Starting phenix.real_space_refine on Sun Mar 10 14:20:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/03_2024/7jzu_22574.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/03_2024/7jzu_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_22574/03_2024/7jzu_22574.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/03_2024/7jzu_22574.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/03_2024/7jzu_22574.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzu_22574/03_2024/7jzu_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-dev-5265/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: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.78, per 1000 atoms: 0.90 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: 0.96 Conformation dependent library (CDL) restraints added in 379.8 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: 0.25 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: 0.49 Time building geometry restraints manager: 0.99 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: 1169 13.82 - 27.64: 52 27.64 - 41.46: 17 41.46 - 55.27: 4 55.27 - 69.09: 2 Dihedral angle restraints: 1244 sinusoidal: 519 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 1241 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: 2.590 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: 12.350 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.370 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- 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 : 9.379 69.093 770 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 : 0.226 Fit side-chains REVERT: B 361 CYS cc_start: 0.6296 (p) cc_final: 0.5724 (p) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1728 time to fit residues: 9.6488 Evaluate side-chains 32 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 0.3980 chunk 11 optimal weight: 0.0970 chunk 14 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 overall best weight: 0.2178 ------------------------------------------------------------------------------- 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: 0.7384 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2034 Z= 0.254 Angle : 0.580 6.421 2760 Z= 0.302 Chirality : 0.044 0.156 304 Planarity : 0.004 0.037 355 Dihedral : 4.291 15.074 334 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.15 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: 0.43 (0.54), residues: 244 helix: -0.00 (0.59), residues: 79 sheet: 0.61 (0.77), residues: 48 loop : 0.57 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.005 0.003 HIS A 21 PHE 0.012 0.002 PHE B 497 TYR 0.025 0.002 TYR B 495 ARG 0.003 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 44 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.230 Fit side-chains REVERT: A 13 MET cc_start: 0.8451 (ptm) cc_final: 0.8048 (ptt) REVERT: A 29 SER cc_start: 0.8115 (t) cc_final: 0.7775 (p) REVERT: B 361 CYS cc_start: 0.6275 (p) cc_final: 0.5637 (p) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.1218 time to fit residues: 6.3594 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 0.0470 chunk 23 optimal weight: 0.3980 chunk 20 optimal weight: 0.3980 overall best weight: 0.1856 ------------------------------------------------------------------------------- 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: 0.7411 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2034 Z= 0.216 Angle : 0.526 5.249 2760 Z= 0.272 Chirality : 0.043 0.136 304 Planarity : 0.004 0.049 355 Dihedral : 4.105 16.581 334 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.47 % Allowed : 6.37 % 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: 0.54 (0.55), residues: 244 helix: 0.32 (0.62), residues: 81 sheet: 0.55 (0.77), residues: 48 loop : 0.51 (0.59), residues: 115 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 0.007 0.001 PHE B 456 TYR 0.021 0.002 TYR B 495 ARG 0.003 0.000 ARG B 403 *********************** 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 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.227 Fit side-chains REVERT: A 29 SER cc_start: 0.8121 (t) cc_final: 0.7724 (p) REVERT: B 361 CYS cc_start: 0.6382 (p) cc_final: 0.5752 (p) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 0.1632 time to fit residues: 7.3720 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 0.0470 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.0010 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.0000 chunk 9 optimal weight: 0.0370 chunk 16 optimal weight: 0.0770 chunk 11 optimal weight: 0.4980 chunk 20 optimal weight: 0.0980 chunk 5 optimal weight: 0.0870 chunk 7 optimal weight: 0.4980 overall best weight: 0.0324 ------------------------------------------------------------------------------- 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: 0.7328 moved from start: 0.3088 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= 