Starting phenix.real_space_refine on Sun Mar 10 16:27:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/03_2024/7e3b_30978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/03_2024/7e3b_30978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/03_2024/7e3b_30978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/03_2024/7e3b_30978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/03_2024/7e3b_30978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/03_2024/7e3b_30978.pdb" } resolution = 4.2 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= 0.001 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 2095 2.51 5 N 541 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3299 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "A" 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: 2.30, per 1000 atoms: 0.70 Number of scatterers: 3299 At special positions: 0 Unit cell: (68.481, 85.873, 72.829, 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 649 8.00 N 541 7.00 C 2095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 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 A 601 " - " ASN A 343 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 570.5 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.6% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.331A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.364A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.136A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.561A pdb=" N SER B 35 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.918A pdb=" N THR C 97 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 111 hydrogen bonds defined for protein. 255 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: 0.89 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1049 1.35 - 1.48: 968 1.48 - 1.60: 1352 1.60 - 1.73: 0 1.73 - 1.85: 16 Bond restraints: 3385 Sorted by residual: bond pdb=" CB PHE B 78 " pdb=" CG PHE B 78 " ideal model delta sigma weight residual 1.502 1.454 0.048 2.30e-02 1.89e+03 4.40e+00 bond pdb=" N TRP B 112 " pdb=" CA TRP B 112 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.88e+00 bond pdb=" CD2 PHE B 78 " pdb=" CE2 PHE B 78 " ideal model delta sigma weight residual 1.382 1.338 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB TRP B 112 " pdb=" CG TRP B 112 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.12e+00 bond pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 1.808 1.854 -0.046 3.30e-02 9.18e+02 1.97e+00 ... (remaining 3380 not shown) Histogram of bond angle deviations from ideal: 101.25 - 107.80: 141 107.80 - 114.35: 1826 114.35 - 120.90: 1493 120.90 - 127.45: 1117 127.45 - 134.00: 33 Bond angle restraints: 4610 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 124.84 -10.44 2.30e+00 1.89e-01 2.06e+01 angle pdb=" CB LYS B 13 " pdb=" CG LYS B 13 " pdb=" CD LYS B 13 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" C ILE C 83 " pdb=" N ALA C 84 " pdb=" CA ALA C 84 " ideal model delta sigma weight residual 122.09 116.48 5.61 1.86e+00 2.89e-01 9.11e+00 angle pdb=" N CYS A 432 " pdb=" CA CYS A 432 " pdb=" C CYS A 432 " ideal model delta sigma weight residual 108.60 112.87 -4.27 1.46e+00 4.69e-01 8.54e+00 angle pdb=" C GLY A 431 " pdb=" N CYS A 432 " pdb=" CA CYS A 432 " ideal model delta sigma weight residual 121.80 116.95 4.85 1.71e+00 3.42e-01 8.04e+00 ... (remaining 4605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 1814 17.19 - 34.37: 147 34.37 - 51.55: 26 51.55 - 68.74: 7 68.74 - 85.92: 3 Dihedral angle restraints: 1997 sinusoidal: 779 harmonic: 1218 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP B 110 " pdb=" C ASP B 110 " pdb=" N ILE B 111 " pdb=" CA ILE B 111 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 1994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 280 0.033 - 0.066: 146 0.066 - 0.099: 41 0.099 - 0.132: 23 0.132 - 0.165: 10 Chirality restraints: 500 Sorted by residual: chirality pdb=" CA ILE C 29 " pdb=" N ILE C 29 " pdb=" C ILE C 29 " pdb=" CB ILE C 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CB ILE B 111 " pdb=" CA ILE B 111 " pdb=" CG1 ILE B 111 " pdb=" CG2 ILE B 111 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 497 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 34 " -0.025 2.00e-02 2.50e+03 1.61e-02 6.50e+00 pdb=" CG TRP B 34 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP