Starting phenix.real_space_refine on Fri Aug 2 19:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vae_43089/08_2024/8vae_43089.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vae_43089/08_2024/8vae_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vae_43089/08_2024/8vae_43089.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vae_43089/08_2024/8vae_43089.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vae_43089/08_2024/8vae_43089.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vae_43089/08_2024/8vae_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 Residue "A GLU 60": "OE1" <-> "OE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 4.16, per 1000 atoms: 0.89 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 - 3.50 Amino acid : False - 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: 1.75 Conformation dependent library (CDL) restraints added in 819.3 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: 0.43 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: 1.25 Time building geometry restraints manager: 1.94 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: 99.05 - 106.04: 86 106.04 - 113.02: 2541 113.02 - 120.01: 1722 120.01 - 127.00: 2006 127.00 - 133.98: 41 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: 4.020 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.640 Find NCS groups from input model: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.558 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: 0.1690 time to fit residues: 12.4661 Evaluate side-chains 37 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.545 Fit side-chains REVERT: A 522 GLN cc_start: 0.7935 (mm110) cc_final: 0.7712 (mt0) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1699 time to fit residues: 10.7701 Evaluate side-chains 36 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 29 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4743 Z= 0.229 Angle : 0.631 11.762 6396 Z= 0.317 Chirality : 0.043 0.228 706 Planarity : 0.003 0.026 834 Dihedral : 5.273 56.320 625 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.57 % Allowed : 10.63 % Favored : 87.80 % 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: 1.72 (0.35), residues: 579 helix: 1.68 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.21 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 242 PHE 0.012 0.001 PHE A 127 TYR 0.016 0.002 TYR A 150 ARG 0.004 0.001 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 48 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.426 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.1295 time to fit residues: 8.7404 Evaluate side-chains 33 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2029 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= 0.185 Angle : 0.622 12.870 6396 Z= 0.309 Chirality : 0.041 0.224 706 Planarity : 0.003 0.026 834 Dihedral : 5.089 50.508 625 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.17 % Allowed : 12.01 % Favored : 85.83 % 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: 418 sheet: None (None), residues: 0 loop : -0.14 (0.52), 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 0.010 0.001 PHE A 127 TYR 0.016 0.002 TYR A 370 ARG 0.003 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 46 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.540 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 45 average time/residue: 0.1150 time to fit residues: 7.7199 Evaluate side-chains 35 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 CYS 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 41 optimal weight: 0.0270 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 0.026 4743 Z= 0.175 Angle : 0.613 13.550 6396 Z= 0.303 Chirality : 0.041 0.216 706 Planarity : 0.003 0.029 834 Dihedral : 4.882 46.778 625 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.97 % Allowed : 14.17 % Favored : 83.86 % 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: 1.86 (0.36), residues: 579 helix: 1.77 (0.26), residues: 419 sheet: None (None), residues: 0 loop : -0.11 (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 288 PHE 0.008 0.001 PHE A 127 TYR 0.017 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 47 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 298 MET cc_start: 0.7324 (tpt) cc_final: 0.7046 (tpt) REVERT: A 501 GLU cc_start: 0.7539 (tp30) cc_final: 0.7333 (tp30) REVERT: A 554 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6774 (t80) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.1176 time to fit residues: 8.1129 Evaluate side-chains 37 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 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 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 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4743 Z= 0.171 Angle : 0.626 13.966 6396 Z= 0.307 Chirality : 0.041 0.294 706 Planarity : 0.003 0.033 834 Dihedral : 4.756 45.284 625 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.56 % Allowed : 14.96 % Favored : 82.48 % 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: 1.99 (0.36), residues: 579 helix: 1.87 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.07 (0.53), 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 0.008 0.001 PHE A 568 TYR 0.017 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 46 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 33 time to evaluate : 0.571 Fit side-chains REVERT: A 178 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7411 (tt) REVERT: A 380 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 554 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6703 (t80) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.1063 time to fit residues: 7.6537 Evaluate side-chains 40 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4743 Z= 0.198 Angle : 0.633 14.300 6396 Z= 0.312 Chirality : 0.042 0.248 706 