Starting phenix.real_space_refine on Thu Mar 6 07:40:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl8_25194/03_2025/7sl8_25194_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl8_25194/03_2025/7sl8_25194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2025/7sl8_25194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2025/7sl8_25194.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2025/7sl8_25194_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl8_25194/03_2025/7sl8_25194_neut.cif" } resolution = 3.4 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= 0.003 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 34 5.16 5 C 3493 2.51 5 N 844 2.21 5 O 924 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: 5295 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4362 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 22, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 905 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.57, per 1000 atoms: 0.67 Number of scatterers: 5295 At special positions: 0 Unit cell: (109.18, 78.44, 90.1, 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 34 16.00 O 924 8.00 N 844 7.00 C 3493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 652.3 milliseconds 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1284 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 63.6% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 25 through 49 removed outlier: 4.188A pdb=" N ILE A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.900A pdb=" N SER A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.734A pdb=" N TRP A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.540A pdb=" N ALA A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 138 through 157 removed outlier: 4.599A pdb=" N GLN A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 174 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.613A pdb=" N SER A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 195 " --> pdb=" O TYR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 227 removed outlier: 3.727A pdb=" N GLY A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.582A pdb=" N TYR A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.397A pdb=" N TYR A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.779A pdb=" N CYS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.572A pdb=" N ALA A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.853A pdb=" N VAL A 329 " --> pdb=" O MET A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.699A pdb=" N MET A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 4.692A pdb=" N LYS A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.598A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 409 removed outlier: 3.569A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'A' and resid 418 through 440 removed outlier: 3.504A pdb=" N ALA A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.532A pdb=" N VAL A 444 " --> pdb=" O TRP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 477 removed outlier: 3.991A pdb=" N SER A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.555A pdb=" N TRP A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 505 removed outlier: 3.863A pdb=" N TRP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 527 through 548 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.901A pdb=" N HIS A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 666 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.575A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.728A pdb=" N VAL B 14 " --> pdb=" O SER B 119 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 912 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: 1.50 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1579 1.34 - 1.46: 1073 1.46 - 1.58: 2721 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 5426 Sorted by residual: bond pdb=" C LEU A 323 " pdb=" N PRO A 324 " ideal model delta sigma weight residual 1.334 1.405 -0.071 2.34e-02 1.83e+03 9.11e+00 bond pdb=" C TRP A 276 " pdb=" N PRO A 277 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" C13 CLR A 701 " pdb=" C17 CLR A 701 " ideal model delta sigma weight residual 1.550 1.517 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C10 CLR A 701 " pdb=" C9 CLR A 701 " ideal model delta sigma weight residual 1.551 1.519 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C VAL A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.27e+00 ... (remaining 5421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 7106 2.17 - 4.34: 251 4.34 - 6.51: 40 6.51 - 8.68: 14 8.68 - 10.85: 1 Bond angle restraints: 7412 Sorted by residual: angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 108.12 118.97 -10.85 1.44e+00 4.82e-01 5.68e+01 angle pdb=" N VAL A 329 " pdb=" CA VAL A 329 " pdb=" C VAL A 329 " ideal model delta sigma weight residual 113.71 109.05 4.66 9.50e-01 1.11e+00 2.40e+01 angle pdb=" N LEU A 527 " pdb=" CA LEU A 527 " pdb=" C LEU A 527 " ideal model delta sigma weight residual 113.55 108.18 5.37 1.26e+00 6.30e-01 1.82e+01 angle pdb=" N LYS A 358 " pdb=" CA LYS A 358 " pdb=" C LYS A 358 " ideal model delta sigma weight residual 111.28 115.50 -4.22 1.09e+00 8.42e-01 1.50e+01 angle pdb=" N ALA A 464 " pdb=" CA ALA A 464 " pdb=" C ALA A 464 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.49e+01 ... (remaining 7407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2754 15.96 - 31.92: 332 31.92 - 47.87: 83 47.87 - 63.83: 8 63.83 - 79.79: 4 Dihedral angle