B 34 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 34 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 34 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 34 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 34 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 34 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 34 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 8 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO B 9 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 78 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C PHE B 78 " -0.027 2.00e-02 2.50e+03 pdb=" O PHE B 78 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 79 " 0.009 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 746 2.77 - 3.30: 3195 3.30 - 3.84: 5475 3.84 - 4.37: 6437 4.37 - 4.90: 11064 Nonbonded interactions: 26917 Sorted by model distance: nonbonded pdb=" OD1 ASP B 98 " pdb=" N ARG B 99 " model vdw 2.241 2.520 nonbonded pdb=" NH2 ARG A 346 " pdb=" OD2 ASP B 98 " model vdw 2.250 2.520 nonbonded pdb=" OD1 ASN A 450 " pdb=" OH TYR B 50 " model vdw 2.275 2.440 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.290 2.520 nonbonded pdb=" NH1 ARG C 18 " pdb=" OG1 THR C 20 " model vdw 2.296 2.520 ... (remaining 26912 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 group one per residue 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: 1.360 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: 0.000 Extract box with map and model: 6.580 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 0.048 3385 Z= 0.400 Angle : 0.810 10.437 4610 Z= 0.459 Chirality : 0.049 0.165 500 Planarity : 0.004 0.041 594 Dihedral : 13.333 85.922 1209 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.38), residues: 415 helix: -3.08 (0.86), residues: 26 sheet: -1.07 (0.45), residues: 130 loop : -1.32 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 34 HIS 0.001 0.001 HIS A 519 PHE 0.019 0.002 PHE B 78 TYR 0.022 0.002 TYR A 365 ARG 0.006 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.365 Fit side-chains REVERT: A 467 ASP cc_start: 0.8499 (t70) cc_final: 0.8014 (p0) REVERT: B 89 ASP cc_start: 0.9199 (m-30) cc_final: 0.8902 (m-30) REVERT: B 110 ASP cc_start: 0.8840 (t0) cc_final: 0.8568 (t0) REVERT: C 83 ILE cc_start: 0.9384 (mt) cc_final: 0.9178 (tt) REVERT: C 88 CYS cc_start: 0.6457 (p) cc_final: 0.6036 (p) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1665 time to fit residues: 17.0055 Evaluate side-chains 76 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- 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: 0.8290 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3385 Z= 0.225 Angle : 0.617 10.254 4610 Z= 0.325 Chirality : 0.046 0.159 500 Planarity : 0.004 0.031 594 Dihedral : 5.509 29.428 485 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.71 (0.40), residues: 415 helix: -2.17 (0.92), residues: 27 sheet: -0.83 (0.46), residues: 132 loop : -1.18 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 PHE 0.014 0.001 PHE B 78 TYR 0.022 0.001 TYR B 53 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.391 Fit side-chains REVERT: A 410 ILE cc_start: 0.9322 (mp) cc_final: 0.9112 (mm) REVERT: A 467 ASP cc_start: 0.8469 (t70) cc_final: 0.8011 (p0) REVERT: B 2 VAL cc_start: 0.9219 (t) cc_final: 0.8984 (t) REVERT: B 53 TYR cc_start: 0.8620 (p90) cc_final: 0.8216 (p90) REVERT: B 110 ASP cc_start: 0.8921 (t0) cc_final: 0.8680 (t0) REVERT: C 49 TYR cc_start: 0.8439 (p90) cc_final: 0.8152 (p90) REVERT: C 81 GLU cc_start: 0.8710 (pp20) cc_final: 0.8488 (pp20) REVERT: C 82 ASP cc_start: 0.8732 (m-30) cc_final: 0.8472 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1633 time to fit residues: 18.8763 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3385 Z= 0.223 Angle : 0.612 10.058 4610 Z= 0.319 Chirality : 0.046 0.182 500 Planarity : 0.004 0.032 594 Dihedral : 5.113 27.552 485 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.58 (0.40), residues: 415 helix: -2.20 (0.89), residues: 27 sheet: -0.63 (0.47), residues: 132 loop : -1.14 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 PHE 0.011 0.001 PHE B 78 TYR 0.014 0.001 TYR B 53 ARG 0.004 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.380 Fit side-chains REVERT: A 410 ILE cc_start: 0.9279 (mp) cc_final: 0.9013 (mm) REVERT: A 452 LEU cc_start: 0.9456 (mt) cc_final: 0.9180 (mt) REVERT: