Starting phenix.real_space_refine on Tue Feb 13 09:04:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hin_34823/02_2024/8hin_34823_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.014 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 37 5.16 5 C 3155 2.51 5 N 778 2.21 5 O 818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 645": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4788 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4512 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain breaks: 2 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'LN9': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.35, per 1000 atoms: 0.70 Number of scatterers: 4788 At special positions: 0 Unit cell: (83.6992, 78.468, 92.8538, 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 37 16.00 O 818 8.00 N 778 7.00 C 3155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 255 " - pdb=" SG CYS A 511 " distance=2.25 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 351 " distance=2.31 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 361 " distance=2.31 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 522 " distance=2.39 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: 2.08 Conformation dependent library (CDL) restraints added in 898.0 milliseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 0 sheets defined 70.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 23 through 46 removed outlier: 3.799A pdb=" N ILE A 37 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.766A pdb=" N LEU A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 94 through 111 removed outlier: 3.939A pdb=" N LEU A 103 " --> pdb=" O TRP A 100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 104 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.650A pdb=" N TYR A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.632A pdb=" N LEU A 229 " --> pdb=" O GLY A 225 " (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: 3.991A pdb=" N ILE A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.593A pdb=" N GLY A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 340 through 343 No H-bonds generated for 'chain 'A' and resid 340 through 343' Processing helix chain 'A' and resid 348 through 355 removed outlier: 3.630A pdb=" N ARG A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 removed outlier: 4.589A pdb=" N TYR A 366 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 3.538A pdb=" N VAL A 371 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS A 372 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 removed outlier: 3.817A pdb=" N LEU A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 445 removed outlier: 3.970A pdb=" N VAL A 430 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 452 through 463 Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 482 through 506 removed outlier: 3.681A pdb=" N MET A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Proline residue: A 502 - end of helix Processing helix chain 'A' and resid 526 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 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 647 through 671 removed outlier: 3.504A pdb=" N TYR A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 53 284 hydrogen bonds defined for protein. 810 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: 1.37 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 713 1.28 - 1.43: 1374 1.43 - 1.57: 2769 1.57 - 1.72: 1 1.72 - 1.86: 57 Bond restraints: 4914 Sorted by residual: bond pdb=" C PHE A 72 " pdb=" O PHE A 72 " ideal model delta sigma weight residual 1.236 1.140 0.096 1.15e-02 7.56e+03 6.95e+01 bond pdb=" C THR A 403 " pdb=" O THR A 403 " ideal model delta sigma weight residual 1.236 1.144 0.093 1.15e-02 7.56e+03 6.48e+01 bond pdb=" C TRP A 276 " pdb=" O TRP A 276 " ideal model delta sigma weight residual 1.241 1.171 0.071 9.80e-03 1.04e+04 5.19e+01 bond pdb=" C PRO A 66 " pdb=" O PRO A 66 