Starting phenix.real_space_refine on Thu Mar 6 03:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vae_43089/03_2025/8vae_43089.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vae_43089/03_2025/8vae_43089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vae_43089/03_2025/8vae_43089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vae_43089/03_2025/8vae_43089.map" model { file = "/net/cci-nas-00/data/ceres_data/8vae_43089/03_2025/8vae_43089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vae_43089/03_2025/8vae_43089.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 2939 2.51 5 N 782 2.21 5 O 891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4653 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4623 Classifications: {'peptide': 581} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 556} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'SAL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.51, per 1000 atoms: 0.97 Number of scatterers: 4653 At special positions: 0 Unit cell: (66.788, 91.692, 95.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 891 8.00 N 782 7.00 C 2939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 169 " distance=2.04 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 177 " distance=2.02 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 279 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 289 " distance=2.04 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 438 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 448 " distance=2.03 Simple disulfide: pdb=" SG CYS A 461 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 559 " distance=1.86 Simple disulfide: pdb=" SG CYS A 558 " - pdb=" SG CYS A 567 " distance=2.01 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: 1.40 Conformation dependent library (CDL) restraints added in 576.7 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 15 through 31 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.949A pdb=" N THR A 76 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 119 through 130 Processing helix chain 'A' and resid 131 through 146 Processing helix chain 'A' and resid 150 through 168 Processing helix chain 'A' and resid 174 through 223 removed outlier: 3.761A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 7.432A pdb=" N GLU A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ARG A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 247 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 267 through 272 removed outlier: 3.607A pdb=" N ILE A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.594A pdb=" N LYS A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 277 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 removed outlier: 3.526A pdb=" N GLU A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.672A pdb=" N PHE A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 310' Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 322 through 338 removed outlier: 3.565A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.636A pdb=" N CYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.887A pdb=" N ASP A 375 " --> pdb=" O LYS A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 399 removed outlier: 4.191A pdb=" N LEU A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.533A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 415 Processing helix chain 'A' and resid 419 through 438 removed outlier: 3.880A pdb=" N GLY A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 466 removed outlier: 4.163A pdb=" N MET A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Proline residue: A 447 - end of helix removed outlier: 3.928A pdb=" N LYS A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.609A pdb=" N THR A 506 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 517 through 536 Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 563 through 582 removed outlier: 3.634A pdb=" N CYS A 567 " --> pdb=" O ASP A 563 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 945 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: 1.21 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1538 1.34 - 1.46: 1008 1.46 - 1.58: 2150 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4743 Sorted by residual: bond pdb=" C1 SAL A 603 " pdb=" C2 SAL A 603 " ideal model delta sigma weight residual 1.409 1.485 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 SAL A 602 " pdb=" C2 SAL A 602 " ideal model delta sigma weight residual 1.409 1.480 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C2 SAL A 601 " pdb=" O2 SAL A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" N CYS A 558 " pdb=" CA CYS A 558 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.18e+00 bond pdb=" N CYS A 559 " pdb=" CA CYS A 559 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.27e-02 6.20e+03 5.75e+00 ... (remaining 4738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6180 1.64 - 3.29: 167 3.29 - 4.93: 38 4.93 - 6.58: 6 6.58 - 8.22: 5 Bond angle restraints: 6396 Sorted by residual: angle pdb=" N CYS A 559 " pdb=" CA CYS A 559 " pdb=" C CYS A 559 " ideal model delta sigma weight residual 113.41 106.51 6.90 1.22e+00 6.72e-01 3.20e+01 angle pdb=" C LYS A 557 " pdb=" N CYS A 558 " pdb=" CA CYS A 558 " ideal model delta sigma weight residual 122.60 114.38 8.22 1.56e+00 4.11e-01 