Planarity : 0.003 0.030 834 Dihedral : 4.819 43.976 625 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.76 % Allowed : 16.34 % Favored : 80.91 % 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: 1.93 (0.36), residues: 579 helix: 1.85 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.13 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 214 HIS 0.003 0.001 HIS A 288 PHE 0.007 0.001 PHE A 488 TYR 0.015 0.001 TYR A 370 ARG 0.001 0.000 ARG A 186 *********************** 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 45 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 31 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 178 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7360 (tp) REVERT: A 380 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8727 (mp) REVERT: A 554 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6674 (t80) outliers start: 14 outliers final: 6 residues processed: 44 average time/residue: 0.1000 time to fit residues: 6.9149 Evaluate side-chains 42 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2520 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= 0.168 Angle : 0.624 15.114 6396 Z= 0.304 Chirality : 0.041 0.226 706 Planarity : 0.003 0.031 834 Dihedral : 4.819 44.139 625 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.76 % Allowed : 16.73 % Favored : 80.51 % 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: 2.02 (0.36), residues: 579 helix: 1.93 (0.26), residues: 417 sheet: None (None), residues: 0 loop : -0.15 (0.52), 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 488 TYR 0.016 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 *********************** 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 51 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.543 Fit side-chains REVERT: A 178 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7318 (tt) REVERT: A 380 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 554 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6497 (t80) outliers start: 14 outliers final: 8 residues processed: 50 average time/residue: 0.1026 time to fit residues: 7.9995 Evaluate side-chains 46 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain A residue 433 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2671 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= 0.190 Angle : 0.639 15.494 6396 Z= 0.312 Chirality : 0.042 0.243 706 Planarity : 0.003 0.031 834 Dihedral : 4.921 44.017 625 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.36 % Allowed : 17.13 % Favored : 80.51 % 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: 1.89 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -0.19 (0.52), 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 288 PHE 0.007 0.001 PHE A 488 TYR 0.016 0.002 TYR A 370 ARG 0.002 0.000 ARG A 197 *********************** 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 48 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.512 Fit side-chains REVERT: A 178 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7508 (tt) REVERT: A 380 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 554 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6580 (t80) outliers start: 12 outliers final: 8 residues processed: 47 average time/residue: 0.1084 time to fit residues: 7.9251 Evaluate side-chains 45 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain A residue 433 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 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4743 Z= 0.197 Angle : 0.665 15.603 6396 Z= 0.323 Chirality : 0.042 0.242 706 Planarity : 0.003 0.031 834 Dihedral : 4.955 44.098 625 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.17 % Allowed : 17.72 % Favored : 80.12 % 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: 1.92 (0.36), residues: 579 helix: 1.85 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.20 (0.53), residues: 161 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 488 TYR 0.016 0.002 TYR A 370 ARG 0.002 0.000 ARG A 197 ********************** 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 fitting. rotamer outliers: 11 poor density : 34 time to evaluate : 0.555 Fit side-chains REVERT: A 178 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7553 (tt) REVERT: A 380 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8735 (mp) REVERT: A 554 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6579 (t80) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.1110 time to fit residues: 7.5929 Evaluate side-chains 42 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 380 LEU Chi-restraints excluded: chain A residue 433 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 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.2980 chunk 30 optimal weight: 0.0050 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.101857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.082440 restraints weight = 12162.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.084792 restraints weight = 7017.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086487 restraints weight = 4893.735| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2699 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= 0.162 Angle : 0.638 15.985 6396 Z= 0.308 Chirality : 0.041 0.219 706 Planarity : 0.003 0.032 834 Dihedral : 4.838 44.003 625 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.36 % Allowed : 17.13 % Favored : 80.51 % 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: 1.99 (0.36), residues: 579 helix: 1.91 (0.25), residues: 418 sheet: None (None), residues: 0 loop : -0.19 (0.53), residues: 161 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 0.006 0.001 PHE A 127 TYR 0.019 0.001 TYR A 370 ARG 0.002 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1301.40 seconds wall clock time: 23 minutes 54.25 seconds (1434.25 seconds total)