Starting phenix.real_space_refine on Thu Dec 7 15:58:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/12_2023/7jzm_22533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/12_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_22533/12_2023/7jzm_22533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/12_2023/7jzm_22533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/12_2023/7jzm_22533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/12_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-1.21rc1-5172/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.17, per 1000 atoms: 2.05 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: 1.37 Conformation dependent library (CDL) restraints added in 854.0 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: 0.25 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: 0.45 Time building geometry restraints manager: 1.47 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: 1191 14.30 - 28.59: 48 28.59 - 42.89: 8 42.89 - 57.18: 5 57.18 - 71.48: 3 Dihedral angle restraints: 1255 sinusoidal: 496 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 1252 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: 2.670 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: 12.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- 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 : 9.632 71.478 757 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.005 TRP B 353 HIS 0.002 0.001 HIS A 6 PHE 0.013 0.002 PHE B 342 TYR 0.036 0.006 TYR B 495 ARG 0.003 0.000 ARG B 355 *********************** 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 : 0.541 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1916 time to fit residues: 14.1559 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.174 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2340 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2082 Z= 0.167 Angle : 0.607 7.778 2830 Z= 0.315 Chirality : 0.042 0.142 318 Planarity : 0.004 0.039 363 Dihedral : 6.138 57.599 327 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 : 3.48 % Allowed : 8.46 % 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: 1.11 (0.54), residues: 254 helix: 1.17 (0.58), residues: 87 sheet: 0.63 (0.78), residues: 49 loop : 0.64 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 6 PHE 0.015 0.002 PHE A 33 TYR 0.016 0.001 TYR B 495 ARG 0.002 0.000 ARG B 408 *********************** 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 46 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.242 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.1695 time to fit residues: 8.4583 Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.210 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0207 time to fit residues: 0.4561 ------------------------------------------------------------------------------- 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: 0.0670 chunk 22 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 overall best weight: 0.2496 ------------------------------------------------------------------------------- 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: 0.7712 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2082 Z= 0.230 Angle : 0.562 6.109 2830 Z= 0.291 Chirality : 0.042 0.141 318 Planarity : 0.004 0.039 363 Dihedral : 6.219 59.074 327 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.50 % Allowed : 9.95 % Favored : 89.55 % 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: 0.78 (0.53), residues: 254 helix: 1.14 (0.57), residues: 88 sheet: 0.17 (0.74), residues: 49 loop : 0.35 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.002 0.001 HIS A 6 PHE 0.009 0.001 PHE B 429 TYR 0.016 0.002 TYR B 495 ARG 0.001 0.000 ARG A 45 *********************** 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 40 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.235 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.1286 time to fit residues: 6.1672 Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3076 ------------------------------------------------------------------------------- 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: 0.6980 chunk 11 optimal weight: 0.0060 chunk 21 optimal weight: 0.0980 chunk 6 optimal weight: 0.0170 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 overall best weight: 0.1612 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2082 Z= 0.162 Angle : 0.528 5.411 2830 Z= 0.269 Chirality : 0.041 0.135 318 Planarity : 0.003 0.039 363 Dihedral : 6.136 59.968 327 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.49 % Allowed : 11.44 % Favored : 87.06 % 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: 0.71 (0.53), residues: 254 helix: 1.16 (0.57), residues: 88 sheet: -0.04 (0.73), residues: 49 loop : 0.34 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.001 HIS A 18 PHE 0.009 0.001 PHE A 33 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG A 45 *********************** 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 41 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.231 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 0.1298 time to fit residues: 6.0891 Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0233 time to fit residues: 0.3648 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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: 0.7824 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 2082 Z= 0.377 Angle : 0.642 6.409 2830 Z= 0.336 Chirality : 0.046 0.144 318 Planarity : 0.004 0.039 363 Dihedral : 6.328 55.721 327 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: 0.31 (0.53), residues: 254 helix: 1.01 (0.57), residues: 89 sheet: -0.40 (0.76), residues: 49 loop : 0.00 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.002 0.001 HIS A 18 PHE 0.016 0.002 PHE B 429 TYR 0.018 0.002 TYR B 453 ARG 0.002 0.000 ARG B 457 *********************** 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 43 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.239 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.1538 time to fit residues: 7.5680 Evaluate side-chains 41 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.235 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0256 time to fit residues: 0.4066 ------------------------------------------------------------------------------- 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: 0.3980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2082 Z= 0.242 Angle : 0.600 7.431 2830 Z= 0.301 Chirality : 0.043 0.131 318 Planarity : 0.004 0.040 363 Dihedral : 6.046 54.680 327 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: 0.23 (0.53), residues: 254 helix: 1.04 (0.57), residues: 88 sheet: -0.61 (0.75), residues: 49 loop : -0.04 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.001 0.001 HIS A 6 PHE 0.007 0.001 PHE A 33 TYR 