Starting phenix.real_space_refine on Mon Sep 23 12:05:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/09_2024/7jzm_22533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/09_2024/7jzm_22533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/09_2024/7jzm_22533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/09_2024/7jzm_22533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/09_2024/7jzm_22533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/09_2024/7jzm_22533.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1310 2.51 5 N 340 2.21 5 O 373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2033 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 495 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1500 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.14, per 1000 atoms: 1.54 Number of scatterers: 2033 At special positions: 0 Unit cell: (66.15, 68.25, 69.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 373 8.00 N 340 7.00 C 1310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.28 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.68 Conformation dependent library (CDL) restraints added in 241.7 milliseconds 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 38.4% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 1 through 17 Processing helix chain 'A' and resid 22 through 42 Processing helix chain 'A' and resid 44 through 64 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.514A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.158A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.670A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.479A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 93 hydrogen bonds defined for protein. 240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 591 1.33 - 1.46: 586 1.46 - 1.59: 893 1.59 - 1.72: 0 1.72 - 1.85: 12 Bond restraints: 2082 Sorted by residual: bond pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 1.473 1.337 0.136 1.40e-02 5.10e+03 9.45e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CG GLN B 506 " pdb=" CD GLN B 506 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.74e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C5 FUC C 3 " pdb=" O5 FUC C 3 " ideal model delta sigma weight residual 1.423 1.477 -0.054 2.00e-02 2.50e+03 7.29e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 2649 2.56 - 5.12: 157 5.12 - 7.69: 20 7.69 - 10.25: 3 10.25 - 12.81: 1 Bond angle restraints: 2830 Sorted by residual: angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" CB PRO B 499 " ideal model delta sigma weight residual 103.41 96.76 6.65 9.40e-01 1.13e+00 5.01e+01 angle pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 112.00 120.93 -8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.01 -6.45 1.02e+00 9.61e-01 4.00e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.31 -6.44 1.04e+00 9.25e-01 3.84e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.65 -6.09 1.01e+00 9.80e-01 3.64e+01 ... (remaining 2825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1208 14.30 - 28.59: 48 28.59 - 42.89: 8 42.89 - 57.18: 5 57.18 - 71.48: 3 Dihedral angle restraints: 1272 sinusoidal: 513 harmonic: 759 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 51.36 41.64 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CB GLU B 484 " pdb=" CG GLU B 484 " pdb=" CD GLU B 484 " pdb=" OE1 GLU B 484 " ideal model delta sinusoidal sigma weight residual 0.00 71.48 -71.48 1 3.00e+01 1.11e-03 7.28e+00 dihedral pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta harmonic sigma weight residual 180.00 166.92 13.08 0 5.00e+00 4.00e-02 6.85e+00 ... (remaining 1269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 230 0.082 - 0.164: 69 0.164 - 0.245: 15 0.245 - 0.327: 3 0.327 - 0.409: 1 Chirality restraints: 318 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.38e+01 chirality pdb=" C1 FUC C 3 " pdb=" O6 NAG C 1 " pdb=" C2 FUC C 3 " pdb=" O5 FUC C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.68e+01 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.90 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 315 not shown) Planarity restraints: 364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR B 495 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " 0.025 2.00e-02 2.50e+03 1.34e-02 3.57e+00 pdb=" CG TYR B 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.016 2.00e-02 2.50e+03 1.65e-02 3.40e+00 pdb=" CG ASN B 343 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 361 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 880 2.92 - 3.41: 1816 3.41 - 3.91: 3445 3.91 - 4.40: 3881 4.40 - 4.90: 6261 Nonbonded interactions: 16283 Sorted by model distance: nonbonded pdb=" O ASP A 2 " pdb=" OD1 ASP A 2 " model vdw 2.420 3.040 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.566 3.120 nonbonded pdb=" O ASN B 501 " pdb=" NE2 GLN B 506 " model vdw 2.568 3.120 nonbonded pdb=" O5 NAG C 1 " pdb=" O6 NAG C 1 " model vdw 2.569 2.432 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.574 2.560 ... (remaining 16278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.350 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.010 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.136 2082 Z= 0.952 Angle : 1.378 12.810 2830 Z= 0.921 Chirality : 0.084 0.409 318 Planarity : 0.005 0.026 363 Dihedral : 9.533 71.478 774 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.52), residues: 254 helix: 0.21 (0.51), residues: 85 