Starting phenix.real_space_refine (version: dev) on Sun Dec 11 14:09:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/12_2022/7e3b_30978.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/12_2022/7e3b_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_30978/12_2022/7e3b_30978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/12_2022/7e3b_30978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/12_2022/7e3b_30978.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3b_30978/12_2022/7e3b_30978.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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 chiralities: 1 Time building chain proxies: 2.44, per 1000 atoms: 0.74 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: 1.24 Conformation dependent library (CDL) restraints added in 456.2 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: 0.25 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: 0.88 Time building geometry restraints manager: 1.30 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: 1803 17.19 - 34.37: 145 34.37 - 51.56: 24 51.56 - 68.74: 7 68.74 - 85.92: 3 Dihedral angle restraints: 1982 sinusoidal: 764 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 1979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 282 0.033 - 0.066: 145 0.066 - 0.099: 40 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 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. 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: 1.240 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: 6.520 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 14.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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= 0.397 Angle : 0.805 10.437 4610 Z= 0.458 Chirality : 0.049 0.165 500 Planarity : 0.004 0.041 594 Dihedral : 13.258 85.922 1194 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 % 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 *********************** 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 : 0.410 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1598 time to fit residues: 16.4185 Evaluate side-chains 76 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5211 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.4566 ------------------------------------------------------------------------------- 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: 0.8320 moved from start: 0.1048 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= 0.213 Angle : 0.616 10.189 4610 Z= 0.326 Chirality : 0.046 0.171 500 Planarity : 0.004 0.031 594 Dihedral : 5.049 22.696 470 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.00 % 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: -1.73 (0.39), residues: 415 helix: -2.16 (0.91), residues: 27 sheet: -0.84 (0.46), residues: 132 loop : -1.19 (0.36), residues: 256 *********************** 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 : 0.407 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1620 time to fit residues: 18.7093 Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5458 ------------------------------------------------------------------------------- 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: 0.7980 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.8313 moved from start: 0.1404 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= 0.210 Angle : 0.606 10.071 4610 Z= 0.317 Chirality : 0.047 0.178 500 Planarity : 0.004 0.032 594 Dihedral : 4.817 22.849 470 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: -1.50 (0.40), residues: 415 helix: -2.11 (0.91), residues: 27 sheet: -0.57 (0.48), residues: 132 loop : -1.10 (0.36), residues: 256 *********************** 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 : 0.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1672 time to fit residues: 19.3215 Evaluate side-chains 81 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4896 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3385 Z= 0.277 Angle : 0.630 9.812 4610 Z= 0.328 Chirality : 0.047 0.201 500 Planarity : 0.004 0.034 594 Dihedral : 4.892 23.863 470 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.00 % 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 (0.40), residues: 415 helix: -2.13 (0.92), residues: 27 sheet: -0.65 (0.47), residues: 132 loop : -1.11 (0.36), residues: 256 *********************** 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 96 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1767 time to fit residues: 20.2749 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5388 ------------------------------------------------------------------------------- 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: 0.7980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1715 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= 0.219 Angle : 0.603 9.613 4610 Z= 0.315 Chirality : 0.046 0.211 500 Planarity : 0.004 0.033 594 Dihedral : 4.730 23.051 470 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: -1.46 (0.40), residues: 415 helix: -2.06 (0.91), residues: 27 sheet: -0.54 (0.48), residues: 132 loop : -1.08 (0.36), residues: 256 *********************** 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 102 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.454 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1716 time to fit residues: 21.0078 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5330 ------------------------------------------------------------------------------- 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: 0.1980 chunk 9 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 0.045 3385 Z= 0.190 Angle : 0.619 9.402 4610 Z= 0.318 Chirality : 0.046 0.220 500 Planarity : 0.004 0.034 594 Dihedral : 4.632 22.542 470 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.00 % 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: -1.40 (0.40), residues: 415 helix: -2.04 (0.89), residues: 27 sheet: -0.47 (0.48), residues: 132 loop : -1.04 (0.36), residues: 256 *********************** 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 : 0.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1458 time to fit residues: 17.9607 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6290 ------------------------------------------------------------------------------- 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: 0.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 15 optimal weight: 0.0670 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 3385 Z= 0.165 Angle : 0.610 9.115 4610 Z= 0.310 Chirality : 0.046 0.227 500 Planarity : 0.004 0.036 594 Dihedral : 4.485 21.765 470 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.00 % 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: -1.20 (0.40), residues: 415 helix: -2.09 (0.91), residues: 27 sheet: -0.26 (0.49), residues: 132 loop : -0.92 (0.37), residues: 256 *********************** 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 103 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1523 time to fit residues: 19.1414 Evaluate side-chains 85 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6068 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8320 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3385 Z= 0.290 Angle : 0.662 9.270 4610 Z= 0.338 Chirality : 0.048 0.237 500 Planarity : 0.004 0.036 594 Dihedral : 4.663 23.873 470 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 0.00 % 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: -1.28 (0.40), residues: 415 helix: -2.20 (0.91), residues: 27 sheet: -0.38 (0.48), residues: 132 loop : -0.94 (0.36), residues: 256 *********************** 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 101 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1437 time to fit residues: 17.8334 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5344 ------------------------------------------------------------------------------- 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: 4.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2079 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= 0.299 Angle : 0.669 9.394 4610 Z= 0.342 Chirality : 0.048 0.240 500 Planarity : 0.004 0.035 594 Dihedral : 4.802 24.062 470 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer Outliers : 0.00 % 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: -1.31 (0.41), residues: 415 helix: -2.25 (0.93), residues: 27 sheet: -0.39 (0.48), residues: 132 loop : -0.95 (0.37), residues: 256 *********************** 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 99 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.417 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1420 time to fit residues: 17.3006 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5357 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8316 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3385 Z= 0.249 Angle : 0.671 9.415 4610 Z= 0.339 Chirality : 0.048 0.251 500 Planarity : 0.004 0.035 594 Dihedral : 4.675 23.324 470 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.00 % 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: -1.31 (0.40), residues: 415 helix: -2.28 (0.92), residues: 27 sheet: -0.42 (0.48), residues: 132 loop : -0.93 (0.37), residues: 256 ********************** 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 100 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.381 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1516 time to fit residues: 18.7567 Evaluate side-chains 82 residues out of total 364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5328 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.0020 chunk 40 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.059128 restraints weight = 8524.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.061132 restraints weight = 4890.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.062386 restraints weight = 3335.037| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3385 Z= 0.248 Angle : 0.659 9.351 4610 Z= 0.335 Chirality : 0.048 0.245 500 Planarity : 0.004 0.035 594 Dihedral : 4.728 23.342 470 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 0.00 % 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: -1.24 (0.41), residues: 415 helix: -2.34 (0.90), residues: 27 sheet: -0.30 (0.49), residues: 132 loop : -0.92 (0.37), residues: 256 =============================================================================== Job complete usr+sys time: 1325.48 seconds wall clock time: 24 minutes 32.80 seconds (1472.80 seconds total)