_2026/9jg5_61451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jg5_61451/07_2026/9jg5_61451.map" model { file = "/net/cci-nas-00/data/ceres_data/9jg5_61451/07_2026/9jg5_61451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jg5_61451/07_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-dev-6108/lib/python3.11/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, 6 Ad-hoc single atom residues: {' CL': 1} Classifications: {'water': 6} Link IDs: {None: 5} Chain breaks: 1 Time building chain proxies: 1.20, per 1000 atoms: 0.28 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: 0.38 Conformation dependent library (CDL) restraints added in 162.5 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: 0.07 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: 0.47 Time building geometry restraints manager: 0.51 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: 1.870 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.700 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 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/Z covalent geometry : bond 0.00181 / 0.11 ( 4461) covalent geometry : angle 0.50273 / 0.29 ( 6086) SS BOND : bond 0.00184 / 0.10 ( 1) SS BOND : angle 0.77147 / 0.45 ( 2) hydrogen bonds : bond 0.15710 / 10.54 ( 281) hydrogen bonds : angle 6.65986 / 4.63 ( 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 : 0.167 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: 0.0536 time to fit residues: 8.0032 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 : 0.155 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.206035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188775 restraints weight = 5000.784| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.69 r_work: 0.4137 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4462 Z= 0.129 Angle : 0.529 9.129 6088 Z= 0.259 Chirality : 0.040 0.140 670 Planarity : 0.004 0.032 744 Dihedral : 8.075 58.570 617 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.53 % Allowed : 10.34 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.36), residues: 538 helix: 1.57 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -1.20 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.018 0.001 TYR A 137 PHE 0.016 0.001 PHE A 520 TRP 0.014 0.001 TRP A 113 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4461) covalent geometry : angle 0.52805 / 0.26 ( 6086) SS BOND : bond 0.00287 / 0.15 ( 1) SS BOND : angle 1.54038 / 0.87 ( 2) hydrogen bonds : bond 0.04162 / 2.67 ( 281) hydrogen bonds : angle 4.23140 / 2.86 ( 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 97 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.5869 (p90) REVERT: A 104 TYR cc_start: 0.7373 (t80) cc_final: 0.7074 (t80) REVERT: A 172 MET cc_start: 0.5709 (ttm) cc_final: 0.5371 (mtm) REVERT: A 200 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7346 (tt0) REVERT: A 394 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7368 (ppp) REVERT: A 482 ILE cc_start: 0.5795 (mm) cc_final: 0.5199 (mm) REVERT: A 559 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6875 (mm) REVERT: A 587 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.3361 (mtm-85) outliers start: 21 outliers final: 9 residues processed: 89 average time/residue: 0.0463 time to fit residues: 5.6548 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 : 0.145 ------------------------------------------------------------------------------- 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 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 587 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 GLN ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.204071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.186535 restraints weight = 4977.664| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.68 r_work: 0.4105 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4462 Z= 0.122 Angle : 0.513 8.131 6088 Z= 0.252 Chirality : 0.039 0.144 670 Planarity : 0.004 0.032 744 Dihedral : 7.095 59.282 609 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.96 % Allowed : 12.72 % Favored : 82.33 % 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: 1.38 (0.37), residues: 538 helix: 1.77 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.36 (0.48), 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 0.026 0.001 PHE A 386 TRP 0.012 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4461) covalent geometry : angle 0.51247 / 0.25 ( 6086) SS BOND : bond 0.00258 / 0.14 ( 1) SS BOND : angle 1.31366 / 0.74 ( 2) hydrogen bonds : bond 0.04012 / 2.59 ( 281) hydrogen bonds : angle 4.10947 / 2.81 ( 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: 23 poor density : 70 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6300 (p90) REVERT: A 172 MET cc_start: 0.5869 (ttm) cc_final: 0.5488 (mtm) REVERT: A 200 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7428 (tt0) REVERT: A 455 PHE cc_start: 0.8067 (t80) cc_final: 0.7851 (t80) REVERT: A 482 ILE cc_start: 0.5878 (mm) cc_final: 0.5230 (mm) REVERT: A 559 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.6868 (mm) REVERT: A 563 ILE cc_start: 0.5129 (mt) cc_final: 0.4429 (mt) REVERT: A 567 GLN cc_start: 0.5814 (mt0) cc_final: 0.5521 (pt0) REVERT: A 587 ARG cc_start: 0.4812 (OUTLIER) cc_final: 0.3247 (mtm-85) outliers start: 23 outliers final: 10 residues processed: 86 average time/residue: 0.0419 time to fit residues: 5.0049 Evaluate side-chains 78 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 101 ILE 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 