Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 16:48:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/10_2023/7jzm_22533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/10_2023/7jzm_22533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/10_2023/7jzm_22533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/10_2023/7jzm_22533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/10_2023/7jzm_22533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/10_2023/7jzm_22533.pdb" } resolution = 3.5 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= 0.022 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 10 5.16 5 C 1310 2.51 5 N 340 2.21 5 O 373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 2033 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 495 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1500 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.71, per 1000 atoms: 0.84 Number of scatterers: 2033 At special positions: 0 Unit cell: (66.15, 68.25, 69.3, 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 10 16.00 O 373 8.00 N 340 7.00 C 1310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.28 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN B 343 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 312.7 milliseconds 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 38.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 Processing helix chain 'A' and resid 22 through 42 Processing helix chain 'A' and resid 44 through 64 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.514A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.158A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.479A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 93 hydrogen bonds defined for protein. 240 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: 0.49 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 591 1.33 - 1.46: 586 1.46 - 1.59: 893 1.59 - 1.72: 0 1.72 - 1.85: 12 Bond restraints: 2082 Sorted by residual: bond pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 1.473 1.337 0.136 1.40e-02 5.10e+03 9.45e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CG GLN B 506 " pdb=" CD GLN B 506 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.74e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.477 -0.054 2.00e-02 2.50e+03 7.29e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.19: 27 104.19 - 111.62: 885 111.62 - 119.06: 722 119.06 - 126.49: 1185 126.49 - 133.92: 11 Bond angle restraints: 2830 Sorted by residual: angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" CB PRO B 499 " ideal model delta sigma weight residual 103.41 96.76 6.65 9.40e-01 1.13e+00 5.01e+01 angle pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 112.00 120.93 -8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.01 -6.45 1.02e+00 9.61e-01 4.00e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.31 -6.44 1.04e+00 9.25e-01 3.84e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.65 -6.09 1.01e+00 9.80e-01 3.64e+01 ... (remaining 2825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1154 14.30 - 28.59: 45 28.59 - 42.89: 8 42.89 - 57.18: 5 57.18 - 71.48: 1 Dihedral angle restraints: 1213 sinusoidal: 454 harmonic: 759 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 51.36 41.64 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB GLU B 484 " pdb=" CG GLU B 484 " pdb=" CD GLU B 484 " pdb=" OE1 GLU B 484 " ideal model delta sinusoidal sigma weight residual 0.00 71.48 -71.48 1 3.00e+01 1.11e-03 7.28e+00 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual 180.00 166.92 13.08 0 5.00e+00 4.00e-02 6.85e+00 ... (remaining 1210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 230 0.082 - 0.164: 69 0.164 - 0.245: 15 0.245 - 0.327: 3 0.327 - 0.409: 1 Chirality restraints: 318 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.38e+01 chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.68e+01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.90 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 315 not shown) Planarity restraints: 364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR B 495 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " 0.025 2.00e-02 2.50e+03 1.34e-02 3.57e+00 pdb=" CG TYR B 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.016 2.00e-02 2.50e+03 1.65e-02 3.40e+00 pdb=" CG ASN B 343 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 361 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 880 2.92 - 3.41: 1816 3.41 - 3.91: 3445 3.91 - 4.40: 3881 4.40 - 4.90: 6261 Nonbonded interactions: 16283 Sorted by model distance: nonbonded pdb=" O ASP A 2 " pdb=" OD1 ASP A 2 " model vdw 2.420 3.040 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.566 2.520 nonbonded pdb=" O ASN B 501 " pdb=" NE2 GLN B 506 " model vdw 2.568 2.520 nonbonded pdb=" O5 NAG C 1 " pdb=" O6 NAG C 1 " model vdw 2.569 2.432 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.574 2.560 ... (remaining 16278 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: 3.540 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: 12.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.670 Find NCS groups from input model: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 0.015 0.136 2082 Z= 0.952 Angle : 1.378 12.810 2830 Z= 0.921 Chirality : 0.084 0.409 318 Planarity : 0.005 0.026 363 Dihedral : 9.289 71.478 715 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.52), residues: 254 helix: 0.21 (0.51), residues: 85 sheet: 0.78 (0.76), residues: 52 loop : 0.82 (0.60), residues: 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1799 time to fit residues: 13.3830 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 0.0980 overall best weight: 0.1114 ------------------------------------------------------------------------------- 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: 0.7625 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2082 Z= 0.172 Angle : 0.613 8.177 2830 Z= 0.315 Chirality : 0.042 0.141 318 Planarity : 0.004 0.038 363 Dihedral : 4.178 17.340 285 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.49 % Allowed : 9.45 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.54), residues: 254 helix: 1.18 (0.58), residues: 87 sheet: 0.62 (0.78), residues: 49 loop : 0.65 (0.57), residues: 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.224 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1691 time to fit residues: 8.2046 Evaluate side-chains 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0248 time to fit residues: 0.4847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.0870 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 18 optimal weight: 0.0670 chunk 17 optimal weight: 0.0770 chunk 11 optimal weight: 0.0270 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 overall best weight: 0.0712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2082 Z= 0.131 Angle : 0.535 6.383 2830 Z= 0.269 Chirality : 0.041 0.134 318 Planarity : 0.003 0.039 363 Dihedral : 3.920 17.282 285 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.50 % Allowed : 10.95 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.52), residues: 254 helix: 1.24 (0.57), residues: 88 sheet: 0.39 (0.74), residues: 49 loop : 0.47 (0.57), residues: 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.230 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1289 time to fit residues: 5.5798 Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.7780 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2082 Z= 0.340 Angle : 0.620 6.182 2830 Z= 0.327 Chirality : 0.044 0.145 318 Planarity : 0.004 0.040 363 Dihedral : 4.336 18.085 285 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 9.95 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.53), residues: 254 helix: 1.11 (0.57), residues: 89 sheet: -0.15 (0.73), residues: 49 loop : 0.15 (0.57), residues: 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.232 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.1397 time to fit residues: 7.2535 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0326 time to fit residues: 0.