Starting phenix.real_space_refine on Thu Dec 7 15:49:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/12_2023/7jzu_22574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/12_2023/7jzu_22574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/12_2023/7jzu_22574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/12_2023/7jzu_22574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/12_2023/7jzu_22574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/12_2023/7jzu_22574.pdb" } resolution = 3.1 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= 0.031 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 11 5.16 5 C 1270 2.51 5 N 325 2.21 5 O 381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B TYR 421": "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 ASP 467": "OD1" <-> "OD2" 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" 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: 1987 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1512 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 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: 1.65, per 1000 atoms: 0.83 Number of scatterers: 1987 At special positions: 0 Unit cell: (59.85, 71.4, 66.15, 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 11 16.00 O 381 8.00 N 325 7.00 C 1270 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=2.09 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.16 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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: 0.93 Conformation dependent library (CDL) restraints added in 383.5 milliseconds 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 462 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 36.7% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.566A pdb=" N LEU A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.781A pdb=" N LEU A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 removed outlier: 4.251A pdb=" N GLU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.716A 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 390 removed outlier: 4.979A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.459A 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: 3.944A 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: 6.591A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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 80 hydrogen bonds defined for protein. 204 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: 0.47 Time building geometry restraints manager: 0.97 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: 571 1.33 - 1.46: 603 1.46 - 1.59: 846 1.59 - 1.73: 0 1.73 - 1.86: 14 Bond restraints: 2034 Sorted by residual: bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" CB ASN B 487 " pdb=" CG ASN B 487 " ideal model delta sigma weight residual 1.516 1.442 0.074 2.50e-02 1.60e+03 8.85e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.03e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.469 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.476 -0.053 2.00e-02 2.50e+03 7.13e+00 ... (remaining 2029 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.09: 64 107.09 - 113.85: 1042 113.85 - 120.61: 950 120.61 - 127.37: 694 127.37 - 134.13: 10 Bond angle restraints: 2760 Sorted by residual: angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.56 126.07 -6.51 1.02e+00 9.61e-01 4.08e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.95 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C LEU B 425 " pdb=" N PRO B 426 " pdb=" CA PRO B 426 " ideal model delta sigma weight residual 120.03 126.20 -6.17 9.90e-01 1.02e+00 3.89e+01 angle pdb=" C THR B 478 " pdb=" N PRO B 479 " pdb=" CA PRO B 479 " ideal model delta sigma weight residual 119.78 126.05 -6.27 1.03e+00 9.43e-01 3.71e+01 angle pdb=" C ALA B 411 " pdb=" N PRO B 412 " pdb=" CA PRO B 412 " ideal model delta sigma weight residual 119.76 125.81 -6.05 1.03e+00 9.43e-01 3.45e+01 ... (remaining 2755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.82: 1152 13.82 - 27.64: 52 27.64 - 41.46: 17 41.46 - 55.27: 4 55.27 - 69.09: 2 Dihedral angle restraints: 1227 sinusoidal: 502 harmonic: 725 Sorted by residual: dihedral pdb=" C TYR B 495 " pdb=" N TYR B 495 " pdb=" CA TYR B 495 " pdb=" CB TYR B 495 " ideal model delta harmonic sigma weight residual -122.60 -114.96 -7.64 0 2.50e+00 1.60e-01 9.34e+00 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 93.00 116.81 -23.81 1 1.00e+01 1.00e-02 8.17e+00 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 69.09 -69.09 1 3.00e+01 1.11e-03 6.86e+00 ... (remaining 1224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 199 0.074 - 0.149: 81 0.149 - 0.223: 18 0.223 - 0.298: 4 0.298 - 0.372: 2 Chirality restraints: 304 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 -2.58 0.18 2.00e-02 2.50e+03 7.72e+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 -2.47 0.07 2.00e-02 2.50e+03 1.21e+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 -2.86 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 301 not shown) Planarity restraints: 356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.043 2.00e-02 2.50e+03 2.19e-02 9.57e+00 pdb=" CG TYR B 495 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.018 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 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 449 " 0.025 2.00e-02 2.50e+03 1.47e-02 4.34e+00 pdb=" CG TYR B 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 449 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR B 449 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 449 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 449 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 505 " -0.026 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 505 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 505 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 505 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 505 