587 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.202165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.184369 restraints weight = 4934.984| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.68 r_work: 0.4074 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4462 Z= 0.119 Angle : 0.509 8.132 6088 Z= 0.249 Chirality : 0.039 0.120 670 Planarity : 0.004 0.035 744 Dihedral : 6.809 58.942 606 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.31 % Allowed : 13.79 % Favored : 81.90 % 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: 1.48 (0.37), residues: 538 helix: 1.87 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.41 (0.47), residues: 152 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 0.023 0.001 PHE A 572 TRP 0.010 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 4461) covalent geometry : angle 0.50844 / 0.25 ( 6086) SS BOND : bond 0.00254 / 0.13 ( 1) SS BOND : angle 1.12176 / 0.63 ( 2) hydrogen bonds : bond 0.03813 / 2.49 ( 281) hydrogen bonds : angle 4.06392 / 2.79 ( 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 93 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.6932 (OUTLIER) cc_final: 0.6578 (p90) REVERT: A 172 MET cc_start: 0.5879 (ttm) cc_final: 0.5510 (mtm) REVERT: A 200 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7434 (tt0) REVERT: A 482 ILE cc_start: 0.5955 (mm) cc_final: 0.5247 (mm) REVERT: A 496 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6472 (mt) REVERT: A 559 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6868 (mm) REVERT: A 563 ILE cc_start: 0.5178 (mt) cc_final: 0.4577 (mt) REVERT: A 567 GLN cc_start: 0.6072 (mt0) cc_final: 0.5708 (pt0) REVERT: A 587 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.3196 (mtm-85) outliers start: 20 outliers final: 10 residues processed: 86 average time/residue: 0.0390 time to fit residues: 4.8603 Evaluate side-chains 81 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 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 216 LEU Chi-restraints excluded: chain A residue 229 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 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 587 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.238962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.222965 restraints weight = 5226.942| |-----------------------------------------------------------------------------| r_work (start): 0.4538 rms_B_bonded: 1.57 r_work: 0.4433 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4309 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4462 Z= 0.112 Angle : 0.500 8.131 6088 Z= 0.244 Chirality : 0.039 0.118 670 Planarity : 0.004 0.037 744 Dihedral : 6.699 59.584 605 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.88 % Allowed : 14.66 % Favored : 81.47 % 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: 1.58 (0.37), residues: 538 helix: 1.94 (0.27), residues: 386 sheet: None (None), residues: 0 loop : -1.37 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 575 TYR 0.015 0.001 TYR A 69 PHE 0.022 0.001 PHE A 520 TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 4461) covalent geometry : angle 0.49933 / 0.24 ( 6086) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 1.07874 / 0.61 ( 2) hydrogen bonds : bond 0.03626 / 2.34 ( 281) hydrogen bonds : angle 3.99557 / 2.75 ( 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 90 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6885 (p90) REVERT: A 172 MET cc_start: 0.5949 (ttm) cc_final: 0.5647 (mtm) REVERT: A 200 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7662 (tt0) REVERT: A 316 ASN cc_start: 0.7709 (m110) cc_final: 0.7075 (m110) REVERT: A 482 ILE cc_start: 0.6432 (mm) cc_final: 0.5760 (mm) REVERT: A 521 ILE cc_start: 0.8298 (mm) cc_final: 0.8093 (mt) REVERT: A 559 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7012 (mm) REVERT: A 563 ILE cc_start: 0.5188 (mt) cc_final: 0.4879 (mt) REVERT: A 587 ARG cc_start: 0.5053 (OUTLIER) cc_final: 0.3318 (mtm-85) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.0436 time to fit residues: 5.1611 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 : 0.149 ------------------------------------------------------------------------------- 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 101 ILE 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 535 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU 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: 2.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.186816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.163427 restraints weight = 5192.130| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.22 r_work: 0.3699 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4462 Z= 0.153 Angle : 0.549 8.137 6088 Z= 0.271 Chirality : 0.041 0.136 670 Planarity : 0.004 0.036 744 Dihedral : 6.792 57.704 605 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.88 % Allowed : 16.81 % Favored : 79.31 % 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: 1.33 (0.37), residues: 538 helix: 1.78 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.39 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 201 TYR 0.020 0.002 TYR A 69 PHE 0.023 0.001 PHE A 455 TRP 0.010 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 4461) covalent geometry : angle 0.54859 / 0.27 ( 6086) SS BOND : bond 0.00297 / 0.16 ( 1) SS BOND : angle 1.51264 / 0.85 ( 2) hydrogen bonds : bond 0.04250 / 2.75 ( 281) hydrogen bonds : angle 4.21835 / 2.91 ( 