sheet: 0.78 (0.76), residues: 52 loop : 0.82 (0.60), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.005 TRP B 353 HIS 0.002 0.001 HIS A 6 PHE 0.013 0.002 PHE B 342 TYR 0.036 0.006 TYR B 495 ARG 0.003 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.229 Fit side-chains REVERT: B 469 SER cc_start: 0.8421 (t) cc_final: 0.7854 (p) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1686 time to fit residues: 12.4728 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.0030 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 overall best weight: 0.1988 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2082 Z= 0.209 Angle : 0.624 7.574 2830 Z= 0.328 Chirality : 0.043 0.144 318 Planarity : 0.004 0.038 363 Dihedral : 6.145 57.866 344 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.49 % Allowed : 9.45 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.53), residues: 254 helix: 0.98 (0.58), residues: 88 sheet: 0.45 (0.77), residues: 49 loop : 0.51 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.001 0.001 HIS A 6 PHE 0.015 0.002 PHE A 33 TYR 0.018 0.002 TYR B 495 ARG 0.003 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8107 (mm) cc_final: 0.7724 (mt) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 0.1558 time to fit residues: 7.4629 Evaluate side-chains 41 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.0040 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.0970 chunk 17 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.0040 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2082 Z= 0.200 Angle : 0.558 5.877 2830 Z= 0.290 Chirality : 0.042 0.137 318 Planarity : 0.004 0.039 363 Dihedral : 6.055 58.830 344 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.49 % Allowed : 8.46 % Favored : 89.05 % 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 (0.53), residues: 254 helix: 1.12 (0.57), residues: 89 sheet: -0.00 (0.75), residues: 49 loop : 0.35 (0.58), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.001 0.000 HIS A 18 PHE 0.007 0.001 PHE A 19 TYR 0.015 0.001 TYR B 495 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 25 ILE cc_start: 0.8234 (mm) cc_final: 0.7890 (mt) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.1523 time to fit residues: 7.7892 Evaluate side-chains 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.0060 chunk 6 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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: 0.7760 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2082 Z= 0.279 Angle : 0.593 6.404 2830 Z= 0.311 Chirality : 0.044 0.139 318 Planarity : 0.004 0.041 363 Dihedral : 6.180 59.185 344 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.99 % Allowed : 10.95 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.52), residues: 254 helix: 0.96 (0.56), residues: 89 sheet: -0.30 (0.74), residues: 49 loop : 0.26 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.003 0.001 HIS A 6 PHE 0.011 0.001 PHE B 429 TYR 0.014 0.002 TYR B 495 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.226 Fit side-chains REVERT: A 25 ILE cc_start: 0.8371 (mm) cc_final: 0.8019 (mt) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1483 time to fit residues: 8.1174 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 8 optimal weight: 0.0770 chunk 4 optimal weight: 0.0870 chunk 14 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS B 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2082 Z= 0.175 Angle : 0.565 6.532 2830 Z= 0.288 Chirality : 0.042 0.131 318 Planarity : 0.004 0.042 363 Dihedral : 5.961 58.153 344 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 14.43 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.53), residues: 254 helix: 0.97 (0.57), residues: 89 sheet: -0.40 (0.74), residues: 49 loop : 0.26 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.002 0.001 HIS A 18 PHE 0.009 0.001 PHE A 33 TYR 0.011 0.001 TYR B 495 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.303 Fit side-chains REVERT: A 25 ILE cc_start: 0.8404 (mm) cc_final: 0.8062 (mt) REVERT: B 489 TYR cc_start: 0.7531 (m-80) cc_final: 0.7302 (m-80) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.1274 time to fit residues: 6.1316 Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.0980 chunk 8 optimal weight: 0.3980 chunk 12 optimal weight: 0.1980 chunk 23 optimal weight: 0.0980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.2980 chunk 11 optimal weight: 0.0060 overall best weight: 0.0974 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2082 Z= 0.137 Angle : 0.593 9.420 2830 Z= 0.291 Chirality : 0.042 0.130 318 Planarity : 0.004 0.043 363 Dihedral : 5.840 58.001 344 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 16.42 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.53), residues: 254 helix: 1.12 (0.57), residues: 88 sheet: -0.34 (0.75), residues: 49 loop : 0.28 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 6 PHE 0.011 0.001 PHE A 33 TYR 0.010 0.001 TYR A 14 ARG 0.004 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.231 Fit side-chains REVERT: A 25 ILE cc_start: 0.8347 (mm) cc_final: 0.7996 (mt) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1393 time to fit residues: 6.3810 Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 4 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 16 optimal weight: 0.0170 chunk 11 optimal weight: 0.3980 chunk 2 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 23 optimal weight: 0.0970 