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.26e-02 6.30e+03 4.39e+01 bond pdb=" C GLY A 68 " pdb=" O GLY A 68 " ideal model delta sigma weight residual 1.234 1.156 0.078 1.19e-02 7.06e+03 4.27e+01 ... (remaining 4909 not shown) Histogram of bond angle deviations from ideal: 92.98 - 101.54: 50 101.54 - 110.11: 1099 110.11 - 118.68: 3099 118.68 - 127.25: 2363 127.25 - 135.82: 90 Bond angle restraints: 6701 Sorted by residual: angle pdb=" C ASN A 101 " pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " ideal model delta sigma weight residual 110.67 92.98 17.69 1.92e+00 2.71e-01 8.49e+01 angle pdb=" N THR A 411 " pdb=" CA THR A 411 " pdb=" C THR A 411 " ideal model delta sigma weight residual 111.07 101.26 9.81 1.07e+00 8.73e-01 8.41e+01 angle pdb=" C PRO A 518 " pdb=" CA PRO A 518 " pdb=" CB PRO A 518 " ideal model delta sigma weight residual 110.20 96.90 13.30 1.46e+00 4.69e-01 8.30e+01 angle pdb=" N GLY A 418 " pdb=" CA GLY A 418 " pdb=" C GLY A 418 " ideal model delta sigma weight residual 111.03 98.32 12.71 1.40e+00 5.10e-01 8.25e+01 angle pdb=" C PHE A 453 " pdb=" CA PHE A 453 " pdb=" CB PHE A 453 " ideal model delta sigma weight residual 110.81 96.80 14.01 1.60e+00 3.91e-01 7.66e+01 ... (remaining 6696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2453 17.64 - 35.28: 296 35.28 - 52.92: 71 52.92 - 70.56: 19 70.56 - 88.20: 8 Dihedral angle restraints: 2847 sinusoidal: 1087 harmonic: 1760 Sorted by residual: dihedral pdb=" CB CYS A 345 " pdb=" SG CYS A 345 " pdb=" SG CYS A 351 " pdb=" CB CYS A 351 " ideal model delta sinusoidal sigma weight residual -86.00 -171.52 85.52 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -161.56 75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" C ASN A 101 " pdb=" N ASN A 101 " pdb=" CA ASN A 101 " pdb=" CB ASN A 101 " ideal model delta harmonic sigma weight residual -122.60 -105.38 -17.22 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 2844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 412 0.068 - 0.137: 252 0.137 - 0.205: 89 0.205 - 0.274: 24 0.274 - 0.342: 4 Chirality restraints: 781 Sorted by residual: chirality pdb=" CA PRO A 367 " pdb=" N PRO A 367 " pdb=" C PRO A 367 " pdb=" CB PRO A 367 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA LEU A 170 " pdb=" N LEU A 170 " pdb=" C LEU A 170 " pdb=" CB LEU A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA ASN A 75 " pdb=" N ASN A 75 " pdb=" C ASN A 75 " pdb=" CB ASN A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 778 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 445 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C GLN A 445 " -0.083 2.00e-02 2.50e+03 pdb=" O GLN A 445 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA A 446 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 504 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C PHE A 504 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE A 504 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A 505 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 499 " -0.266 9.50e-02 1.11e+02 1.19e-01 8.72e+00 pdb=" NE ARG A 499 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 499 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 499 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 499 " -0.010 2.00e-02 2.50e+03 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 514 2.76 - 3.30: 5088 3.30 - 3.83: 7690 3.83 - 4.37: 10135 4.37 - 4.90: 16119 Nonbonded interactions: 39546 Sorted by model distance: nonbonded pdb=" O GLY A 77 " pdb=" N GLY A 79 " model vdw 2.228 2.520 nonbonded pdb=" ND2 ASN A 250 " pdb=" C1 NAG A 801 " model vdw 2.236 3.550 nonbonded pdb=" O GLY A 77 " pdb=" N HIS A 80 " model vdw 2.246 2.520 nonbonded pdb=" N MET A 62 " pdb=" O MET A 62 " model vdw 2.298 2.496 nonbonded pdb=" O PRO A 246 " pdb=" CB ALA A 247 " model vdw 2.299 3.460 ... (remaining 39541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.017 0.104 4914 Z= 1.124 Angle : 2.476 17.694 6701 Z= 1.796 Chirality : 0.096 0.342 781 Planarity : 0.008 0.119 821 Dihedral : 16.966 88.204 1711 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.73 % Favored : 92.61 % Rotamer: Outliers : 4.58 % Allowed : 14.74 % Favored : 80.68 % Cbeta Deviations : 1.07 % 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: -3.91 (0.28), residues: 609 helix: -2.24 (0.20), residues: 444 sheet: None (None), residues: 0 loop : -3.08 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP A 276 HIS 0.005 0.002 HIS A 264 PHE 0.026 0.004 PHE A 476 TYR 0.040 0.004 TYR A 455 ARG 0.012 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.545 Fit side-chains REVERT: A 101 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7366 (t0) REVERT: A 117 TYR cc_start: 0.8260 (m-10) cc_final: 0.8018 (m-80) REVERT: A 125 MET cc_start: 0.6594 (ttp) cc_final: 0.6379 (ttp) REVERT: A 130 ARG cc_start: 0.6746 (ttp80) cc_final: 0.6381 (ttt-90) REVERT: A 330 MET cc_start: 0.8358 (mtt) cc_final: 0.8140 (mtt) REVERT: A 333 MET cc_start: 0.8450 (mtp) cc_final: 0.7664 (mtp) REVERT: A 382 MET cc_start: 0.6783 (tpt) cc_final: 0.6356 (tpp) REVERT: A 422 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5354 (mt) REVERT: A 506 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 570 ARG cc_start: 0.5734 (ptt-90) cc_final: 0.5463 (ptt-90) REVERT: B 28 GLN cc_start: 0.5671 (OUTLIER) cc_final: 0.5408 (tp40) REVERT: B 31 MET cc_start: 0.6562 (mmm) cc_final: 0.5633 (ptt) REVERT: B 54 TRP cc_start: 0.5243 (m100) cc_final: 0.4961 (m100) outliers start: 23 outliers final: 6 residues processed: 115 average time/residue: 0.1955 time to fit residues: 27.7992 Evaluate side-chains 88 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain B residue 28 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.0570 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4914 Z= 0.194 Angle : 0.664 8.403 6701 Z= 0.332 Chirality : 0.043 0.197 781 Planarity : 0.005 0.051 821 Dihedral : 7.825 68.101 712 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.78 % Allowed : 16.33 % Favored : 79.88 % 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: -0.68 (0.34), residues: 609 helix: 0.06 (0.24), residues: 455 sheet: None (None), residues: 0 loop : -1.74 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 30 HIS 0.004 0.001 HIS A 268 PHE 0.019 0.002 PHE A 453 TYR 0.010 0.001 TYR A 256 ARG 0.004 0.001 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.517 Fit side-chains REVERT: A 60 ARG cc_start: 0.6310 (ptm-80) cc_final: 0.5838 (ttt-90) REVERT: A 125 MET cc_start: 0.6340 (ttp) cc_final: 0.6090 (ttp) REVERT: A 325 MET cc_start: 0.8212 (tmm) cc_final: 0.7844 (tpp) REVERT: A 427 ARG cc_start: 0.5908 (mtt-85) cc_final: 0.5305 (mtp180) REVERT: A 506 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 31 MET cc_start: 0.6277 (mmm) cc_final: 0.5447 (ptt) outliers start: 19 outliers final: 13 residues processed: 96 average time/residue: 0.1928 time to fit residues: 23.1774 Evaluate side-chains 82 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 655 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 250 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4914 Z= 0.260 Angle : 0.661 8.153 6701 Z= 0.327 Chirality : 0.044 0.192 781 Planarity : 0.005 0.057 821 Dihedral : 6.183 56.478 700 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.38 % Allowed : 18.53 % Favored : 77.09 % 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: 0.10 (0.35), residues: 609 helix: 0.62 (0.25), residues: 455 sheet: None (None), residues: 0 loop : -1.42 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 30 HIS 0.005 0.001 HIS A 555 PHE 0.015 0.001 PHE A 230 TYR 0.014 0.001 TYR A 256 ARG 0.006 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.546 Fit side-chains REVERT: A 60 ARG cc_start: 0.6321 (ptm-80) cc_final: 0.5889 (ttt-90) REVERT: A 112 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 125 MET cc_start: 0.6401 (ttp) cc_final: 0.6187 (ttp) REVERT: A 209 LEU cc_start: 