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 86 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.151 Fit side-chains REVERT: A 69 TYR cc_start: 0.6720 (OUTLIER) cc_final: 0.6388 (p90) REVERT: A 172 MET cc_start: 0.5709 (ttm) cc_final: 0.5283 (mtm) REVERT: A 200 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6830 (tt0) REVERT: A 446 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7594 (mtm) REVERT: A 482 ILE cc_start: 0.5041 (mm) cc_final: 0.4332 (mm) REVERT: A 559 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6592 (mm) REVERT: A 567 GLN cc_start: 0.5652 (mt0) cc_final: 0.4964 (pt0) REVERT: A 587 ARG cc_start: 0.4839 (OUTLIER) cc_final: 0.3020 (mtm-85) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 0.0456 time to fit residues: 5.1815 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 : 0.152 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 229 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 535 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 590 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.194936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.176364 restraints weight = 5037.105| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.68 r_work: 0.4008 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3893 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4462 Z= 0.143 Angle : 0.539 8.047 6088 Z= 0.268 Chirality : 0.040 0.130 670 Planarity : 0.004 0.038 744 Dihedral : 6.761 57.112 605 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.88 % Allowed : 17.67 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.37), residues: 538 helix: 1.78 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.46 (0.47), residues: 158 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 404 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4461) covalent geometry : angle 0.53856 / 0.27 ( 6086) SS BOND : bond 0.00263 / 0.14 ( 1) SS BOND : angle 1.31766 / 0.74 ( 2) hydrogen bonds : bond 0.04171 / 2.70 ( 281) hydrogen bonds : angle 4.21270 / 2.92 ( 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 88 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7309 (p90) REVERT: A 172 MET cc_start: 0.6002 (ttm) cc_final: 0.5609 (mtm) REVERT: A 200 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7388 (tt0) REVERT: A 316 ASN cc_start: 0.7541 (m110) cc_final: 0.6926 (m110) REVERT: A 446 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7834 (mtm) REVERT: A 482 ILE cc_start: 0.5973 (mm) cc_final: 0.5146 (mm) REVERT: A 559 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7293 (mm) REVERT: A 587 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.3067 (mtm-85) outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 0.0462 time to fit residues: 5.4627 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 : 0.157 ------------------------------------------------------------------------------- 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 229 LEU 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 535 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 590 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.0040 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.4166 r_free = 0.4166 target = 0.197949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.178819 restraints weight = 5078.660| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.80 r_work: 0.4034 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4462 Z= 0.117 Angle : 0.540 11.584 6088 Z= 0.261 Chirality : 0.039 0.118 670 Planarity : 0.004 0.037 744 Dihedral : 6.695 56.654 605 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.23 % Allowed : 19.61 % Favored : 77.16 % 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: 1.95 (0.27), residues: 380 sheet: None (None), residues: 0 loop : -1.42 (0.47), residues: 158 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 0.022 0.001 PHE A 572 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4461) covalent geometry : angle 0.53938 / 0.26 ( 6086) SS BOND : bond 0.00254 / 0.13 ( 1) SS BOND : angle 1.08331 / 0.61 ( 2) hydrogen bonds : bond 0.03756 / 2.43 ( 281) hydrogen bonds : angle 4.09613 / 2.84 ( 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 87 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.158 Fit side-chains REVERT: A 172 MET cc_start: 0.5975 (ttm) cc_final: 0.5584 (mtm) REVERT: A 200 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7442 (tt0) REVERT: A 316 ASN cc_start: 0.7534 (m110) cc_final: 0.6912 (m110) REVERT: A 482 ILE cc_start: 0.6140 (mm) cc_final: 0.5369 (mm) REVERT: A 559 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7388 (mm) REVERT: A 587 ARG cc_start: 0.5061 (OUTLIER) cc_final: 0.3188 (mtm-85) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.0441 time to fit residues: 5.1296 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 : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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 535 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU 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: 3.