0.116 Angle : 0.442 3.477 2760 Z= 0.232 Chirality : 0.042 0.125 304 Planarity : 0.004 0.047 355 Dihedral : 3.854 20.468 334 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 9.31 % 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: 1.07 (0.55), residues: 244 helix: 1.36 (0.67), residues: 67 sheet: 0.38 (0.75), residues: 48 loop : 0.66 (0.57), residues: 129 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 0.004 0.001 PHE B 400 TYR 0.012 0.001 TYR B 495 ARG 0.003 0.000 ARG B 408 *********************** 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: 2 poor density : 41 time to evaluate : 0.147 Fit side-chains REVERT: A 29 SER cc_start: 0.8121 (t) cc_final: 0.7767 (p) REVERT: B 361 CYS cc_start: 0.6219 (p) cc_final: 0.5572 (p) REVERT: B 506 GLN cc_start: 0.8572 (mt0) cc_final: 0.8302 (mt0) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.0936 time to fit residues: 4.6606 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 5 optimal weight: 0.0670 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.0770 chunk 10 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 0.0770 overall best weight: 0.2234 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2034 Z= 0.239 Angle : 0.517 7.031 2760 Z= 0.264 Chirality : 0.044 0.129 304 Planarity : 0.004 0.048 355 Dihedral : 4.054 17.562 334 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 7.84 % Favored : 90.20 % 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: 0.90 (0.55), residues: 244 helix: 1.13 (0.64), residues: 73 sheet: 0.28 (0.76), residues: 48 loop : 0.58 (0.58), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 436 HIS 0.001 0.001 HIS A 21 PHE 0.009 0.001 PHE B 456 TYR 0.022 0.001 TYR B 495 ARG 0.003 0.001 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 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.237 Fit side-chains REVERT: A 29 SER cc_start: 0.8212 (t) cc_final: 0.7848 (p) REVERT: B 361 CYS cc_start: 0.6361 (p) cc_final: 0.5728 (p) outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.1305 time to fit residues: 5.7226 Evaluate side-chains 38 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 10 optimal weight: 0.0870 chunk 9 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.1754 ------------------------------------------------------------------------------- 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: 0.7426 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2034 Z= 0.189 Angle : 0.488 7.210 2760 Z= 0.247 Chirality : 0.043 0.125 304 Planarity : 0.004 0.048 355 Dihedral : 4.153 21.325 334 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.96 % Allowed : 9.31 % Favored : 88.73 % 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: 0.90 (0.55), residues: 244 helix: 1.20 (0.65), residues: 73 sheet: 0.60 (0.88), residues: 38 loop : 0.38 (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 0.002 0.000 ARG B 457 *********************** 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 : 0.256 Fit side-chains REVERT: A 29 SER cc_start: 0.8182 (t) cc_final: 0.7839 (p) REVERT: B 361 CYS cc_start: 0.6346 (p) cc_final: 0.5722 (p) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.1150 time to fit residues: 5.3958 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 2 optimal weight: 0.0770 chunk 18 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 9 optimal weight: 0.0770 overall best weight: 0.1496 ------------------------------------------------------------------------------- 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: 0.7426 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2034 Z= 0.173 Angle : 0.477 7.956 2760 Z= 0.241 Chirality : 0.042 0.122 304 Planarity : 0.004 0.049 355 Dihedral : 4.134 23.606 334 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.96 % Allowed : 9.31 % Favored : 88.73 % 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: 0.92 (0.55), residues: 244 helix: 1.30 (0.65), residues: 73 sheet: 0.58 (0.88), residues: 38 loop : 0.35 (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 0.004 0.001 PHE B 456 TYR 0.016 0.001 TYR B 495 ARG 0.002 0.000 ARG B 457 *********************** 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: 4 poor density : 36 time to evaluate : 0.214 Fit side-chains REVERT: A 29 SER cc_start: 0.8164 (t) cc_final: 0.7819 (p) REVERT: B 361 CYS cc_start: 0.6367 (p) cc_final: 0.5743 (p) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.1125 time to fit residues: 5.1606 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 20 optimal weight: 0.0070 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.2198 ------------------------------------------------------------------------------- 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: 0.7474 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2034 Z= 0.229 Angle : 0.525 8.325 2760 Z= 0.263 Chirality : 0.044 0.130 304 