0.6324 (mm) cc_final: 0.5908 (mm) REVERT: A 325 MET cc_start: 0.8398 (tmm) cc_final: 0.8010 (tpp) REVERT: A 358 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6709 (mm-30) REVERT: A 506 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7077 (t80) REVERT: A 564 ARG cc_start: 0.5952 (ptt-90) cc_final: 0.5739 (ptt90) REVERT: B 31 MET cc_start: 0.6249 (mmm) cc_final: 0.5535 (ptt) REVERT: B 54 TRP cc_start: 0.4717 (m100) cc_final: 0.4384 (m100) outliers start: 22 outliers final: 15 residues processed: 91 average time/residue: 0.1967 time to fit residues: 22.1914 Evaluate side-chains 89 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 72 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4914 Z= 0.199 Angle : 0.604 9.425 6701 Z= 0.299 Chirality : 0.042 0.174 781 Planarity : 0.005 0.057 821 Dihedral : 5.957 54.171 700 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.18 % Allowed : 18.33 % Favored : 76.49 % 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: 0.54 (0.35), residues: 609 helix: 0.95 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -1.32 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 PHE 0.009 0.001 PHE A 534 TYR 0.031 0.001 TYR A 256 ARG 0.006 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.491 Fit side-chains REVERT: A 60 ARG cc_start: 0.6385 (ptm-80) cc_final: 0.5919 (tmt170) REVERT: A 112 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7476 (tt) REVERT: A 125 MET cc_start: 0.6348 (ttp) cc_final: 0.6101 (ttp) REVERT: A 150 TYR cc_start: 0.6886 (m-10) cc_final: 0.6581 (m-10) REVERT: A 209 LEU cc_start: 0.6106 (mm) cc_final: 0.5711 (mm) REVERT: A 325 MET cc_start: 0.8390 (tmm) cc_final: 0.8045 (tpp) REVERT: A 333 MET cc_start: 0.8308 (mtp) cc_final: 0.8069 (mtp) REVERT: A 374 MET cc_start: 0.7589 (mtt) cc_final: 0.7302 (mtp) REVERT: A 564 ARG cc_start: 0.5892 (ptt-90) cc_final: 0.5672 (ptt90) REVERT: B 31 MET cc_start: 0.6118 (mmm) cc_final: 0.5486 (ptt) outliers start: 26 outliers final: 20 residues processed: 94 average time/residue: 0.1805 time to fit residues: 21.2275 Evaluate side-chains 96 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.0470 chunk 49 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4914 Z= 0.154 Angle : 0.550 8.061 6701 Z= 0.271 Chirality : 0.039 0.166 781 Planarity : 0.004 0.055 821 Dihedral : 5.620 52.403 700 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.18 % Allowed : 20.12 % Favored : 75.70 % 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: 1.08 (0.36), residues: 609 helix: 1.40 (0.25), residues: 448 sheet: None (None), residues: 0 loop : -1.20 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 30 HIS 0.002 0.000 HIS A 555 PHE 0.008 0.001 PHE A 398 TYR 0.023 0.001 TYR A 256 ARG 0.003 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 0.537 Fit side-chains REVERT: A 32 TYR cc_start: 0.7579 (t80) cc_final: 0.7298 (t80) REVERT: A 60 ARG cc_start: 0.6380 (ptm-80) cc_final: 0.5878 (tmt170) REVERT: A 112 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7599 (tt) REVERT: A 150 TYR cc_start: 0.6738 (m-10) cc_final: 0.6416 (m-10) REVERT: A 325 MET cc_start: 0.8353 (tmm) cc_final: 0.8023 (tpp) REVERT: A 333 MET cc_start: 0.8195 (mtp) cc_final: 0.7940 (mtp) REVERT: A 358 GLU cc_start: 0.6637 (mm-30) cc_final: 0.6290 (mm-30) REVERT: A 374 MET cc_start: 0.7578 (mtt) cc_final: 0.7281 (mtp) REVERT: A 552 PRO cc_start: 0.6153 (Cg_exo) cc_final: 0.5872 (Cg_endo) REVERT: A 564 ARG cc_start: 0.5956 (ptt-90) cc_final: 0.5723 (ptt90) outliers start: 21 outliers final: 12 residues processed: 89 average time/residue: 0.1913 time to fit residues: 21.3632 Evaluate side-chains 88 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0070 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4914 Z= 0.151 Angle : 0.534 7.303 6701 Z= 0.263 Chirality : 0.039 0.163 781 Planarity : 0.004 0.050 821 Dihedral : 5.090 52.441 697 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.18 % Allowed : 20.72 % Favored : 