restraints: 3181 sinusoidal: 1172 harmonic: 2009 Sorted by residual: dihedral pdb=" CA PRO A 518 " pdb=" C PRO A 518 " pdb=" N THR A 519 " pdb=" CA THR A 519 " ideal model delta harmonic sigma weight residual -180.00 -158.39 -21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR B 101 " pdb=" C TYR B 101 " pdb=" N THR B 102 " pdb=" CA THR B 102 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA TYR B 61 " pdb=" C TYR B 61 " pdb=" N ALA B 62 " pdb=" CA ALA B 62 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 652 0.055 - 0.109: 180 0.109 - 0.164: 38 0.164 - 0.218: 12 0.218 - 0.273: 2 Chirality restraints: 884 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.66 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA CYS A 361 " pdb=" N CYS A 361 " pdb=" C CYS A 361 " pdb=" CB CYS A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL A 98 " pdb=" CA VAL A 98 " pdb=" CG1 VAL A 98 " pdb=" CG2 VAL A 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 881 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 465 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO A 466 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 330 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 331 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 331 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 331 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 102 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO B 103 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " 0.032 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1750 2.83 - 3.35: 4902 3.35 - 3.87: 8745 3.87 - 4.38: 9429 4.38 - 4.90: 16804 Nonbonded interactions: 41630 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR B 101 " model vdw 2.316 3.040 nonbonded pdb=" O SER A 446 " pdb=" OG SER A 446 " model vdw 2.321 3.040 nonbonded pdb=" O LEU A 152 " pdb=" OG1 THR A 156 " model vdw 2.327 3.040 nonbonded pdb=" CD2 TYR A 319 " pdb=" C24 CLR A 701 " model vdw 2.330 3.740 nonbonded pdb=" O LEU A 190 " pdb=" OG1 THR A 194 " model vdw 2.342 3.040 ... (remaining 41625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.030 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5426 Z= 0.365 Angle : 0.968 10.854 7412 Z= 0.543 Chirality : 0.057 0.273 884 Planarity : 0.008 0.066 902 Dihedral : 14.662 79.791 1882 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.92 % Allowed : 11.28 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.09 (0.25), residues: 692 helix: -2.46 (0.19), residues: 413 sheet: -2.41 (0.66), residues: 49 loop : -2.90 (0.36), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 68 HIS 0.003 0.001 HIS A 525 PHE 0.016 0.002 PHE B 49 TYR 0.010 0.002 TYR A 144 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 333 MET cc_start: 0.8006 (mtm) cc_final: 0.7752 (mtm) REVERT: B 7 GLN cc_start: 0.7438 (mp10) cc_final: 0.7085 (mp10) outliers start: 5 outliers final: 2 residues processed: 131 average time/residue: 0.1783 time to fit residues: 29.8739 Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 142 GLN A 525 HIS A 648 ASN A 666 ASN B 121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.133924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.113371 restraints weight = 9682.091| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.69 r_work: 0.3667 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5426 Z= 0.177 Angle : 0.642 7.491 7412 Z= 0.335 Chirality : 0.040 0.154 884 Planarity : 0.005 0.049 902 Dihedral : 6.134 57.838 814 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.77 % Allowed : 16.27 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.06 (0.30), residues: 692 helix: -0.51 (0.24), residues: 412 sheet: -1.80 (0.68), residues: 48 loop : -2.73 (0.36), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 276 HIS 0.002 0.000 HIS B 121 PHE 0.013 0.001 PHE A 432 TYR 0.021 0.001 TYR B 61 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.9448 (mt) cc_final: 0.9188 (mp) REVERT: B 87 LEU cc_start: 0.7815 (mm) cc_final: 0.7475 (mm) REVERT: B 90 GLU cc_start: 0.7515 (pm20) cc_final: 0.6903 (pm20) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.1554 time to fit residues: 24.0072 Evaluate side-chains 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 54 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.134249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113869 restraints weight = 9837.050| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.71 r_work: 0.3653 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5426 Z= 0.197 Angle : 0.599 6.278 7412 Z= 0.312 Chirality : 0.040 0.145 884 Planarity : 0.005 0.047 902 Dihedral : 5.903 58.564 814 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.07 % Allowed : 18.48 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.32), residues: 692 helix: 0.29 (0.26), residues: 411 sheet: -1.24 (0.71), residues: 48 loop : -2.55 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 487 HIS 0.001 0.000 HIS A 555 PHE 0.019 0.001 PHE A 658 TYR 0.015 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8184 (mmm) cc_final: 0.7727 (mtt) REVERT: A 325 MET cc_start: 0.8904 (tpp) cc_final: 0.8702 (tpp) REVERT: A 349 SER cc_start: 0.9165 (m) cc_final: 0.8838 (p) REVERT: A 525 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.7738 (t70) REVERT: B 84 MET cc_start: 0.7949 (ptp) cc_final: 0.7634 (ptp) REVERT: B 88 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8688 (pttm) outliers start: 22 outliers final: 16 residues processed: 121 average