Starting phenix.real_space_refine on Tue Feb 11 11:05:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sl8_25194/02_2025/7sl8_25194_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sl8_25194/02_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_25194/02_2025/7sl8_25194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sl8_25194/02_2025/7sl8_25194.map" model { file = "/net/cci-nas-00/data/ceres_data/7sl8_25194/02_2025/7sl8_25194_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sl8_25194/02_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-5592/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: 3.93, per 1000 atoms: 0.74 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: 1.21 Conformation dependent library (CDL) restraints added in 607.5 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: 0.52 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: 1.77 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: 0.430 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: 0.030 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- 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 : 0.544 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: 0.1922 time to fit residues: 31.7778 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 : 0.573 ------------------------------------------------------------------------------- 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 = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.113369 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 : 0.522 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: 0.1567 time to fit residues: 24.0289 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 : 0.533 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.134027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.113529 restraints weight = 9847.369| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.72 r_work: 0.3652 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 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 = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2103 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= 0.199 Angle : 0.600 6.118 7412 Z= 0.313 Chirality : 0.040 0.143 884 Planarity : 0.005 0.048 902 Dihedral : 5.895 58.548 814 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.25 % Allowed : 18.67 % Favored : 77.08 % 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: -1.14 (0.32), residues: 692 helix: 0.30 (0.26), residues: 412 sheet: -1.21 (0.71), residues: 48 loop : -2.56 (0.38), residues: 232 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 0.020 0.001 PHE A 658 TYR 0.015 0.001 TYR B 61 ARG 0.003 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 129 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8187 (mmm) cc_final: 0.7742 (mtt) REVERT: A 349 SER cc_start: 0.9165 (m) cc_final: 0.8833 (p) REVERT: A 525 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.7859 (t70) REVERT: B 84 MET cc_start: 0.8045 (ptp) cc_final: 0.7816 (ptp) REVERT: B 88 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8696 (pttm) outliers start: 23 outliers final: 15 residues processed: 123 average time/residue: 0.1505 time to fit residues: 24.5789 Evaluate side-chains 107 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 66 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3878 r_free = 0.3878 target = 0.130328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110915 restraints weight = 9215.206| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.41 r_work: 0.3546 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2391 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= 0.186 Angle : 0.613 9.135 7412 Z= 0.313 Chirality : 0.040 0.145 884 Planarity : 0.005 0.048 902 Dihedral : 5.739 58.202 813 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.47 % Allowed : 19.41 % Favored : 74.12 % 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: -0.64 (0.33), residues: 692 helix: 0.78 (0.27), residues: 406 sheet: -0.96 (0.70), residues: 48 loop : -2.46 (0.38), 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 49 TYR 0.014 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 132 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8110 (mmm) cc_final: 0.7653 (mtt) REVERT: A 347 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8690 (m) REVERT: A 349 SER cc_start: 0.9114 (m) cc_final: 0.8797 (p) REVERT: A 525 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8071 (t70) REVERT: B 88 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8662 (pttm) outliers start: 35 outliers final: 20 residues processed: 122 average time/residue: 0.1523 time to fit residues: 24.8183 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 : 0.574 ------------------------------------------------------------------------------- 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 357 THR 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 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: 3.