Starting phenix.real_space_refine on Sun Mar 10 15:02:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mji_23874/03_2024/7mji_23874.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mji_23874/03_2024/7mji_23874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mji_23874/03_2024/7mji_23874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mji_23874/03_2024/7mji_23874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mji_23874/03_2024/7mji_23874.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mji_23874/03_2024/7mji_23874.pdb" } resolution = 2.81 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= 0.024 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 14 5.16 5 C 1597 2.51 5 N 425 2.21 5 O 486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2522 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1547 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "E" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 961 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 1.96, per 1000 atoms: 0.78 Number of scatterers: 2522 At special positions: 0 Unit cell: (84, 59, 79, 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 14 16.00 O 486 8.00 N 425 7.00 C 1597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 116 " distance=2.02 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 475.3 milliseconds 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 582 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 16.6% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.648A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.555A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.614A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 removed outlier: 4.400A pdb=" N ASP E 52 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 53 " --> pdb=" O PHE E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 49 through 53' Processing helix chain 'E' and resid 84 through 86 No H-bonds generated for 'chain 'E' and resid 84 through 86' Processing helix chain 'E' and resid 107 through 111 removed outlier: 3.511A pdb=" N THR E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.835A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 28 removed outlier: 3.644A pdb=" N LEU E 99 " --> pdb=" O CYS E 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.611A pdb=" N MET E 55 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG E 71 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 57 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 32 through 33 removed outlier: 4.140A pdb=" N VAL E 134 " --> pdb=" O ARG E 118 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 210 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: 0.66 Time building geometry restraints manager: 1.02 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: 813 1.34 - 1.46: 685 1.46 - 1.58: 1070 1.58 - 1.71: 0 1.71 - 1.83: 18 Bond restraints: 2586 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" CG LEU E 41 " pdb=" CD1 LEU E 41 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.52e+00 bond pdb=" C TYR B 505 " pdb=" N GLN B 506 " ideal model delta sigma weight residual 1.340 1.266 0.074 5.87e-02 2.90e+02 1.58e+00 bond pdb=" CG1 ILE E 69 " pdb=" CD1 ILE E 69 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 ... (remaining 2581 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.96: 48 104.96 - 112.22: 1180 112.22 - 119.47: 879 119.47 - 126.73: 1373 126.73 - 133.99: 35 Bond angle restraints: 3515 Sorted by residual: angle pdb=" CA ASN B 360 " pdb=" CB ASN B 360 " pdb=" CG ASN B 360 " ideal model delta sigma weight residual 112.60 115.23 -2.63 1.00e+00 1.00e+00 6.90e+00 angle pdb=" CA LEU E 84 " pdb=" CB LEU E 84 " pdb=" CG LEU E 84 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" C LYS E 96 " pdb=" N ASN E 97 " pdb=" CA ASN E 97 " ideal model delta sigma weight residual 122.36 125.96 -3.60 1.42e+00 4.96e-01 6.41e+00 angle pdb=" C SER B 359 " pdb=" N ASN B 360 " pdb=" CA ASN B 360 " ideal model delta sigma weight residual 122.93 126.73 -3.80 1.51e+00 4.39e-01 6.33e+00 angle pdb=" CB ARG E 59 " pdb=" CG ARG E 59 " pdb=" CD ARG E 59 " ideal model delta sigma weight residual 111.30 116.91 -5.61 2.30e+00 1.89e-01 5.95e+00 ... (remaining 3510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1393 15.39 - 30.77: 110 30.77 - 46.15: 20 46.15 - 61.54: 6 61.54 - 76.92: 5 Dihedral angle restraints: 1534 sinusoidal: 610 harmonic: 924 Sorted by residual: dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" N GLY B 404 " pdb=" CA GLY B 404 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 515 " pdb=" C PHE B 515 " pdb=" N GLU B 516 " pdb=" CA GLU B 516 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 175 0.032 - 0.063: 114 0.063 - 0.095: 52 0.095 - 0.127: 26 0.127 - 0.158: 7 Chirality restraints: 374 Sorted by residual: chirality pdb=" CA VAL E 58 " pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CB VAL E 58 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 371 not shown) Planarity restraints: 459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 103 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C MET E 103 " 0.040 2.00e-02 2.50e+03 pdb=" O MET E 103 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN E 104 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 43 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C CYS E 43 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS E 43 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 44 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO B 521 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " -0.030 