Starting phenix.real_space_refine on Fri Apr 5 20:32:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/04_2024/7sl8_25194_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/04_2024/7sl8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/04_2024/7sl8_25194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/04_2024/7sl8_25194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/04_2024/7sl8_25194_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl8_25194/04_2024/7sl8_25194_neut_updated.pdb" } 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 Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 135": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 267": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 379": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 3.32, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 840.9 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... running ksdssp... Secondary structure from input PDB file: 28 helices and 3 sheets defined 55.7% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 26 through 48 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 68 through 75 removed outlier: 3.900A pdb=" N SER A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.559A pdb=" N LEU A 108 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 139 through 156 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 230 through 237 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) Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 276 through 293 removed outlier: 3.779A pdb=" N CYS A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.651A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 348 through 354 removed outlier: 4.692A pdb=" N LYS A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 370 removed outlier: 4.500A pdb=" N TYR A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 379 through 408 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 410 through 413 No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.504A pdb=" N ALA A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 453 through 476 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 Processing helix chain 'A' and resid 482 through 504 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 519 through 522 No H-bonds generated for 'chain 'A' and resid 519 through 522' Processing helix chain 'A' and resid 528 through 547 Processing helix chain 'A' and resid 553 through 555 No H-bonds generated for 'chain 'A' and resid 553 through 555' Processing helix chain 'A' and resid 639 through 665 Processing sheet with id= A, 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) removed outlier: 4.520A pdb=" N THR B 79 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 74 " --> pdb=" O THR B 79 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.502A pdb=" N THR B 117 " --> pdb=" O VAL B 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 39 through 41 271 hydrogen bonds defined for protein. 756 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: 1.31 Time building geometry restraints manager: 2.35 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: 99.41 - 106.40: 146 106.40 - 113.38: 2961 113.38 - 120.37: 2214 120.37 - 127.35: 2023 127.35 - 134.34: 68 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: 1752 2.83 - 3.35: 4932 3.35 - 3.87: 8781 3.87 - 4.38: 9502 4.38 - 4.90: 16815 Nonbonded interactions: 41782 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR B 101 " model vdw 2.316 2.440 nonbonded pdb=" O SER A 446 " pdb=" OG SER A 446 " model vdw 2.321 2.440 nonbonded pdb=" O LEU A 152 " pdb=" OG1 THR A 156 " model vdw 2.327 2.440 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 2.440 ... (remaining 41777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.520 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: 1.900 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.710 Find NCS groups from input model: 0.140 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- 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= 0.358 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 fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.631 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: 0.1982 time to fit residues: 33.0659 Evaluate side-chains 97 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 448 GLN A 525 HIS A 648 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5426 Z= 0.176 Angle : 0.613 7.566 7412 Z= 0.316 Chirality : 0.039 0.145 884 Planarity : 0.005 0.048 902 Dihedral : 5.981 53.433 814 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.51 % Allowed : 16.64 % Favored : 79.85 % 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: -2.04 (0.30), residues: 692 helix: -0.42 (0.25), residues: 397 sheet: -1.79 (0.68), residues: 48 loop : -2.75 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 289 HIS 0.002 0.000 HIS B 121 PHE 0.015 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 127 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8583 (tt) cc_final: 0.8349 (tt) REVERT: A 374 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7502 (mtm) REVERT: A 382 MET cc_start: 0.8301 (tpt) cc_final: 0.8013 (tpt) REVERT: B 22 LEU cc_start: 0.9334 (mt) cc_final: 0.9128 (mp) REVERT: B 87 LEU cc_start: 0.7840 (mm) cc_final: 0.7551 (mm) REVERT: B 90 GLU cc_start: 0.7396 (pm20) cc_final: 0.6776 (pm20) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.1550 time to fit residues: 24.2135 Evaluate side-chains 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 480 VAL 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 52 THR Chi-restraints excluded: chain B residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2005 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= 0.227 Angle : 0.599 5.973 7412 Z= 0.308 Chirality : 0.040 0.139 884 Planarity : 0.004 0.046 902 Dihedral : 5.888 57.168 814 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.55 % Allowed : 17.01 % 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: -1.26 (0.32), residues: 692 helix: 0.21 (0.27), residues: 398 sheet: -1.16 (0.72), residues: 48 loop : -2.51 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 487 HIS 0.001 0.000 HIS A 555 PHE 0.013 0.001 PHE A 432 TYR 0.014 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 125 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.8062 (mmm) cc_final: 