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.0030 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.0020 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2082 Z= 0.199 Angle : 0.564 6.987 2830 Z= 0.286 Chirality : 0.042 0.135 318 Planarity : 0.004 0.040 363 Dihedral : 4.118 17.362 285 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.53), residues: 254 helix: 1.10 (0.57), residues: 88 sheet: -0.37 (0.73), residues: 49 loop : 0.11 (0.58), residues: 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.238 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.1381 time to fit residues: 7.0926 Evaluate side-chains 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0263 time to fit residues: 0.3839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 14 optimal weight: 0.0980 chunk 11 optimal weight: 0.0970 overall best weight: 0.1876 ------------------------------------------------------------------------------- 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: 0.7758 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2082 Z= 0.187 Angle : 0.597 9.221 2830 Z= 0.300 Chirality : 0.042 0.130 318 Planarity : 0.004 0.040 363 Dihedral : 4.082 16.818 285 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.00 % Allowed : 12.94 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.53), residues: 254 helix: 1.04 (0.57), residues: 88 sheet: -0.40 (0.76), residues: 49 loop : 0.06 (0.58), residues: 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.202 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1199 time to fit residues: 5.9384 Evaluate side-chains 40 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.223 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0223 time to fit residues: 0.3396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.0010 chunk 7 optimal weight: 0.3980 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.1980 chunk 18 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 23 optimal weight: 0.1980 overall best weight: 0.1586 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2082 Z= 0.171 Angle : 0.600 9.200 2830 Z= 0.293 Chirality : 0.042 0.130 318 Planarity : 0.004 0.040 363 Dihedral : 4.057 16.356 285 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.00 % Allowed : 14.43 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.54), residues: 254 helix: 0.95 (0.57), residues: 88 sheet: -0.31 (0.78), residues: 49 loop : 0.03 (0.58), residues: 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.238 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1229 time to fit residues: 6.1238 Evaluate side-chains 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.229 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0231 time to fit residues: 0.3504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0070 chunk 22 optimal weight: 0.0970 chunk 23 optimal weight: 0.0980 chunk 13 optimal weight: 0.0010 chunk 9 optimal weight: 0.0040 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.0770 chunk 16 optimal weight: 0.0980 overall best weight: 0.0372 ------------------------------------------------------------------------------- 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: 0.7685 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 2082 Z= 0.128 Angle : 0.652 11.546 2830 Z= 0.302 Chirality : 0.041 0.127 318 Planarity : 0.003 0.040 363 Dihedral : 3.995 15.581 285 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.00 % Allowed : 15.42 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.54), residues: 254 helix: 0.91 (0.58), residues: 88 sheet: -0.03 (0.81), residues: 47 loop : -0.07 (0.57), residues: 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.237 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1253 time to fit residues: 6.2308 Evaluate side-chains 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0242 time to fit residues: 0.3605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 2 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 21 optimal weight: 0.1980 chunk 6 optimal weight: 0.3980 chunk 18 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 overall best weight: 0.1116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2082 Z= 0.151 Angle : 0.658 10.205 2830 Z= 0.308 Chirality : 0.041 0.129 318 Planarity : 0.003 0.040 363 Dihedral : 3.953 17.830 285 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.55), residues: 254 helix: 1.42 (0.59), residues: 88 sheet: 0.01 (0.81), residues: 49 loop : -0.08 (0.58), residues: 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1297 time to fit residues: 5.9503 Evaluate side-chains 38 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.0030 chunk 0 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2082 Z= 0.294 Angle : 0.685 9.806 2830 Z= 0.335 Chirality : 0.044 0.132 318 Planarity : 0.004 0.042 363 Dihedral : 4.352 19.203 285 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 17.91 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.54), residues: 254 helix: 1.31 (0.58), residues: 88 sheet: -0.35 (0.77), residues: 49 loop : -0.28 (0.57), residues: 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.236 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1304 time to fit residues: 5.8358 Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.1980 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.0870 chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 0.0870 chunk 6 optimal weight: 0.1980 overall best weight: 0.1536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111279 restraints weight = 2990.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114113 restraints weight = 1658.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116004 restraints weight = 1125.782| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2082 Z= 0.170 Angle : 0.651 10.010 2830 Z= 0.307 Chirality : 0.042 0.130 318 Planarity : 0.004 0.042 363 Dihedral : 4.141 18.336 285 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 18.91 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.54), residues: 254 helix: 1.26 (0.58), residues: 88 sheet: -0.33 (0.78), residues: 49 loop : -0.23 (0.58), residues: 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.69 seconds wall clock time: 22 minutes 41.93 seconds (1361.93 seconds total)