5.00e-02 4.00e+02 ... (remaining 456 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 917 2.87 - 3.38: 2025 3.38 - 3.89: 4248 3.89 - 4.39: 4808 4.39 - 4.90: 8495 Nonbonded interactions: 20493 Sorted by model distance: nonbonded pdb=" OG SER B 366 " pdb=" OD1 ASN B 388 " model vdw 2.367 2.440 nonbonded pdb=" NE ARG E 71 " pdb=" OD2 ASP E 119 " model vdw 2.373 2.520 nonbonded pdb=" NE2 GLN E 60 " pdb=" O LYS E 64 " model vdw 2.446 2.520 nonbonded pdb=" OH TYR B 489 " pdb=" NH2 ARG E 124 " model vdw 2.474 2.520 nonbonded pdb=" NE ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.492 2.520 ... (remaining 20488 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: 3.470 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: 12.940 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.006 0.074 2586 Z= 0.385 Angle : 0.808 9.063 3515 Z= 0.427 Chirality : 0.053 0.158 374 Planarity : 0.008 0.070 458 Dihedral : 12.491 76.924 937 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.44), residues: 316 helix: -4.87 (0.21), residues: 27 sheet: 0.26 (0.55), residues: 93 loop : -0.23 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.017 0.002 PHE B 377 TYR 0.021 0.002 TYR B 495 ARG 0.017 0.002 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.301 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.0055 time to fit residues: 76.3450 Evaluate side-chains 63 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 388 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2586 Z= 0.213 Angle : 0.505 4.274 3515 Z= 0.263 Chirality : 0.042 0.128 374 Planarity : 0.004 0.030 458 Dihedral : 5.757 48.251 380 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 11.40 % Favored : 85.29 % 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: -0.15 (0.46), residues: 316 helix: -4.12 (0.45), residues: 28 sheet: 0.69 (0.57), residues: 89 loop : 0.25 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 57 HIS 0.001 0.001 HIS B 519 PHE 0.010 0.001 PHE B 377 TYR 0.014 0.001 TYR B 365 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.327 Fit side-chains REVERT: B 360 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8238 (t0) REVERT: E 42 SER cc_start: 0.8521 (m) cc_final: 0.8288 (p) REVERT: E 77 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.7904 (ptp90) outliers start: 9 outliers final: 4 residues processed: 75 average time/residue: 0.9779 time to fit residues: 75.3504 Evaluate side-chains 73 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN B 498 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2586 Z= 0.280 Angle : 0.525 4.620 3515 Z= 0.275 Chirality : 0.044 0.149 374 Planarity : 0.004 0.028 458 Dihedral : 6.001 54.530 380 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.21 % Allowed : 16.18 % Favored : 81.62 % 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 (0.47), residues: 316 helix: -3.43 (0.73), residues: 28 sheet: 0.57 (0.57), residues: 89 loop : 0.33 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 377 TYR 0.014 0.001 TYR B 495 ARG 0.006 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.283 Fit side-chains REVERT: E 42 SER cc_start: 0.8393 (m) cc_final: 0.8084 (p) outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.9102 time to fit residues: 69.3712 Evaluate side-chains 74 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN B 409 GLN E 94 ASN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2586 Z= 0.248 Angle : 0.512 4.948 3515 Z= 0.264 Chirality : 0.043 0.133 374 Planarity : 0.003 0.027 458 Dihedral : 5.996 56.914 380 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.31 % Allowed : 15.44 % Favored : 81.25 % 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: 0.02 (0.47), residues: 316 helix: -3.14 (0.85), residues: 28 sheet: 0.21 (0.57), residues: 84 loop : 0.55 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 515 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.001 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.279 Fit side-chains REVERT: E 42 SER cc_start: 0.8392 (m) cc_final: 0.8054 (p) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.9764 time to fit residues: 74.1786 Evaluate side-chains 74 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2586 Z= 0.186 Angle : 0.496 5.149 3515 Z= 0.257 Chirality : 0.043 0.137 374 Planarity : 0.003 0.027 458 Dihedral : 5.722 54.067 380 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.47), residues: 316 helix: -3.01 (0.89), residues: 28 sheet: 0.18 (0.57), residues: 84 loop : 0.64 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.011 0.001 PHE B 392 TYR 0.010 0.001 TYR B 495 ARG 0.003 0.001 ARG E 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.287 Fit side-chains REVERT: B 360 ASN cc_start: 0.8649 (t0) cc_final: 0.8240 (t0) REVERT: B 424 LYS cc_start: 0.8898 (tptp) cc_final: 0.8615 (tppp) REVERT: E 92 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7948 (ttp-110) REVERT: E 132 MET cc_start: 0.8516 (mmt) cc_final: 0.7619 (mmt) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 1.0016 time to fit residues: 69.0083 Evaluate side-chains 68 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8243 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2586 Z= 0.274 Angle : 0.529 6.358 3515 Z= 0.272 Chirality : 0.044 0.132 374 Planarity : 0.003 0.027 458 Dihedral : 6.187 59.096 380 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.41 % Allowed : 16.54 % Favored : 79.04 % 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: 0.07 (0.47), residues: 316 helix: -2.85 (0.92), residues: 28 sheet: 0.19 (0.58), residues: 84 loop : 0.56 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 