0.7572 (mtt) REVERT: A 233 MET cc_start: 0.8621 (mtm) cc_final: 0.8249 (mtt) REVERT: A 325 MET cc_start: 0.8883 (tpp) cc_final: 0.8667 (tpp) REVERT: A 349 SER cc_start: 0.8863 (m) cc_final: 0.8613 (p) REVERT: A 382 MET cc_start: 0.8290 (tpt) cc_final: 0.7962 (tpt) REVERT: B 88 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8656 (pttm) outliers start: 30 outliers final: 18 residues processed: 117 average time/residue: 0.1544 time to fit residues: 24.3580 Evaluate side-chains 104 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 171 LEU Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 PHE 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 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 52 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2283 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= 0.176 Angle : 0.594 11.213 7412 Z= 0.298 Chirality : 0.039 0.141 884 Planarity : 0.004 0.046 902 Dihedral : 5.712 56.945 813 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 5.91 % Allowed : 18.67 % Favored : 75.42 % 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: -0.83 (0.33), residues: 692 helix: 0.54 (0.27), residues: 397 sheet: -0.75 (0.75), residues: 48 loop : -2.34 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.001 0.000 HIS A 309 PHE 0.012 0.001 PHE A 432 TYR 0.014 0.001 TYR B 61 ARG 0.004 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 134 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.7946 (mmm) cc_final: 0.7555 (mtt) REVERT: A 218 LEU cc_start: 0.8571 (tt) cc_final: 0.8307 (tt) REVERT: A 233 MET cc_start: 0.8595 (mtm) cc_final: 0.8259 (mtt) REVERT: A 349 SER cc_start: 0.8884 (m) cc_final: 0.8615 (p) REVERT: A 382 MET cc_start: 0.8262 (tpt) cc_final: 0.7786 (tpt) REVERT: A 525 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7861 (t70) REVERT: B 88 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8655 (pttm) outliers start: 32 outliers final: 19 residues processed: 125 average time/residue: 0.1553 time to fit residues: 25.9784 Evaluate side-chains 110 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 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 319 TYR Chi-restraints excluded: chain A residue 339 PHE 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 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 5 GLN Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 52 THR 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 49 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5426 Z= 0.176 Angle : 0.603 10.118 7412 Z= 0.301 Chirality : 0.041 0.256 884 Planarity : 0.004 0.043 902 Dihedral : 5.363 57.318 811 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.36 % Allowed : 21.44 % 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: -0.57 (0.33), residues: 692 helix: 0.75 (0.27), residues: 397 sheet: -0.51 (0.77), residues: 48 loop : -2.26 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.009 0.001 HIS A 224 PHE 0.024 0.001 PHE B 69 TYR 0.012 0.001 TYR B 61 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 124 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.7922 (mmm) cc_final: 0.7581 (mtt) REVERT: A 218 LEU cc_start: 0.8579 (tt) cc_final: 0.8306 (tt) REVERT: A 349 SER cc_start: 0.8918 (m) cc_final: 0.8625 (p) REVERT: A 382 MET cc_start: 0.8192 (tpt) cc_final: 0.7686 (tpt) REVERT: A 525 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7990 (t70) REVERT: B 88 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (pttm) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.1539 time to fit residues: 24.6609 Evaluate side-chains 108 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS 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 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 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 52 THR 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 39 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2587 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= 0.208 Angle : 0.607 8.482 7412 Z= 0.304 Chirality : 0.041 0.229 884 Planarity : 0.004 0.045 902 Dihedral : 5.379 57.297 811 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.36 % Allowed : 22.37 % 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: -0.42 (0.33), residues: 692 helix: 0.85 (0.27), residues: 398 sheet: -0.24 (0.79), residues: 48 loop : -2.21 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.006 0.001 HIS A 224 PHE 0.023 0.001 PHE B 69 TYR 0.012 0.001 TYR A 229 ARG 0.003 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 119 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.7932 (mmm) cc_final: 0.7626 (mtt) REVERT: A 233 MET cc_start: 0.8379 (mtt) cc_final: 0.8148 (mtt) REVERT: A 349 SER cc_start: 0.8932 (m) cc_final: 0.8607 (p) REVERT: A 382 MET cc_start: 0.8223 (tpt) cc_final: 0.7851 (tpt) REVERT: A 525 HIS cc_start: 0.8334 (OUTLIER) cc_final: 0.7999 (t70) REVERT: B 88 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8618 (pttm) outliers start: 29 outliers final: 25 residues processed: 111 average time/residue: 0.1595 time to fit residues: 23.7691 Evaluate side-chains 111 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU 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 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 PHE 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 470 VAL 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 52 THR 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 48 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5426 Z= 0.215 Angle : 0.619 9.916 7412 Z= 0.309 Chirality : 0.041 0.218 884 Planarity : 0.004 0.046 902 Dihedral : 5.342 56.822 811 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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: -0.29 (0.34), residues: 692 helix: 0.95 (0.27), residues: 398 sheet: -0.14 (0.81), residues: 48 loop : -2.15 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.012 0.001 HIS A 224 PHE 0.018 0.001 PHE B 69 TYR 0.011 0.001 TYR B 61 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 121 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 0.617 Fit side-chains REVERT: A 65 MET cc_start: 0.7925 (mmm) cc_final: 0.7634 (mtt) REVERT: A 233 MET cc_start: 0.8379 (mtt) cc_final: 0.8162 (mtt) REVERT: A 349 SER cc_start: 0.8803 (m) cc_final: 0.8519 (p) REVERT: A 382 MET cc_start: 0.8136 (tpt) cc_final: 0.7810 (tpt) REVERT: A 525 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7999 (t70) REVERT: B 88 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8614 (pttm) outliers start: 31 outliers final: 26 residues processed: 112 average time/residue: 0.1470 time to fit residues: 22.4329 Evaluate side-chains 111 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 357 THR 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 470 VAL 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 52 THR 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 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 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 ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2777 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= 0.187 Angle : 0.624 11.910 7412 Z= 0.310 Chirality : 0.041 0.220 884 Planarity : 0.004 0.046 902 Dihedral : 5.298 55.707 811 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.36 % Allowed : 24.03 % Favored : 70.61 % 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: -0.16 (0.34), residues: 692 helix: 1.09 (0.28), residues: 398 sheet: 0.01 (0.83), residues: 48 loop : -2.18 (0.40), residues: 246 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 0.035 0.002 PHE B 69 TYR 0.014 0.001 TYR B 61 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 121 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 92 time to evaluate : 0.612 Fit side-chains REVERT: A 65 MET cc_start: 0.7900 (mmm) cc_final: 0.7627 (mtt) REVERT: A 349 SER cc_start: 0.8846 (m) cc_final: 0.8574 (p) REVERT: A 382 MET cc_start: 0.8066 (tpt) cc_final: 0.7771 (tpt) REVERT: A 525 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7952 (t70) REVERT: B 60 ASN cc_start: 0.8074 (t0) cc_final: 0.7873 (t0) REVERT: B 88 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8595 (pttm) outliers start: 29 outliers final: 24 residues processed: 112 average time/residue: 0.1521 time to fit residues: 22.8579 Evaluate side-chains 112 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 PHE Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 357 THR 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 470 VAL 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 52 THR 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: 0.7980 chunk 48 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2893 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= 0.181 Angle : 0.623 14.416 7412 Z= 0.307 Chirality : 0.040 0.214 884 Planarity : 0.004 0.041 902 Dihedral : 5.211 54.870 811 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.55 % Allowed : 24.03 % 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: -0.08 (0.34), residues: 692 helix: 1.22 (0.28), residues: 398 sheet: -0.42 (0.76), residues: 48 loop : -2.16 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 660 HIS 0.003 0.001 HIS A 224 PHE 0.020 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 118 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 88 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.7893 (mmm) cc_final: 0.7659 (mtt) REVERT: A 349 SER cc_start: 0.8781 (m) cc_final: 0.8544 (p) REVERT: A 525 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.7977 (t70) outliers start: 30 outliers final: 27 residues processed: 111 average time/residue: 0.1433 time to fit residues: 21.8631 Evaluate side-chains 113 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 PHE 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 470 VAL 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 52 THR Chi-restraints excluded: chain B residue 66 LYS 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 68 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2979 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= 0.185 Angle : 0.633 14.566 7412 Z= 0.311 Chirality : 0.040 0.211 884 Planarity : 0.004 0.042 902 Dihedral : 5.137 54.673 811 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.18 % Allowed : 24.21 % Favored : 70.61 % 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: 0.01 (0.34), residues: 692 helix: 1.30 (0.28), residues: 398 sheet: -0.18 (0.79), residues: 48 loop : -2.19 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 660 HIS 0.010 0.001 HIS A 224 PHE 0.017 0.001 PHE A 168 TYR 0.010 0.001 TYR A 557 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 111 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.7885 (mmm) cc_final: 0.7656 (mtt) REVERT: A 233 MET cc_start: 0.8398 (mtt) cc_final: 0.8194 (mtt) REVERT: A 349 SER cc_start: 0.8789 (m) cc_final: 0.8555 (p) REVERT: A 382 MET cc_start: 0.8160 (tpt) cc_final: 0.7810 (tpt) REVERT: A 525 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.8063 (t70) REVERT: B 88 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8584 (pttp) outliers start: 28 outliers final: 25 residues processed: 105 average time/residue: 0.1415 time to fit residues: 20.2549 Evaluate side-chains 107 residues out of total 585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 80 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 224 HIS Chi-restraints excluded: chain A residue 264 HIS Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 339 PHE 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 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 52 THR Chi-restraints excluded: chain B residue 66 LYS 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 15 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 HIS ** B 83 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.128784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.108432 restraints weight = 9925.815| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.74 r_work: 0.3585 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5426 Z= 0.191 Angle : 0.632 14.753 7412 Z= 0.311 Chirality : 0.041 0.199 884 Planarity : 0.004 0.043 902 Dihedral : 5.082 54.591 811 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.36 % Allowed : 23.84 % Favored : 70.79 % 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: 0.04 (0.34), residues: 692 helix: 1.33 (0.28), residues: 398 sheet: -0.24 (0.78), residues: 48 loop : -2.19 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 660 HIS 0.013 0.001 HIS A 224 PHE 0.016 0.001 PHE A 168 TYR 0.018 0.001 TYR A 557 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: 1463.73 seconds wall clock time: 27 minutes 10.26 seconds (1630.26 seconds total)