2.78e+01 angle pdb=" N VAL A 469 " pdb=" CA VAL A 469 " pdb=" C VAL A 469 " ideal model delta sigma weight residual 113.71 109.69 4.02 9.50e-01 1.11e+00 1.79e+01 angle pdb=" C VAL A 315 " pdb=" N CYS A 316 " pdb=" CA CYS A 316 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.06e+00 angle pdb=" C ALA A 569 " pdb=" N GLU A 570 " pdb=" CA GLU A 570 " ideal model delta sigma weight residual 121.52 116.39 5.13 1.84e+00 2.95e-01 7.77e+00 ... (remaining 6391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 2608 17.56 - 35.12: 293 35.12 - 52.68: 58 52.68 - 70.24: 10 70.24 - 87.79: 13 Dihedral angle restraints: 2982 sinusoidal: 1244 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS A 514 " pdb=" SG CYS A 514 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -1.59 -84.41 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS A 558 " pdb=" SG CYS A 558 " pdb=" SG CYS A 567 " pdb=" CB CYS A 567 " ideal model delta sinusoidal sigma weight residual 93.00 174.19 -81.19 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual -86.00 -166.30 80.30 1 1.00e+01 1.00e-02 7.98e+01 ... (remaining 2979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 516 0.040 - 0.079: 142 0.079 - 0.119: 40 0.119 - 0.158: 6 0.158 - 0.198: 2 Chirality restraints: 706 Sorted by residual: chirality pdb=" CB THR A 467 " pdb=" CA THR A 467 " pdb=" OG1 THR A 467 " pdb=" CG2 THR A 467 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA GLU A 570 " pdb=" N GLU A 570 " pdb=" C GLU A 570 " pdb=" CB GLU A 570 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 703 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 568 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C PHE A 568 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE A 568 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA A 569 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 567 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C CYS A 567 " 0.024 2.00e-02 2.50e+03 pdb=" O CYS A 567 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE A 568 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 370 " -0.008 2.00e-02 2.50e+03 7.84e-03 1.23e+00 pdb=" CG TYR A 370 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 370 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 370 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 370 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 370 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 370 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 370 " 0.001 2.00e-02 2.50e+03 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1027 2.78 - 3.31: 4832 3.31 - 3.84: 7879 3.84 - 4.37: 8460 4.37 - 4.90: 14909 Nonbonded interactions: 37107 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OE2 GLU A 358 " model vdw 2.251 3.040 nonbonded pdb=" NH1 ARG A 81 " pdb=" O GLY A 85 " model vdw 2.282 3.120 nonbonded pdb=" NE2 GLN A 221 " pdb=" O PRO A 339 " model vdw 2.312 3.120 nonbonded pdb=" NH2 ARG A 160 " pdb=" OE1 GLU A 188 " model vdw 2.379 3.120 nonbonded pdb=" ND2 ASN A 391 " pdb=" C6 SAL A 601 " model vdw 2.398 3.420 ... (remaining 37102 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 group one per residue 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: 6.930 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.880 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4743 Z= 0.235 Angle : 0.675 8.222 6396 Z= 0.364 Chirality : 0.041 0.198 706 Planarity : 0.003 0.027 834 Dihedral : 15.274 87.795 1791 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.35), residues: 579 helix: 1.68 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.002 0.001 HIS A 242 PHE 0.017 0.001 PHE A 134 TYR 0.020 0.002 TYR A 370 ARG 0.002 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.563 Fit side-chains REVERT: A 174 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7981 (mmtt) REVERT: A 467 THR cc_start: 0.8772 (t) cc_final: 0.8524 (p) REVERT: A 501 GLU cc_start: 0.7690 (tp30) cc_final: 0.7386 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1808 time to fit residues: 13.1915 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084232 restraints weight = 11876.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086610 restraints weight = 7051.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.088194 restraints weight = 4956.745| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4743 Z= 0.203 Angle : 0.630 11.424 6396 Z= 0.320 Chirality : 0.042 0.230 706 Planarity : 0.004 0.027 834 Dihedral : 5.518 63.741 625 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.18 % Allowed : 6.50 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.36), residues: 579 helix: 1.77 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.12 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 338 PHE 0.022 0.001 PHE A 127 TYR 0.017 0.002 TYR A 370 ARG 0.003 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.597 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1763 time to fit residues: 11.0258 Evaluate side-chains 35 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.102927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.083440 restraints weight = 12062.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.085791 restraints weight = 7209.