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 505 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 505 " -0.023 2.00e-02 2.50e+03 ... (remaining 353 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1044 2.99 - 3.47: 1816 3.47 - 3.94: 3369 3.94 - 4.42: 3931 4.42 - 4.90: 6085 Nonbonded interactions: 16245 Sorted by model distance: nonbonded pdb=" N ALA B 520 " pdb=" O ALA B 520 " model vdw 2.509 2.496 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.573 2.520 nonbonded pdb=" N ASN B 440 " pdb=" OD1 ASN B 440 " model vdw 2.586 2.520 nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.597 2.496 nonbonded pdb=" N GLN B 506 " pdb=" O GLN B 506 " model vdw 2.617 2.496 ... (remaining 16240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.960 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.800 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 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 0.074 2034 Z= 0.953 Angle : 1.344 7.124 2760 Z= 0.904 Chirality : 0.085 0.372 304 Planarity : 0.005 0.022 355 Dihedral : 9.478 69.093 753 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 (0.52), residues: 244 helix: -1.00 (0.53), residues: 78 sheet: 0.98 (0.75), residues: 49 loop : 0.87 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP B 353 HIS 0.002 0.001 HIS A 21 PHE 0.014 0.003 PHE B 497 TYR 0.043 0.006 TYR B 495 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1702 time to fit residues: 9.5228 Evaluate side-chains 31 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.221 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.0970 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.2578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN B 487 ASN B 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2034 Z= 0.286 Angle : 0.610 7.261 2760 Z= 0.313 Chirality : 0.045 0.158 304 Planarity : 0.005 0.042 355 Dihedral : 4.544 16.741 317 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 5.39 % Favored : 93.63 % 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 (0.54), residues: 244 helix: -0.04 (0.61), residues: 75 sheet: 0.55 (0.77), residues: 48 loop : 0.64 (0.56), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.003 HIS A 21 PHE 0.014 0.002 PHE B 497 TYR 0.024 0.002 TYR B 505 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.210 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.1129 time to fit residues: 5.6221 Evaluate side-chains 37 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0257 time to fit residues: 0.3506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.0670 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 0.0870 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 20 optimal weight: 0.0870 overall best weight: 0.0872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2034 Z= 0.145 Angle : 0.470 3.540 2760 Z= 0.250 Chirality : 0.042 0.128 304 Planarity : 0.004 0.046 355 Dihedral : 4.099 18.221 317 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 6.37 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.55), residues: 244 helix: 0.80 (0.64), residues: 73 sheet: 0.43 (0.75), residues: 48 loop : 0.65 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.003 0.002 HIS A 21 PHE 0.005 0.001 PHE B 497 TYR 0.017 0.001 TYR B 495 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.213 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 44 average time/residue: 0.1371 time to fit residues: 7.1472 Evaluate side-chains 43 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.228 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0237 time to fit residues: 0.4106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.3980 chunk 19 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.0670 chunk 16 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 20 optimal weight: 0.0970 chunk 5 optimal weight: 0.0270 chunk 7 optimal weight: 0.5980 overall best weight: 0.1574 ------------------------------------------------------------------------------- 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: 0.7399 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2034 Z= 0.188 Angle : 0.480 3.720 2760 Z= 0.252 Chirality : 0.043 0.130 304 Planarity : 0.004 0.045 355 Dihedral : 4.140 18.064 317 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.47 % Allowed : 6.86 % Favored : 91.67 % 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: 0.76 (0.55), residues: 244 helix: 1.03 (0.64), residues: 73 sheet: 0.13 (0.74), residues: 50 loop : 0.52 (0.58), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 PHE 0.008 0.001 PHE B 456 TYR 0.019 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.223 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 40 average time/residue: 0.1414 time to fit residues: 6.6764 Evaluate side-chains 42 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.222 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0237 time to fit residues: 0.4292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 10 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2034 Z= 0.231 Angle : 0.512 6.130 2760 Z= 0.261 Chirality : 0.043 0.125 304 Planarity : 0.004 0.049 355 Dihedral : 4.376 19.516 317 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.49 % Allowed : 7.35 % Favored : 92.16 % 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: 0.81 (0.56), residues: 244 helix: 1.23 (0.65), residues: 73 sheet: 0.30 (0.76), residues: 48 loop : 0.35 (0.59), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 PHE 0.007 0.001 PHE B 456 TYR 0.019 0.001 TYR B 495 ARG 0.003 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.228 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 41 average time/residue: 0.1576 time to fit residues: 7.5247 Evaluate side-chains 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0226 time to fit residues: 0.3241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0670 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.2118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2034 