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.128267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107867 restraints weight = 10041.818| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.76 r_work: 0.3580 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5426 Z= 0.192 Angle : 0.621 11.662 7412 Z= 0.315 Chirality : 0.041 0.332 884 Planarity : 0.004 0.047 902 Dihedral : 5.487 58.023 811 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.28 % Allowed : 20.52 % Favored : 73.20 % 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: -0.31 (0.33), residues: 692 helix: 1.03 (0.27), residues: 406 sheet: -0.72 (0.72), residues: 48 loop : -2.32 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.010 0.001 HIS A 224 PHE 0.012 0.001 PHE B 49 TYR 0.018 0.001 TYR A 229 ARG 0.004 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 131 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8159 (mmm) cc_final: 0.7730 (mtt) REVERT: A 233 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8304 (mtt) REVERT: A 347 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8696 (m) REVERT: A 349 SER cc_start: 0.9172 (m) cc_final: 0.8861 (p) REVERT: A 373 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 525 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8192 (t70) REVERT: B 88 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8653 (pttm) outliers start: 34 outliers final: 24 residues processed: 119 average time/residue: 0.1522 time to fit residues: 24.4118 Evaluate side-chains 121 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.127947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108549 restraints weight = 9105.635| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.39 r_work: 0.3519 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.004 0.034 5426 Z= 0.235 Angle : 0.632 10.098 7412 Z= 0.321 Chirality : 0.042 0.289 884 Planarity : 0.005 0.049 902 Dihedral : 5.435 58.189 811 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.84 % Allowed : 21.63 % 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: -0.13 (0.33), residues: 692 helix: 1.16 (0.27), residues: 406 sheet: -0.61 (0.74), residues: 48 loop : -2.23 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.001 0.000 HIS A 555 PHE 0.012 0.001 PHE B 49 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 132 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8219 (mmm) cc_final: 0.7795 (mtt) REVERT: A 233 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8526 (mtt) REVERT: A 347 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8760 (m) REVERT: A 349 SER cc_start: 0.9206 (m) cc_final: 0.8896 (p) REVERT: A 373 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 88 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8625 (pttm) outliers start: 37 outliers final: 23 residues processed: 119 average time/residue: 0.1554 time to fit residues: 24.7223 Evaluate side-chains 114 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 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 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 = 0.3869 r_free = 0.3869 target = 0.129635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109933 restraints weight = 9021.702| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.49 r_work: 0.3553 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2793 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= 0.195 Angle : 0.622 9.367 7412 Z= 0.316 Chirality : 0.041 0.265 884 Planarity : 0.004 0.048 902 Dihedral : 5.349 56.737 811 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 6.28 % Allowed : 21.63 % 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: 0.06 (0.34), residues: 692 helix: 1.32 (0.27), residues: 407 sheet: -0.49 (0.75), residues: 48 loop : -2.19 (0.41), 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 0.014 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 131 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8100 (mmm) cc_final: 0.7682 (mtt) REVERT: A 347 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8706 (m) REVERT: A 349 SER cc_start: 0.9097 (m) cc_final: 0.8784 (p) REVERT: A 373 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8240 (tt) REVERT: B 60 ASN cc_start: 0.8159 (t0) cc_final: 0.7910 (t0) REVERT: B 88 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8542 (pttm) REVERT: B 90 GLU cc_start: 0.7437 (pm20) cc_final: 0.7189 (pm20) outliers start: 34 outliers final: 23 residues processed: 120 average time/residue: 0.1509 time to fit residues: 24.3299 Evaluate side-chains 115 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 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 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: 0.1980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3963 r_free = 0.3963 target = 0.129218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108968 restraints weight = 9917.549| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.73 r_work: 0.3581 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5426 Z= 0.189 Angle : 0.624 11.641 7412 Z= 0.315 Chirality : 0.040 0.242 884 Planarity : 0.004 0.048 902 Dihedral : 5.268 56.146 811 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.73 % Allowed : 22.55 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.34), residues: 692 helix: 1.45 (0.27), residues: 407 sheet: -0.47 (0.75), 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 0.012 0.002 HIS A 224 PHE 0.012 0.001 PHE B 49 TYR 0.013 