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.196953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.179100 restraints weight = 5066.306| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.75 r_work: 0.3743 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4462 Z= 0.146 Angle : 0.571 9.774 6088 Z= 0.282 Chirality : 0.040 0.116 670 Planarity : 0.004 0.037 744 Dihedral : 6.469 56.231 603 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.45 % Allowed : 20.04 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.37), residues: 538 helix: 1.73 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.40 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.022 0.002 TYR A 374 PHE 0.019 0.001 PHE A 404 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4461) covalent geometry : angle 0.57041 / 0.28 ( 6086) SS BOND : bond 0.00243 / 0.13 ( 1) SS BOND : angle 1.32122 / 0.74 ( 2) hydrogen bonds : bond 0.04230 / 2.74 ( 281) hydrogen bonds : angle 4.20879 / 2.92 ( 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 87 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.153 Fit side-chains REVERT: A 138 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 172 MET cc_start: 0.5824 (ttm) cc_final: 0.5398 (mtm) REVERT: A 200 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7115 (tt0) REVERT: A 316 ASN cc_start: 0.7206 (m110) cc_final: 0.6514 (m110) REVERT: A 394 MET cc_start: 0.7259 (tmm) cc_final: 0.6761 (ptt) REVERT: A 397 LEU cc_start: 0.6368 (mt) cc_final: 0.6168 (mt) REVERT: A 446 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: A 482 ILE cc_start: 0.5543 (mm) cc_final: 0.4766 (mm) REVERT: A 559 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7099 (mm) REVERT: A 587 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.3070 (mtm-85) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.0449 time to fit residues: 5.3018 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 : 0.178 ------------------------------------------------------------------------------- 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 85 ILE Chi-restraints excluded: chain A residue 138 TYR Chi-restraints excluded: chain A residue 216 LEU 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 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 587 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4146 r_free = 0.4146 target = 0.195186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.176654 restraints weight = 5125.912| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.67 r_work: 0.4013 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4466 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= 0.143 Angle : 0.576 8.965 6088 Z= 0.287 Chirality : 0.040 0.119 670 Planarity : 0.004 0.037 744 Dihedral : 6.490 56.076 603 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.23 % Allowed : 20.47 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.37), residues: 538 helix: 1.67 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.41 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 201 TYR 0.018 0.001 TYR A 69 PHE 0.028 0.002 PHE A 404 TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4461) covalent geometry : angle 0.57610 / 0.29 ( 6086) SS BOND : bond 0.00240 / 0.13 ( 1) SS BOND : angle 1.24775 / 0.70 ( 2) hydrogen bonds : bond 0.04193 / 2.71 ( 281) hydrogen bonds : angle 4.21803 / 2.94 ( 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 85 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.090 Fit side-chains REVERT: A 101 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.6990 (mm) REVERT: A 138 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 172 MET cc_start: 0.6071 (ttm) cc_final: 0.5768 (mtm) REVERT: A 200 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7371 (tt0) REVERT: A 316 ASN cc_start: 0.7499 (m110) cc_final: 0.6842 (m110) REVERT: A 380 MET cc_start: 0.7162 (tpt) cc_final: 0.6943 (tpt) REVERT: A 394 MET cc_start: 0.7662 (tmm) cc_final: 0.7115 (ptt) REVERT: A 482 ILE cc_start: 0.6008 (mm) cc_final: 0.5224 (mm) REVERT: A 559 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7346 (mm) REVERT: A 567 GLN cc_start: 0.6072 (mt0) cc_final: 0.5413 (pt0) REVERT: A 587 ARG cc_start: 0.5143 (OUTLIER) cc_final: 0.3186 (mtm-85) outliers start: 15 outliers final: 10 residues processed: 78 average time/residue: 0.0434 time to fit residues: 4.8286 Evaluate side-chains 82 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 101 ILE 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 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 535 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 584 GLU 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: 4.9990 chunk 45 optimal weight: 0.0370 chunk 44 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.236051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.220020 restraints weight = 5362.609| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 1.53 r_work: 0.4401 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.4277 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4467 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= 0.127 Angle : 0.557 8.409 6088 Z= 0.277 Chirality : 0.039 0.128 670 Planarity : 0.004 0.038 744 Dihedral : 6.477 57.625 603 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.66 % Allowed : 20.04 % Favored : 76.29 % 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: 1.78 (0.27), residues: 383 sheet: None (None), residues: 0 loop : -1.35 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.016 0.001 TYR A 69 PHE 0.038 0.001 PHE A 404 TRP 0.010 0.001 TRP A 228 HIS 0.001 0.000 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 4461) covalent geometry : angle 0.55697 / 0.28 ( 6086) SS BOND : bond 0.00366 / 0.19 ( 1) SS BOND : angle 1.25517 / 0.68 ( 2) hydrogen bonds : bond 0.03939 / 2.56 ( 281) hydrogen bonds : angle 4.15423 / 2.92 ( 834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.82 seconds wall clock time: 21 minutes 18.13 seconds (1278.13 seconds total)