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087376 restraints weight = 5114.679| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4743 Z= 0.188 Angle : 0.605 11.791 6396 Z= 0.302 Chirality : 0.041 0.229 706 Planarity : 0.003 0.026 834 Dihedral : 5.211 57.648 625 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.38 % Allowed : 10.24 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.35), residues: 579 helix: 1.78 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.18 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 338 PHE 0.013 0.001 PHE A 127 TYR 0.017 0.002 TYR A 370 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.570 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 44 average time/residue: 0.1307 time to fit residues: 8.2904 Evaluate side-chains 33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 1 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.101480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082279 restraints weight = 12214.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084578 restraints weight = 7262.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086210 restraints weight = 5116.973| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4743 Z= 0.192 Angle : 0.620 12.496 6396 Z= 0.303 Chirality : 0.041 0.242 706 Planarity : 0.003 0.026 834 Dihedral : 5.027 50.579 625 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 11.81 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.36), residues: 579 helix: 1.83 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.07 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.009 0.001 PHE A 127 TYR 0.015 0.002 TYR A 370 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 548 MET cc_start: 0.8220 (mmm) cc_final: 0.7928 (mmt) outliers start: 11 outliers final: 3 residues processed: 47 average time/residue: 0.1308 time to fit residues: 8.7694 Evaluate side-chains 33 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.101466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082136 restraints weight = 12286.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.084485 restraints weight = 7324.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086087 restraints weight = 5157.612| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4743 Z= 0.186 Angle : 0.619 13.453 6396 Z= 0.302 Chirality : 0.041 0.240 706 Planarity : 0.003 0.029 834 Dihedral : 4.871 46.849 625 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 13.39 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.36), residues: 579 helix: 1.77 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.06 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.008 0.001 PHE A 127 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.569 Fit side-chains REVERT: A 298 MET cc_start: 0.7382 (tpt) cc_final: 0.7105 (tpt) REVERT: A 548 MET cc_start: 0.8301 (mmm) cc_final: 0.8033 (mmt) REVERT: A 554 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6862 (t80) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 0.1290 time to fit residues: 8.2425 Evaluate side-chains 37 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 50 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.102894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083392 restraints weight = 11947.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085822 restraints weight = 6941.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087554 restraints weight = 4808.886| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4743 Z= 0.158 Angle : 0.622 14.147 6396 Z= 0.302 Chirality : 0.041 0.294 706 Planarity : 0.003 0.033 834 Dihedral : 4.714 45.412 625 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.36 % Allowed : 15.55 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.36), residues: 579 helix: 1.88 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -0.02 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 288 PHE 0.007 0.001 PHE A 568 TYR 0.018 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.563 Fit side-chains REVERT: A 548 MET cc_start: 0.8258 (mmm) cc_final: 0.8006 (mmt) REVERT: A 554 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6765 (t80) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.1378 time to fit residues: 9.1406 Evaluate side-chains 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 28 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 31 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.103991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084813 restraints weight = 12056.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087256 restraints weight = 6996.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088863 restraints weight = 4814.845| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4743 Z= 0.149 Angle : 0.621 14.603 6396 Z= 0.295 Chirality : 0.041 0.295 706 Planarity : 0.003 0.033 834 Dihedral : 4.608 44.286 625 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 16.34 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.36), residues: 579 helix: 1.99 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.08 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 288 PHE 0.007 0.001 PHE A 127 TYR 0.018 0.001 TYR A 370 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.542 Fit side-chains REVERT: A 298 MET cc_start: 0.6673 (tpt) cc_final: 0.6336 (tpt) REVERT: A 380 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8719 (mp) REVERT: A 531 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 548 MET cc_start: 0.8294 (mmm) cc_final: 0.8055 (mmt) REVERT: A 554 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6667 (t80) outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.1375 time to fit residues: 9.4926 Evaluate side-chains 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 chunk 2 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.102298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082613 restraints weight = 12276.