0.001 TYR A 229 ARG 0.004 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 124 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8136 (mmm) cc_final: 0.7755 (mtt) REVERT: A 347 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (m) REVERT: A 349 SER cc_start: 0.9155 (m) cc_final: 0.8792 (p) REVERT: A 373 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8330 (tt) REVERT: B 60 ASN cc_start: 0.8082 (t0) cc_final: 0.7821 (t0) REVERT: B 88 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8579 (pttm) REVERT: B 90 GLU cc_start: 0.7500 (pm20) cc_final: 0.7263 (pm20) outliers start: 31 outliers final: 24 residues processed: 115 average time/residue: 0.1449 time to fit residues: 22.7035 Evaluate side-chains 117 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 524 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 51 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.131800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.112014 restraints weight = 8922.814| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.49 r_work: 0.3575 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5426 Z= 0.178 Angle : 0.636 13.345 7412 Z= 0.319 Chirality : 0.040 0.220 884 Planarity : 0.004 0.044 902 Dihedral : 5.279 55.251 811 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.36 % Allowed : 23.11 % 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: 0.29 (0.34), residues: 692 helix: 1.58 (0.27), residues: 407 sheet: -0.76 (0.71), 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 0.002 0.001 HIS A 224 PHE 0.014 0.001 PHE A 168 TYR 0.013 0.001 TYR B 61 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 123 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8086 (mmm) cc_final: 0.7712 (mtt) REVERT: A 347 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8765 (m) REVERT: A 349 SER cc_start: 0.9125 (m) cc_final: 0.8776 (p) REVERT: A 373 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8466 (tt) REVERT: A 557 TYR cc_start: 0.7662 (m-80) cc_final: 0.7445 (m-80) REVERT: B 60 ASN cc_start: 0.8113 (t0) cc_final: 0.7908 (t0) REVERT: B 88 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8564 (pttm) outliers start: 29 outliers final: 24 residues processed: 112 average time/residue: 0.1611 time to fit residues: 23.9769 Evaluate side-chains 115 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 524 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 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: 10.0000 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 0.0030 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.131658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111013 restraints weight = 9928.250| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.79 r_work: 0.3598 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3153 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= 0.184 Angle : 0.647 14.137 7412 Z= 0.320 Chirality : 0.041 0.259 884 Planarity : 0.004 0.044 902 Dihedral : 5.229 55.210 811 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.18 % Allowed : 23.66 % 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: 0.37 (0.34), residues: 692 helix: 1.63 (0.27), residues: 407 sheet: -0.64 (0.69), residues: 48 loop : -2.12 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.012 0.001 HIS A 224 PHE 0.013 0.001 PHE B 49 TYR 0.012 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 122 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.8148 (mmm) cc_final: 0.7793 (mtt) REVERT: A 133 ARG cc_start: 0.7284 (tpt90) cc_final: 0.6878 (tpt170) REVERT: A 347 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8772 (m) REVERT: A 349 SER cc_start: 0.9130 (m) cc_final: 0.8756 (p) REVERT: A 373 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 557 TYR cc_start: 0.7746 (m-80) cc_final: 0.7461 (m-80) REVERT: B 60 ASN cc_start: 0.8054 (t0) cc_final: 0.7829 (t0) REVERT: B 88 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8570 (pttm) outliers start: 28 outliers final: 25 residues processed: 113 average time/residue: 0.1619 time to fit residues: 24.4044 Evaluate side-chains 118 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 524 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 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 47 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.130926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111325 restraints weight = 9126.283| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.41 r_work: 0.3567 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5426 Z= 0.226 Angle : 0.661 14.368 7412 Z= 0.329 Chirality : 0.041 0.254 884 Planarity : 0.004 0.045 902 Dihedral : 5.251 55.865 811 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.81 % Allowed : 25.32 % Favored : 69.87 % 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: 0.38 (0.34), residues: 692 helix: 1.61 (0.27), residues: 407 sheet: -0.48 (0.70), residues: 48 loop : -2.10 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 68 HIS 0.014 0.002 HIS A 224 PHE 0.013 0.001 PHE B 49 TYR 0.011 0.001 TYR B 61 ARG 0.004 0.000 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.43 seconds wall clock time: 46 minutes 47.88 seconds (2807.88 seconds total)