time/residue: 0.1480 time to fit residues: 23.9820 Evaluate side-chains 110 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111124 restraints weight = 9303.949| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.45 r_work: 0.3537 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5426 Z= 0.199 Angle : 0.615 9.018 7412 Z= 0.315 Chirality : 0.040 0.147 884 Planarity : 0.005 0.049 902 Dihedral : 5.888 58.372 814 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 6.65 % Allowed : 19.41 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.33), residues: 692 helix: 0.76 (0.27), residues: 406 sheet: -1.07 (0.70), residues: 48 loop : -2.44 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.007 0.001 HIS A 224 PHE 0.012 0.001 PHE B 69 TYR 0.013 0.001 TYR B 61 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8123 (mmm) cc_final: 0.7660 (mtt) REVERT: A 347 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8703 (m) REVERT: A 349 SER cc_start: 0.9131 (m) cc_final: 0.8809 (p) REVERT: A 525 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7977 (t70) REVERT: B 88 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8661 (pttm) outliers start: 36 outliers final: 20 residues processed: 124 average time/residue: 0.1462 time to fit residues: 24.2175 Evaluate side-chains 112 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 648 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.127842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107480 restraints weight = 10062.522| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.77 r_work: 0.3554 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5426 Z= 0.203 Angle : 0.630 10.949 7412 Z= 0.319 Chirality : 0.042 0.337 884 Planarity : 0.004 0.047 902 Dihedral : 5.501 58.200 811 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.47 % Allowed : 19.96 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.33), residues: 692 helix: 1.01 (0.27), residues: 406 sheet: -0.82 (0.71), residues: 48 loop : -2.31 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.001 0.000 HIS A 224 PHE 0.011 0.001 PHE B 69 TYR 0.020 0.001 TYR A 229 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8174 (mmm) cc_final: 0.7741 (mtt) REVERT: A 233 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8313 (mtt) REVERT: A 347 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8689 (m) REVERT: A 349 SER cc_start: 0.9177 (m) cc_final: 0.8852 (p) REVERT: A 373 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 525 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.8178 (t70) REVERT: B 88 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8634 (pttm) outliers start: 35 outliers final: 25 residues processed: 118 average time/residue: 0.1390 time to fit residues: 22.1867 Evaluate side-chains 122 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 2 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.110272 restraints weight = 9055.166| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.48 r_work: 0.3544 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5426 Z= 0.190 Angle : 0.617 11.192 7412 Z= 0.310 Chirality : 0.041 0.310 884 Planarity : 0.004 0.048 902 Dihedral : 5.436 57.125 811 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 6.47 % Allowed : 21.26 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.33), residues: 692 helix: 1.19 (0.27), residues: 406 sheet: -0.54 (0.74), residues: 48 loop : -2.27 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.007 0.001 HIS A 224 PHE 0.013 0.001 PHE B 69 TYR 0.017 0.001 TYR A 229 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8106 (mmm) cc_final: 0.7668 (mtt) REVERT: A 233 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8415 (mtt) REVERT: A 347 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 349 SER cc_start: 0.9125 (m) cc_final: 0.8820 (p) REVERT: A 373 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 88 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8608 (pttm) outliers start: 35 outliers final: 25 residues processed: 125 average time/residue: 0.1519 time to fit residues: 25.1396 Evaluate side-chains 120 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS A 666 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.129790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.109445 restraints weight = 9868.542| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.71 r_work: 0.3583 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5426 Z= 0.186 Angle : 0.631 9.481 7412 Z= 0.319 Chirality : 0.041 0.278 884 Planarity : 0.004 0.047 902 Dihedral : 5.358 56.272 811 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.65 % Allowed : 21.26 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.34), residues: 692 helix: 1.35 (0.27), residues: 407 sheet: -0.47 (0.74), residues: 48 loop : -2.28 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.005 0.001 HIS A 224 PHE 0.013 0.001 PHE B 69 TYR 0.015 0.001 TYR A 229 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8138 (mmm) cc_final: 0.7737 (mtt) REVERT: A 347 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8703 (m) REVERT: A 349 SER cc_start: 0.9160 (m) cc_final: 0.8833 (p) REVERT: A 373 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8333 (tt) REVERT: B 60 ASN cc_start: 0.8139 (t0) cc_final: 0.7867 (t0) REVERT: B 88 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8603 (pttm) REVERT: B 90 GLU cc_start: 0.7495 (pm20) cc_final: 0.7270 (pm20) outliers start: 36 outliers final: 27 residues processed: 119 average time/residue: 