overall best weight: 0.1172 ------------------------------------------------------------------------------- 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: 0.7712 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2082 Z= 0.142 Angle : 0.564 7.340 2830 Z= 0.283 Chirality : 0.042 0.131 318 Planarity : 0.004 0.043 363 Dihedral : 5.820 57.196 344 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 15.42 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.54), residues: 254 helix: 1.11 (0.58), residues: 88 sheet: -0.24 (0.77), residues: 49 loop : 0.24 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 6 PHE 0.009 0.001 PHE A 33 TYR 0.009 0.001 TYR A 14 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.230 Fit side-chains REVERT: A 9 MET cc_start: 0.7745 (tmm) cc_final: 0.7427 (ttp) REVERT: A 25 ILE cc_start: 0.8383 (mm) cc_final: 0.8043 (mt) REVERT: A 34 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7639 (mm-30) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.1321 time to fit residues: 5.5734 Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.0870 chunk 22 optimal weight: 0.0870 chunk 23 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 overall best weight: 0.0934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2082 Z= 0.138 Angle : 0.604 11.163 2830 Z= 0.288 Chirality : 0.041 0.130 318 Planarity : 0.003 0.043 363 Dihedral : 5.785 56.696 344 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.99 % Allowed : 14.93 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.54), residues: 254 helix: 1.09 (0.58), residues: 88 sheet: -0.14 (0.79), residues: 49 loop : 0.26 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 6 PHE 0.010 0.001 PHE B 464 TYR 0.009 0.001 TYR A 14 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.227 Fit side-chains REVERT: A 9 MET cc_start: 0.7713 (tmm) cc_final: 0.7374 (ttp) REVERT: A 25 ILE cc_start: 0.8384 (mm) cc_final: 0.8042 (mt) outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 0.1294 time to fit residues: 5.7753 Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 2 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.0970 chunk 6 optimal weight: 0.0670 chunk 18 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 8 optimal weight: 0.0670 overall best weight: 0.1054 ------------------------------------------------------------------------------- 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: 0.7693 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 2082 Z= 0.143 Angle : 0.601 10.686 2830 Z= 0.286 Chirality : 0.041 0.129 318 Planarity : 0.003 0.043 363 Dihedral : 5.703 55.915 344 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.49 % Allowed : 14.93 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.54), residues: 254 helix: 1.10 (0.58), residues: 88 sheet: -0.04 (0.80), residues: 49 loop : 0.25 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS A 6 PHE 0.007 0.001 PHE A 33 TYR 0.009 0.001 TYR A 14 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.229 Fit side-chains REVERT: A 9 MET cc_start: 0.7672 (tmm) cc_final: 0.7380 (ttt) REVERT: A 25 ILE cc_start: 0.8401 (mm) cc_final: 0.8081 (mt) outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.1344 time to fit residues: 5.6579 Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.0970 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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: 0.7771 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2082 Z= 0.269 Angle : 0.660 9.803 2830 Z= 0.324 Chirality : 0.043 0.131 318 Planarity : 0.004 0.044 363 Dihedral : 5.764 53.240 344 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.49 % Allowed : 15.42 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.54), residues: 254 helix: 1.01 (0.58), residues: 89 sheet: -0.32 (0.80), residues: 49 loop : 0.04 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 436 HIS 0.002 0.001 HIS A 6 PHE 0.008 0.001 PHE B 464 TYR 0.013 0.002 TYR B 453 ARG 0.003 0.000 ARG B 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.234 Fit side-chains REVERT: A 9 MET cc_start: 0.7783 (tmm) cc_final: 0.7480 (ttp) REVERT: A 25 ILE cc_start: 0.8536 (mm) cc_final: 0.8206 (mt) outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.1314 time to fit residues: 5.5252 Evaluate side-chains 35 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.0670 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.0870 chunk 6 optimal weight: 0.0770 overall best weight: 0.1454 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.128764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112011 restraints weight = 2945.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114909 restraints weight = 1652.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116805 restraints weight = 1128.010| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2082 Z= 0.167 Angle : 0.632 10.311 2830 Z= 0.302 Chirality : 0.042 0.128 318 Planarity : 0.004 0.045 363 Dihedral : 5.607 52.509 344 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.49 % Allowed : 15.92 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.54), residues: 254 helix: 1.04 (0.58), residues: 88 sheet: -0.28 (0.80), residues: 49 loop : 0.06 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS A 6 PHE 0.009 0.001 PHE A 33 TYR 0.009 0.001 TYR A 14 ARG 0.003 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1224.74 seconds wall clock time: 22 minutes 35.43 seconds (1355.43 seconds total)