75.10 % 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: 1.35 (0.36), residues: 609 helix: 1.57 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -0.99 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 30 HIS 0.002 0.000 HIS A 555 PHE 0.008 0.001 PHE A 534 TYR 0.020 0.001 TYR A 256 ARG 0.004 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.537 Fit side-chains REVERT: A 60 ARG cc_start: 0.6470 (ptm-80) cc_final: 0.6006 (ttt-90) REVERT: A 112 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7522 (tt) REVERT: A 150 TYR cc_start: 0.6930 (m-10) cc_final: 0.6622 (m-10) REVERT: A 325 MET cc_start: 0.8346 (tmm) cc_final: 0.8015 (tpp) REVERT: A 333 MET cc_start: 0.8194 (mtp) cc_final: 0.7940 (mtp) REVERT: A 358 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6370 (mm-30) REVERT: A 374 MET cc_start: 0.7590 (mtt) cc_final: 0.7295 (mtp) REVERT: A 427 ARG cc_start: 0.5886 (mtt-85) cc_final: 0.5193 (mtp180) REVERT: A 552 PRO cc_start: 0.6212 (Cg_exo) cc_final: 0.5991 (Cg_endo) REVERT: A 564 ARG cc_start: 0.5911 (ptt-90) cc_final: 0.5679 (ptt90) outliers start: 21 outliers final: 13 residues processed: 91 average time/residue: 0.1912 time to fit residues: 21.7677 Evaluate side-chains 92 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4914 Z= 0.220 Angle : 0.577 7.080 6701 Z= 0.286 Chirality : 0.041 0.169 781 Planarity : 0.004 0.049 821 Dihedral : 5.254 52.694 697 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.98 % Allowed : 21.51 % Favored : 74.50 % 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: 1.28 (0.36), residues: 609 helix: 1.43 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -0.72 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 30 HIS 0.003 0.001 HIS A 264 PHE 0.013 0.001 PHE A 534 TYR 0.022 0.001 TYR A 256 ARG 0.004 0.000 ARG A 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.522 Fit side-chains REVERT: A 60 ARG cc_start: 0.6460 (ptm-80) cc_final: 0.6008 (tmt170) REVERT: A 112 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7473 (tt) REVERT: A 150 TYR cc_start: 0.6989 (m-10) cc_final: 0.6619 (m-10) REVERT: A 209 LEU cc_start: 0.5874 (mm) cc_final: 0.5513 (mm) REVERT: A 325 MET cc_start: 0.8446 (tmm) cc_final: 0.8040 (tpp) REVERT: A 333 MET cc_start: 0.8294 (mtp) cc_final: 0.8059 (mtp) REVERT: A 358 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6310 (mm-30) REVERT: A 374 MET cc_start: 0.7621 (mtt) cc_final: 0.7319 (mtp) REVERT: A 552 PRO cc_start: 0.6154 (Cg_exo) cc_final: 0.5870 (Cg_endo) outliers start: 20 outliers final: 18 residues processed: 90 average time/residue: 0.1929 time to fit residues: 21.7958 Evaluate side-chains 96 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4914 Z= 0.161 Angle : 0.542 6.701 6701 Z= 0.268 Chirality : 0.040 0.164 781 Planarity : 0.004 0.048 821 Dihedral : 5.134 52.403 697 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.78 % Allowed : 22.11 % Favored : 74.10 % 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: 1.45 (0.36), residues: 609 helix: 1.55 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -0.69 (0.53), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 30 HIS 0.002 0.001 HIS A 555 PHE 0.009 0.001 PHE A 534 TYR 0.020 0.001 TYR A 256 ARG 0.001 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.577 Fit side-chains REVERT: A 32 TYR cc_start: 0.7602 (t80) cc_final: 0.7327 (t80) REVERT: A 60 ARG cc_start: 0.6501 (ptm-80) cc_final: 0.6058 (ttt-90) REVERT: A 112 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7462 (tt) REVERT: A 150 TYR cc_start: 0.6892 (m-10) cc_final: 0.6589 (m-10) REVERT: A 325 MET cc_start: 0.8422 (tmm) cc_final: 0.8080 (tpp) REVERT: A 333 MET cc_start: 0.8242 (mtp) cc_final: 0.8000 (mtp) REVERT: A 358 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6302 (mm-30) REVERT: A 374 MET cc_start: 0.7628 (mtt) cc_final: 0.7321 (mtp) REVERT: A 552 PRO cc_start: 0.6104 (Cg_exo) cc_final: 0.5822 (Cg_endo) outliers start: 19 outliers final: 18 residues