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.085060 restraints weight = 7142.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.086768 restraints weight = 4959.367| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4743 Z= 0.174 Angle : 0.629 14.924 6396 Z= 0.302 Chirality : 0.042 0.325 706 Planarity : 0.003 0.031 834 Dihedral : 4.657 43.830 625 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.76 % Allowed : 15.75 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.36), residues: 579 helix: 2.03 (0.26), residues: 416 sheet: None (None), residues: 0 loop : -0.07 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.007 0.001 PHE A 488 TYR 0.016 0.001 TYR A 370 ARG 0.005 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7360 (tt) REVERT: A 298 MET cc_start: 0.6819 (tpt) cc_final: 0.6524 (tpt) REVERT: A 380 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 531 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 554 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6506 (t80) outliers start: 14 outliers final: 5 residues processed: 48 average time/residue: 0.1136 time to fit residues: 8.1882 Evaluate side-chains 39 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.101339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081679 restraints weight = 12417.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084020 restraints weight = 7299.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085673 restraints weight = 5110.918| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4743 Z= 0.194 Angle : 0.658 15.154 6396 Z= 0.320 Chirality : 0.043 0.316 706 Planarity : 0.003 0.032 834 Dihedral : 4.792 43.291 625 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.36 % Allowed : 16.54 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.36), residues: 579 helix: 1.96 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.11 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.004 0.001 HIS A 288 PHE 0.008 0.001 PHE A 488 TYR 0.015 0.002 TYR A 370 ARG 0.004 0.000 ARG A 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.604 Fit side-chains REVERT: A 178 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7368 (tt) REVERT: A 298 MET cc_start: 0.6885 (tpt) cc_final: 0.6519 (tpt) REVERT: A 554 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6567 (t80) outliers start: 12 outliers final: 7 residues processed: 44 average time/residue: 0.1081 time to fit residues: 7.4401 Evaluate side-chains 40 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.101718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.082204 restraints weight = 12276.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084528 restraints weight = 7186.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086185 restraints weight = 5046.562| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4743 Z= 0.172 Angle : 0.645 14.984 6396 Z= 0.309 Chirality : 0.042 0.264 706 Planarity : 0.003 0.033 834 Dihedral : 4.832 43.440 625 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.77 % Allowed : 16.93 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.36), residues: 579 helix: 1.95 (0.25), residues: 417 sheet: None (None), residues: 0 loop : -0.16 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.007 0.001 PHE A 551 TYR 0.019 0.001 TYR A 370 ARG 0.004 0.000 ARG A 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.576 Fit side-chains REVERT: A 178 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7424 (tt) REVERT: A 298 MET cc_start: 0.6859 (tpt) cc_final: 0.6549 (tpt) REVERT: A 554 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6547 (t80) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.1058 time to fit residues: 7.3914 Evaluate side-chains 42 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 169 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.102162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082351 restraints weight = 12300.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.084735 restraints weight = 7206.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086412 restraints weight = 5061.361| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4743 Z= 0.166 Angle : 0.647 15.547 6396 Z= 0.308 Chirality : 0.042 0.272 706 Planarity : 0.003 0.033 834 Dihedral : 4.832 43.323 625 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.77 % Allowed : 17.13 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.36), residues: 579 helix: 1.94 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.15 (0.54), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.006 0.001 PHE A 165 TYR 0.018 0.002 TYR A 370 ARG 0.004 0.000 ARG A 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.22 seconds wall clock time: 32 minutes 44.89 seconds (1964.89 seconds total)