68 HIS 0.002 0.001 HIS B 519 PHE 0.010 0.001 PHE B 392 TYR 0.012 0.001 TYR B 365 ARG 0.006 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.285 Fit side-chains REVERT: B 424 LYS cc_start: 0.8889 (tptp) cc_final: 0.8598 (tppp) REVERT: E 77 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7915 (ptp90) REVERT: E 132 MET cc_start: 0.8514 (mmt) cc_final: 0.7519 (mmt) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 1.0474 time to fit residues: 73.0565 Evaluate side-chains 71 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2586 Z= 0.234 Angle : 0.517 6.291 3515 Z= 0.266 Chirality : 0.044 0.131 374 Planarity : 0.003 0.028 458 Dihedral : 6.107 59.969 380 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.41 % Allowed : 18.01 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.48), residues: 316 helix: -2.81 (0.92), residues: 28 sheet: 0.20 (0.58), residues: 84 loop : 0.61 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 68 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE B 392 TYR 0.017 0.001 TYR B 365 ARG 0.004 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.254 Fit side-chains REVERT: B 360 ASN cc_start: 0.8774 (t0) cc_final: 0.8325 (t0) REVERT: B 424 LYS cc_start: 0.8896 (tptp) cc_final: 0.8602 (tppp) REVERT: E 92 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7807 (ttp-110) REVERT: E 132 MET cc_start: 0.8549 (mmt) cc_final: 0.7569 (mmt) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.9500 time to fit residues: 65.4660 Evaluate side-chains 69 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 92 ARG Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 139 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 27 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.0270 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2586 Z= 0.164 Angle : 0.493 6.886 3515 Z= 0.252 Chirality : 0.043 0.127 374 Planarity : 0.003 0.028 458 Dihedral : 5.622 53.936 380 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.31 % Allowed : 18.75 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.48), residues: 316 helix: -2.78 (0.93), residues: 28 sheet: 0.22 (0.59), residues: 84 loop : 0.66 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.010 0.001 PHE B 392 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.309 Fit side-chains REVERT: B 360 ASN cc_start: 0.8782 (t0) cc_final: 0.8345 (t0) REVERT: B 424 LYS cc_start: 0.8897 (tptp) cc_final: 0.8611 (tppp) REVERT: E 132 MET cc_start: 0.8605 (mmt) cc_final: 0.7706 (mmt) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.9289 time to fit residues: 64.0900 Evaluate side-chains 67 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.0370 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2586 Z= 0.163 Angle : 0.506 6.859 3515 Z= 0.260 Chirality : 0.043 0.130 374 Planarity : 0.003 0.029 458 Dihedral : 5.508 51.943 380 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.84 % Allowed : 19.85 % Favored : 78.31 % 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: 0.19 (0.47), residues: 316 helix: -3.20 (1.04), residues: 21 sheet: 0.41 (0.60), residues: 82 loop : 0.49 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 392 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.250 Fit side-chains REVERT: B 360 ASN cc_start: 0.8778 (t0) cc_final: 0.8335 (t0) REVERT: B 424 LYS cc_start: 0.8884 (tptp) cc_final: 0.8596 (tppp) REVERT: E 132 MET cc_start: 0.8602 (mmt) cc_final: 0.7694 (mmt) outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 1.0342 time to fit residues: 69.1385 Evaluate side-chains 64 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2586 Z= 0.246 Angle : 0.535 7.367 3515 Z= 0.274 Chirality : 0.044 0.132 374 Planarity : 0.003 0.027 458 Dihedral : 5.990 57.792 380 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.21 % Allowed : 20.59 % Favored : 77.21 % 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: 0.15 (0.48), residues: 316 helix: -2.73 (0.94), residues: 28 sheet: 0.25 (0.58), residues: 84 loop : 0.62 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 PHE 0.007 0.001 PHE B 392 TYR 0.015 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 632 Ramachandran restraints generated. 316 Oldfield, 0 Emsley, 316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.276 Fit side-chains REVERT: B 360 ASN cc_start: 0.8797 (t0) cc_final: 0.8321 (t0) REVERT: B 424 LYS cc_start: 0.8916 (tptp) cc_final: 0.8602 (tppp) REVERT: E 132 MET cc_start: 0.8579 (mmt) cc_final: 0.7599 (mmt) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 1.0380 time to fit residues: 69.2792 Evaluate side-chains 65 residues out of total 272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain E residue 134 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.082892 restraints weight = 4322.370| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.57 r_work: 0.3038 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2586 Z= 0.211 Angle : 0.528 7.292 3515 Z= 0.271 Chirality : 0.044 0.131 374 Planarity : 0.003 0.028 458 Dihedral : 5.920 57.014 380 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.21 % Allowed : 21.69 % Favored : 76.10 % 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: 0.13 (0.48), residues: 316 helix: -3.14 (1.07), residues: 21 sheet: 0.35 (0.60), residues: 82 loop : 0.45 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 68 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE B 515 TYR 0.014 0.001 TYR B 365 ARG 0.007 0.001 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1840.44 seconds wall clock time: 33 minutes 0.20 seconds (1980.20 seconds total)