Z= 0.223 Angle : 0.513 6.922 2760 Z= 0.259 Chirality : 0.044 0.129 304 Planarity : 0.004 0.047 355 Dihedral : 4.540 22.075 317 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.96 % Allowed : 8.82 % Favored : 89.22 % 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: 0.77 (0.55), residues: 244 helix: 1.26 (0.65), residues: 73 sheet: 0.71 (0.88), residues: 38 loop : 0.12 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.006 0.001 PHE B 456 TYR 0.017 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.160 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.0841 time to fit residues: 3.9408 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.160 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0177 time to fit residues: 0.3417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.1980 chunk 14 optimal weight: 0.0970 chunk 15 optimal weight: 0.0970 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 21 optimal weight: 0.0980 chunk 22 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 9 optimal weight: 0.2980 overall best weight: 0.0954 ------------------------------------------------------------------------------- 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: 0.7405 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2034 Z= 0.135 Angle : 0.468 7.968 2760 Z= 0.235 Chirality : 0.042 0.124 304 Planarity : 0.004 0.050 355 Dihedral : 4.381 25.928 317 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.49 % Allowed : 8.82 % Favored : 90.69 % 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: 0.74 (0.55), residues: 244 helix: 1.28 (0.65), residues: 73 sheet: 0.43 (0.87), residues: 38 loop : 0.17 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.003 0.001 PHE B 374 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.273 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.1358 time to fit residues: 6.4359 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.207 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0234 time to fit residues: 0.3297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.4980 chunk 6 optimal weight: 0.0670 chunk 19 optimal weight: 0.0060 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 overall best weight: 0.1134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2034 Z= 0.149 Angle : 0.476 8.263 2760 Z= 0.238 Chirality : 0.042 0.123 304 Planarity : 0.004 0.048 355 Dihedral : 4.368 25.777 317 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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: 0.72 (0.55), residues: 244 helix: 1.38 (0.66), residues: 73 sheet: 0.40 (0.87), residues: 38 loop : 0.08 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 PHE 0.006 0.001 PHE B 456 TYR 0.014 0.001 TYR B 495 ARG 0.001 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1243 time to fit residues: 6.0086 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.0770 chunk 19 optimal weight: 0.1980 chunk 1 optimal weight: 0.1980 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 0.0170 chunk 20 optimal weight: 0.3980 chunk 5 optimal weight: 0.0470 chunk 17 optimal weight: 0.0370 chunk 2 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 overall best weight: 0.0530 ------------------------------------------------------------------------------- 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: 0.7370 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2034 Z= 0.114 Angle : 0.467 8.047 2760 Z= 0.234 Chirality : 0.041 0.121 304 Planarity : 0.004 0.050 355 Dihedral : 4.298 27.781 317 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % 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: 0.69 (0.55), residues: 244 helix: 1.31 (0.66), residues: 73 sheet: 0.33 (0.86), residues: 38 loop : 0.11 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 PHE 0.003 0.001 PHE B 400 TYR 0.011 0.001 TYR B 505 ARG 0.001 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.223 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1280 time to fit residues: 6.4655 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 0.0980 chunk 15 optimal weight: 0.0270 chunk 14 optimal weight: 0.0000 overall best weight: 0.0640 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2034 Z= 0.124 Angle : 0.471 8.098 2760 Z= 0.238 Chirality : 0.042 0.121 304 Planarity : 0.004 0.050 355 Dihedral : 4.242 27.315 317 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % 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: 0.66 (0.55), residues: 244 helix: 1.34 (0.66), residues: 73 sheet: 0.31 (0.85), residues: 38 loop : 0.05 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 PHE 0.003 0.001 PHE B 456 TYR 0.011 0.001 TYR B 495 ARG 0.002 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 488 Ramachandran restraints generated. 244 Oldfield, 0 Emsley, 244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1224 time to fit residues: 5.6800 Evaluate side-chains 37 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 19 optimal weight: 0.0870 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 0.1980 overall best weight: 0.1334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.159328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.148264 restraints weight = 2273.042| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 0.94 r_work: 0.3595 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2034 Z= 0.166 Angle : 0.486 8.258 2760 Z= 0.245 Chirality : 0.042 0.120 304 Planarity : 0.004 0.050 355 Dihedral : 4.283 25.187 317 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.98 % Allowed : 11.76 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.55), residues: 244 helix: 1.34 (0.66), residues: 73 sheet: 0.33 (0.84), residues: 38 loop : -0.02 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.000 0.000 HIS A 21 PHE 0.006 0.001 PHE B 456 TYR 0.015 0.001 TYR B 495 ARG 0.001 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1261.51 seconds wall clock time: 27 minutes 42.29 seconds (1662.29 seconds total)