processed: 89 average time/residue: 0.1935 time to fit residues: 21.6665 Evaluate side-chains 93 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 483 GLN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4914 Z= 0.163 Angle : 0.539 6.596 6701 Z= 0.267 Chirality : 0.039 0.166 781 Planarity : 0.004 0.048 821 Dihedral : 5.087 52.472 697 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.18 % Allowed : 21.91 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.36), residues: 609 helix: 1.62 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -0.61 (0.53), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 30 HIS 0.002 0.001 HIS A 555 PHE 0.009 0.001 PHE A 534 TYR 0.018 0.001 TYR A 256 ARG 0.002 0.000 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.507 Fit side-chains REVERT: A 32 TYR cc_start: 0.7575 (t80) cc_final: 0.7307 (t80) REVERT: A 60 ARG cc_start: 0.6533 (ptm-80) cc_final: 0.6100 (ttt-90) REVERT: A 112 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 150 TYR cc_start: 0.6903 (m-10) cc_final: 0.6549 (m-10) REVERT: A 325 MET cc_start: 0.8444 (tmm) cc_final: 0.8084 (tpp) REVERT: A 333 MET cc_start: 0.8201 (mtp) cc_final: 0.7947 (mtp) REVERT: A 358 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6264 (mm-30) REVERT: A 374 MET cc_start: 0.7631 (mtt) cc_final: 0.7318 (mtp) REVERT: A 552 PRO cc_start: 0.6096 (Cg_exo) cc_final: 0.5817 (Cg_endo) outliers start: 21 outliers final: 17 residues processed: 88 average time/residue: 0.1965 time to fit residues: 21.5979 Evaluate side-chains 91 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4914 Z= 0.173 Angle : 0.546 6.605 6701 Z= 0.272 Chirality : 0.040 0.166 781 Planarity : 0.004 0.048 821 Dihedral : 5.153 52.189 697 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.59 % Allowed : 22.71 % Favored : 73.71 % 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: 1.53 (0.36), residues: 609 helix: 1.59 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -0.56 (0.54), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 PHE 0.010 0.001 PHE A 534 TYR 0.019 0.001 TYR A 256 ARG 0.003 0.000 ARG A 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.518 Fit side-chains REVERT: A 32 TYR cc_start: 0.7580 (t80) cc_final: 0.7312 (t80) REVERT: A 60 ARG cc_start: 0.6498 (ptm-80) cc_final: 0.6074 (ttt-90) REVERT: A 112 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7446 (tt) REVERT: A 150 TYR cc_start: 0.6949 (m-10) cc_final: 0.6613 (m-10) REVERT: A 325 MET cc_start: 0.8462 (tmm) cc_final: 0.8082 (tpp) REVERT: A 333 MET cc_start: 0.8267 (mtp) cc_final: 0.8029 (mtp) REVERT: A 358 GLU cc_start: 0.6546 (mm-30) cc_final: 0.6251 (mm-30) REVERT: A 374 MET cc_start: 0.7594 (mtt) cc_final: 0.7299 (mtp) REVERT: A 552 PRO cc_start: 0.6076 (Cg_exo) cc_final: 0.5794 (Cg_endo) outliers start: 18 outliers final: 17 residues processed: 86 average time/residue: 0.1962 time to fit residues: 21.0279 Evaluate side-chains 92 residues out of total 502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 53 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.145656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120091 restraints weight = 5217.471| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.27 r_work: 0.3135 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4914 Z= 0.196 Angle : 0.562 6.654 6701 Z= 0.280 Chirality : 0.041 0.168 781 Planarity : 0.004 0.048 821 Dihedral : 5.228 52.256 697 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.78 % Allowed : 22.51 % Favored : 73.71 % 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: 1.48 (0.36), residues: 609 helix: 1.53 (0.25), residues: 449 sheet: None (None), residues: 0 loop : -0.51 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 30 HIS 0.003 0.001 HIS A 555 PHE 0.012 0.001 PHE A 534 TYR 0.020 0.001 TYR A 256 ARG 0.001 0.000 ARG A 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1368.34 seconds wall clock time: 25 minutes 13.30 seconds (1513.30 seconds total)