0.011 0.001 TYR A 14 ARG 0.002 0.000 ARG B 457 *********************** 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 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: 2 residues processed: 42 average time/residue: 0.1503 time to fit residues: 7.4412 Evaluate side-chains 40 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.237 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0217 time to fit residues: 0.3686 ------------------------------------------------------------------------------- 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: 0.4980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.0000 chunk 4 optimal weight: 0.0870 chunk 15 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.0020 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 overall best weight: 0.0528 ------------------------------------------------------------------------------- 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: 0.7716 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2082 Z= 0.118 Angle : 0.603 10.420 2830 Z= 0.289 Chirality : 0.041 0.126 318 Planarity : 0.003 0.042 363 Dihedral : 5.858 55.710 327 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.50 % Allowed : 15.92 % 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: 0.36 (0.54), residues: 254 helix: 0.96 (0.57), residues: 88 sheet: -0.28 (0.79), residues: 49 loop : 0.07 (0.59), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.003 0.001 HIS A 6 PHE 0.012 0.001 PHE B 464 TYR 0.009 0.001 TYR A 14 ARG 0.002 0.000 ARG A 45 *********************** 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 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.231 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1307 time to fit residues: 6.0261 Evaluate side-chains 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.244 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0234 time to fit residues: 0.3706 ------------------------------------------------------------------------------- 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: 0.6980 chunk 22 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 9 optimal weight: 0.0670 chunk 17 optimal weight: 0.0970 chunk 6 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 0.0980 overall best weight: 0.0658 ------------------------------------------------------------------------------- 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: 0.7704 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2082 Z= 0.129 Angle : 0.563 7.475 2830 Z= 0.282 Chirality : 0.041 0.127 318 Planarity : 0.003 0.041 363 Dihedral : 5.808 55.635 327 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.50 % Allowed : 15.42 % Favored : 84.08 % 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: 0.46 (0.55), residues: 254 helix: 0.99 (0.58), residues: 88 sheet: -0.08 (0.80), residues: 49 loop : 0.11 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 6 PHE 0.009 0.001 PHE B 464 TYR 0.009 0.001 TYR A 14 ARG 0.002 0.000 ARG A 45 *********************** 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 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.243 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1374 time to fit residues: 6.0350 Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3312 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 0.0050 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 15 optimal weight: 0.3980 chunk 12 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 overall best weight: 0.1994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 2082 Z= 0.191 Angle : 0.618 11.183 2830 Z= 0.300 Chirality : 0.042 0.132 318 Planarity : 0.003 0.042 363 Dihedral : 5.807 54.071 327 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.50 % Allowed : 15.92 % 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: 0.37 (0.54), residues: 254 helix: 0.96 (0.58), residues: 88 sheet: -0.16 (0.81), residues: 49 loop : 0.01 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS A 6 PHE 0.010 0.001 PHE B 486 TYR 0.010 0.001 TYR A 14 ARG 0.001 0.000 ARG A 45 *********************** 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: 1 poor density : 37 time to evaluate : 0.242 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1577 time to fit residues: 7.0176 Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.234 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3161 ------------------------------------------------------------------------------- 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: 0.0570 chunk 3 optimal weight: 0.0980 chunk 17 optimal weight: 0.0030 chunk 1 optimal weight: 0.3980 chunk 14 optimal weight: 0.0670 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 chunk 0 optimal weight: 0.0970 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 overall best weight: 0.0642 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4407 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= 0.127 Angle : 0.616 11.209 2830 Z= 0.291 Chirality : 0.041 0.132 318 Planarity : 0.003 0.041 363 Dihedral : 5.712 54.030 327 Min Nonbonded Distance : 2.199 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: 0.40 (0.54), residues: 254 helix: 1.04 (0.58), residues: 88 sheet: 0.09 (0.85), residues: 47 loop : -0.13 (0.57), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.000 0.000 HIS A 6 PHE 0.012 0.001 PHE B 486 TYR 0.009 0.001 TYR A 14 ARG 0.005 0.000 ARG B 357 ********************** 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 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1371 time to fit residues: 5.6263 Evaluate side-chains 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2625 ------------------------------------------------------------------------------- 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: 0.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 0.0870 chunk 6 optimal weight: 0.0670 overall best weight: 0.1696 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.127829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112061 restraints weight = 2965.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114759 restraints weight = 1685.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.116575 restraints weight = 1161.283| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2082 Z= 0.174 Angle : 0.614 11.070 2830 Z= 0.293 Chirality : 0.041 0.132 318 Planarity : 0.004 0.042 363 Dihedral : 5.671 52.853 327 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 0.43 (0.54), residues: 254 helix: 1.09 (0.58), residues: 88 sheet: -0.03 (0.82), residues: 49 loop : -0.07 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS A 6 PHE 0.012 0.001 PHE B 486 TYR 0.010 0.001 TYR A 14 ARG 0.004 0.000 ARG B 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1231.91 seconds wall clock time: 28 minutes 5.71 seconds (1685.71 seconds total)