0.1396 time to fit residues: 22.6439 Evaluate side-chains 122 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 52 optimal weight: 0.0980 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.111055 restraints weight = 9092.696| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.39 r_work: 0.3538 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5426 Z= 0.211 Angle : 0.638 10.594 7412 Z= 0.320 Chirality : 0.041 0.241 884 Planarity : 0.004 0.048 902 Dihedral : 5.320 56.473 811 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.10 % Allowed : 22.00 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.34), residues: 692 helix: 1.44 (0.27), residues: 407 sheet: -0.40 (0.75), residues: 48 loop : -2.15 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.008 0.001 HIS A 224 PHE 0.011 0.001 PHE B 69 TYR 0.014 0.001 TYR A 229 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8121 (mmm) cc_final: 0.7695 (mtt) REVERT: A 347 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8734 (m) REVERT: A 349 SER cc_start: 0.9138 (m) cc_final: 0.8795 (p) REVERT: A 373 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8382 (tt) REVERT: B 60 ASN cc_start: 0.8124 (t0) cc_final: 0.7872 (t0) REVERT: B 88 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8578 (pttm) REVERT: B 90 GLU cc_start: 0.7470 (pm20) cc_final: 0.7262 (pm20) outliers start: 33 outliers final: 25 residues processed: 116 average time/residue: 0.1377 time to fit residues: 21.9981 Evaluate side-chains 116 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.129427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.108928 restraints weight = 9877.353| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.75 r_work: 0.3574 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5426 Z= 0.203 Angle : 0.652 12.875 7412 Z= 0.328 Chirality : 0.041 0.229 884 Planarity : 0.004 0.045 902 Dihedral : 5.286 56.026 811 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 6.28 % Allowed : 22.18 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.34), residues: 692 helix: 1.52 (0.27), residues: 407 sheet: -0.54 (0.73), residues: 48 loop : -2.11 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.007 0.001 HIS A 224 PHE 0.012 0.001 PHE A 168 TYR 0.011 0.001 TYR A 229 ARG 0.004 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8163 (mmm) cc_final: 0.7764 (mtt) REVERT: A 347 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8741 (m) REVERT: A 349 SER cc_start: 0.9188 (m) cc_final: 0.8804 (p) REVERT: A 373 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8398 (tt) REVERT: B 60 ASN cc_start: 0.8089 (t0) cc_final: 0.7860 (t0) REVERT: B 88 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (pttm) outliers start: 34 outliers final: 28 residues processed: 114 average time/residue: 0.1417 time to fit residues: 22.2468 Evaluate side-chains 121 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 65 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.130859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.111130 restraints weight = 9074.044| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.45 r_work: 0.3571 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5426 Z= 0.193 Angle : 0.661 14.372 7412 Z= 0.327 Chirality : 0.041 0.256 884 Planarity : 0.004 0.044 902 Dihedral : 5.269 55.646 811 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.73 % Allowed : 23.11 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.34), residues: 692 helix: 1.56 (0.27), residues: 407 sheet: -0.64 (0.71), residues: 48 loop : -2.10 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.008 0.001 HIS A 224 PHE 0.010 0.001 PHE A 168 TYR 0.011 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1384 Ramachandran restraints generated. 692 Oldfield, 0 Emsley, 692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8098 (mmm) cc_final: 0.7700 (mtt) REVERT: A 347 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8763 (m) REVERT: A 349 SER cc_start: 0.9124 (m) cc_final: 0.8742 (p) REVERT: A 373 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 557 TYR cc_start: 0.7648 (m-80) cc_final: 0.7400 (m-80) REVERT: B 60 ASN cc_start: 0.8074 (t0) cc_final: 0.7854 (t0) REVERT: B 88 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8562 (pttm) outliers start: 31 outliers final: 26 residues processed: 113 average time/residue: 0.1577 time to fit residues: 23.4950 Evaluate side-chains 118 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 88 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 0.0070 chunk 58 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 0.0010 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.133317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.112707 restraints weight = 9942.656| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.79 r_work: 0.3635 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5426 Z= 0.164 Angle : 0.643 14.148 7412 Z= 0.318 Chirality : 0.041 0.258 884 Planarity : 0.005 0.046 902 Dihedral : 5.130 54.115 811 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.99 % Allowed : 24.58 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.34), residues: 692 helix: 1.64 (0.27), residues: 408 sheet: -0.54 (0.68), residues: 48 loop : -2.07 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 660 HIS 0.008 0.001 HIS A 224 PHE 0.010 0.001 PHE A 432 TYR 0.013 0.001 TYR B 61 ARG 0.010 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2575.14 seconds wall clock time: 45 minutes 5.76 seconds (2705.76 seconds total)