A 467 ASP cc_start: 0.8413 (t70) cc_final: 0.7933 (p0) REVERT: B 2 VAL cc_start: 0.9231 (t) cc_final: 0.8990 (t) REVERT: B 53 TYR cc_start: 0.8627 (p90) cc_final: 0.8255 (p90) REVERT: B 110 ASP cc_start: 0.8912 (t0) cc_final: 0.8651 (t0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1741 time to fit residues: 19.8946 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3385 Z= 0.250 Angle : 0.608 9.856 4610 Z= 0.319 Chirality : 0.046 0.189 500 Planarity : 0.004 0.032 594 Dihedral : 5.037 25.827 485 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.52 (0.40), residues: 415 helix: -2.14 (0.91), residues: 27 sheet: -0.55 (0.48), residues: 132 loop : -1.12 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 PHE 0.012 0.001 PHE A 456 TYR 0.018 0.001 TYR B 52 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.370 Fit side-chains REVERT: A 410 ILE cc_start: 0.9305 (mp) cc_final: 0.9071 (mm) REVERT: A 452 LEU cc_start: 0.9443 (mt) cc_final: 0.9223 (mt) REVERT: A 467 ASP cc_start: 0.8414 (t70) cc_final: 0.7887 (p0) REVERT: B 2 VAL cc_start: 0.9210 (t) cc_final: 0.8962 (t) REVERT: B 53 TYR cc_start: 0.8723 (p90) cc_final: 0.8366 (p90) REVERT: C 23 CYS cc_start: 0.5183 (t) cc_final: 0.4763 (t) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1603 time to fit residues: 19.3133 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN C 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3385 Z= 0.278 Angle : 0.642 9.684 4610 Z= 0.334 Chirality : 0.047 0.221 500 Planarity : 0.004 0.033 594 Dihedral : 5.010 24.701 485 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.56 (0.39), residues: 415 helix: -2.16 (0.90), residues: 27 sheet: -0.62 (0.47), residues: 132 loop : -1.12 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 34 HIS 0.002 0.001 HIS A 519 PHE 0.014 0.001 PHE A 347 TYR 0.011 0.001 TYR B 53 ARG 0.003 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.382 Fit side-chains REVERT: A 410 ILE cc_start: 0.9300 (mp) cc_final: 0.9065 (mm) REVERT: A 452 LEU cc_start: 0.9445 (mt) cc_final: 0.9231 (mt) REVERT: A 467 ASP cc_start: 0.8416 (t70) cc_final: 0.7868 (p0) REVERT: B 53 TYR cc_start: 0.8642 (p90) cc_final: 0.8320 (p90) REVERT: C 23 CYS cc_start: 0.5352 (t) cc_final: 0.4895 (t) REVERT: C 88 CYS cc_start: 0.6063 (p) cc_final: 0.5785 (p) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1625 time to fit residues: 19.4478 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0010 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN C 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3385 Z= 0.189 Angle : 0.613 9.532 4610 Z= 0.316 Chirality : 0.046 0.226 500 Planarity : 0.004 0.033 594 Dihedral : 4.823 24.144 485 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.42 (0.40), residues: 415 helix: -2.12 (0.87), residues: 27 sheet: -0.45 (0.48), residues: 132 loop : -1.07 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 105 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 429 TYR 0.009 0.001 TYR B 53 ARG 0.006 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.378 Fit side-chains REVERT: A 410 ILE cc_start: 0.9272 (mp) cc_final: 0.9049 (mm) REVERT: A 452 LEU cc_start: 0.9414 (mt) cc_final: 0.9190 (mm) REVERT: A 467 ASP cc_start: 0.8411 (t70) cc_final: 0.7861 (p0) REVERT: B 2 VAL cc_start: 0.9221 (t) cc_final: 0.8929 (t) REVERT: B 53 TYR cc_start: 0.8565 (p90) cc_final: 0.8278 (p90) REVERT: C 23 CYS cc_start: 0.5461 (t) cc_final: 0.4127 (t) REVERT: C 88 CYS cc_start: 0.5890 (p) cc_final: 0.5324 (p) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1720 time to fit residues: 20.6889 Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.0050 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3385 Z= 0.224 Angle : 0.626 9.319 4610 Z= 0.324 Chirality : 0.047 0.233 500 Planarity : 0.004 0.041 594 Dihedral : 4.765 23.222 485 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.32 (0.40), residues: 415 helix: -2.02 (0.92), residues: 27 sheet: -0.41 (0.48), residues: 132 loop : -0.99 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 34 HIS 0.001 0.001 HIS A 519 PHE 0.022 0.001 PHE B 78 TYR 0.018 0.001 TYR B 32 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.381 Fit side-chains REVERT: A 410 ILE cc_start: 0.9258 (mp) cc_final: 0.9038 (mm) REVERT: A 452 LEU cc_start: 0.9382 (mt) cc_final: 0.9146 (mm) REVERT: A 467 ASP cc_start: 0.8417 (t70) cc_final: 