Planarity : 0.004 0.048 355 Dihedral : 4.429 22.834 334 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.96 % Allowed : 9.80 % 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: 0.83 (0.55), residues: 244 helix: 1.36 (0.66), residues: 73 sheet: 0.57 (0.87), residues: 38 loop : 0.19 (0.55), residues: 133 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 0.010 0.001 PHE B 456 TYR 0.018 0.002 TYR B 495 ARG 0.002 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 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.232 Fit side-chains REVERT: A 29 SER cc_start: 0.8206 (t) cc_final: 0.7856 (p) REVERT: B 361 CYS cc_start: 0.6257 (p) cc_final: 0.5631 (p) outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.1100 time to fit residues: 5.2256 Evaluate side-chains 40 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 514 SER 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: 0.8980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 0.0980 chunk 5 optimal weight: 0.0870 chunk 17 optimal weight: 0.1980 chunk 2 optimal weight: 0.0970 chunk 7 optimal weight: 0.2980 overall best weight: 0.0914 ------------------------------------------------------------------------------- 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: 0.7412 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2034 Z= 0.129 Angle : 0.465 8.495 2760 Z= 0.232 Chirality : 0.042 0.122 304 Planarity : 0.004 0.050 355 Dihedral : 4.265 27.562 334 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.98 % Allowed : 10.78 % 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: 0.82 (0.55), residues: 244 helix: 1.38 (0.66), residues: 73 sheet: 0.38 (0.86), residues: 38 loop : 0.23 (0.53), 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 0.004 0.001 PHE B 456 TYR 0.011 0.001 TYR B 505 ARG 0.001 0.000 ARG B 457 *********************** 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 41 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.210 Fit side-chains REVERT: A 29 SER cc_start: 0.8138 (t) cc_final: 0.7797 (p) REVERT: B 361 CYS cc_start: 0.6283 (p) cc_final: 0.5663 (p) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.1291 time to fit residues: 6.0005 Evaluate side-chains 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.0020 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 13 optimal weight: 0.0000 chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 0.1980 chunk 0 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 overall best weight: 0.0750 ------------------------------------------------------------------------------- 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: 0.7388 moved from start: 0.3811 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= 0.122 Angle : 0.451 8.353 2760 Z= 0.225 Chirality : 0.042 0.121 304 Planarity : 0.004 0.049 355 Dihedral : 4.158 28.293 334 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.49 % Allowed : 11.27 % 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: 0.87 (0.54), residues: 244 helix: 1.35 (0.66), residues: 73 sheet: 0.44 (0.85), residues: 38 loop : 0.29 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 21 PHE 0.005 0.001 PHE B 497 TYR 0.012 0.001 TYR B 495 ARG 0.002 0.000 ARG B 403 ********************** 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 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.231 Fit side-chains REVERT: A 29 SER cc_start: 0.8044 (t) cc_final: 0.7735 (p) REVERT: A 38 LYS cc_start: 0.5860 (mmmt) cc_final: 0.4732 (tptp) REVERT: B 361 CYS cc_start: 0.6216 (p) cc_final: 0.5569 (p) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.1338 time to fit residues: 6.0930 Evaluate side-chains 39 residues out of total 216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.0010 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.0570 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 chunk 19 optimal weight: 0.1980 chunk 22 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 overall best weight: 0.1042 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.159117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147329 restraints weight = 2317.862| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 0.99 r_work: 0.3584 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2034 Z= 0.137 Angle : 0.451 7.852 2760 Z= 0.228 Chirality : 0.042 0.120 304 Planarity : 0.004 0.051 355 Dihedral : 4.121 27.489 334 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.98 % Allowed : 9.80 % 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: 0.87 (0.55), residues: 244 helix: 1.40 (0.66), residues: 73 sheet: 0.49 (0.85), residues: 38 loop : 0.24 (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 0.005 0.001 PHE B 456 TYR 0.014 0.001 TYR B 505 ARG 0.003 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1324.23 seconds wall clock time: 24 minutes 22.30 seconds (1462.30 seconds total)