0.7867 (p0) REVERT: B 2 VAL cc_start: 0.9206 (t) cc_final: 0.8926 (t) REVERT: C 11 LEU cc_start: 0.9338 (tt) cc_final: 0.9126 (tt) REVERT: C 78 LEU cc_start: 0.9157 (tt) cc_final: 0.8827 (tt) REVERT: C 79 GLN cc_start: 0.8670 (mm110) cc_final: 0.8420 (mm110) REVERT: C 88 CYS cc_start: 0.5881 (p) cc_final: 0.5634 (p) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1627 time to fit residues: 18.7226 Evaluate side-chains 83 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3385 Z= 0.245 Angle : 0.656 9.264 4610 Z= 0.337 Chirality : 0.048 0.238 500 Planarity : 0.004 0.035 594 Dihedral : 4.863 23.262 485 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.40), residues: 415 helix: -2.15 (0.92), residues: 27 sheet: -0.34 (0.49), residues: 132 loop : -1.04 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 34 HIS 0.002 0.001 HIS A 519 PHE 0.017 0.001 PHE B 78 TYR 0.027 0.002 TYR B 52 ARG 0.004 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.348 Fit side-chains REVERT: A 467 ASP cc_start: 0.8425 (t70) cc_final: 0.7830 (p0) REVERT: B 2 VAL cc_start: 0.9198 (t) cc_final: 0.8902 (t) REVERT: C 78 LEU cc_start: 0.9148 (tt) cc_final: 0.8857 (tt) REVERT: C 79 GLN cc_start: 0.8764 (mm110) cc_final: 0.8277 (mm110) REVERT: C 88 CYS cc_start: 0.5516 (p) cc_final: 0.5090 (p) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1717 time to fit residues: 19.2454 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.0370 chunk 24 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3385 Z= 0.216 Angle : 0.635 9.194 4610 Z= 0.324 Chirality : 0.048 0.268 500 Planarity : 0.004 0.034 594 Dihedral : 4.689 22.700 485 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.27 (0.41), residues: 415 helix: -2.14 (0.93), residues: 27 sheet: -0.33 (0.49), residues: 132 loop : -0.96 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 112 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.001 PHE B 78 TYR 0.025 0.001 TYR B 53 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.381 Fit side-chains REVERT: A 467 ASP cc_start: 0.8436 (t70) cc_final: 0.7827 (p0) REVERT: B 2 VAL cc_start: 0.9189 (t) cc_final: 0.8856 (t) REVERT: B 53 TYR cc_start: 0.8757 (p90) cc_final: 0.8350 (p90) REVERT: B 77 GLN cc_start: 0.7747 (mt0) cc_final: 0.7503 (mm-40) REVERT: B 120 VAL cc_start: 0.7660 (p) cc_final: 0.7044 (p) REVERT: C 55 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 78 LEU cc_start: 0.9141 (tt) cc_final: 0.8831 (tt) REVERT: C 79 GLN cc_start: 0.8693 (mm110) cc_final: 0.8424 (mm110) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1613 time to fit residues: 19.0258 Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3385 Z= 0.297 Angle : 0.671 9.277 4610 Z= 0.343 Chirality : 0.049 0.271 500 Planarity : 0.004 0.035 594 Dihedral : 4.866 23.981 485 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.32 (0.41), residues: 415 helix: -2.25 (0.91), residues: 27 sheet: -0.38 (0.49), residues: 132 loop : -0.97 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 105 HIS 0.002 0.001 HIS A 519 PHE 0.016 0.001 PHE B 78 TYR 0.022 0.002 TYR B 53 ARG 0.004 0.001 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 467 ASP cc_start: 0.8415 (t70) cc_final: 0.7766 (p0) REVERT: B 2 VAL cc_start: 0.9187 (t) cc_final: 0.8887 (t) REVERT: B 53 TYR cc_start: 0.8752 (p90) cc_final: 0.8333 (p90) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1634 time to fit residues: 18.2541 Evaluate side-chains 80 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.073719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.060414 restraints weight = 8483.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.062482 restraints weight = 4768.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.063845 restraints weight = 3226.376| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3385 Z= 0.198 Angle : 0.661 9.108 4610 Z= 0.334 Chirality : 0.048 0.277 500 Planarity : 0.004 0.034 594 Dihedral : 4.671 22.438 485 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.41), residues: 415 helix: -2.21 (0.91), residues: 27 sheet: -0.36 (0.48), residues: 132 loop : -0.92 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 112 HIS 0.002 0.001 HIS A 519 PHE 0.012 0.001 PHE B 78 TYR 0.021 0.001 TYR B 53 ARG 0.005 0.001 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.89 seconds wall clock time: 24 minutes 44.67 seconds (1484.67 seconds total)