Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:17:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/04_2022/7jzm_22533.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/04_2022/7jzm_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_22533/04_2022/7jzm_22533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/04_2022/7jzm_22533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/04_2022/7jzm_22533.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzm_22533/04_2022/7jzm_22533.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'NAG': 2, 'FUC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.84, per 1000 atoms: 0.91 Number of scatterers: 2033 At special positions: 0 Unit cell: (66.15, 68.25, 69.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 373 8.00 N 340 7.00 C 1310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.28 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG C 1 " - " ASN B 343 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 322.4 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: 0.14 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: 0.51 Time building geometry restraints manager: 1.09 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 1.435 1.479 -0.044 1.10e-02 8.26e+03 1.59e+01 bond pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " ideal model delta sigma weight residual 1.523 1.555 -0.032 1.00e-02 1.00e+04 1.00e+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 1.435 1.467 -0.032 1.10e-02 8.26e+03 8.63e+00 ... (remaining 2077 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.19: 27 104.19 - 111.62: 885 111.62 - 119.06: 722 119.06 - 126.49: 1185 126.49 - 133.92: 11 Bond angle restraints: 2830 Sorted by residual: angle pdb=" N PRO B 499 " pdb=" CA PRO B 499 " pdb=" CB PRO B 499 " ideal model delta sigma weight residual 103.41 96.76 6.65 9.40e-01 1.13e+00 5.01e+01 angle pdb=" CA PRO B 499 " pdb=" N PRO B 499 " pdb=" CD PRO B 499 " ideal model delta sigma weight residual 112.00 120.93 -8.93 1.40e+00 5.10e-01 4.07e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.01 -6.45 1.02e+00 9.61e-01 4.00e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.31 -6.44 1.04e+00 9.25e-01 3.84e+01 angle pdb=" C PHE B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta sigma weight residual 119.56 125.65 -6.09 1.01e+00 9.80e-01 3.64e+01 ... (remaining 2825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1175 14.30 - 28.59: 45 28.59 - 42.89: 8 42.89 - 57.18: 5 57.18 - 71.48: 1 Dihedral angle restraints: 1234 sinusoidal: 475 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 1231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 233 0.082 - 0.164: 68 0.164 - 0.246: 13 0.246 - 0.328: 3 0.328 - 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 4.19e+00 ... (remaining 315 not shown) Planarity restraints: 364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR B 495 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " 0.025 2.00e-02 2.50e+03 1.34e-02 3.57e+00 pdb=" CG TYR B 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.016 2.00e-02 2.50e+03 1.65e-02 3.40e+00 pdb=" CG ASN B 343 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 361 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 880 2.92 - 3.41: 1816 3.41 - 3.91: 3445 3.91 - 4.40: 3881 4.40 - 4.90: 6261 Nonbonded interactions: 16283 Sorted by model distance: nonbonded pdb=" O ASP A 2 " pdb=" OD1 ASP A 2 " model vdw 2.420 3.040 nonbonded pdb=" N ASP B 428 " pdb=" OD1 ASP B 428 " model vdw 2.566 2.520 nonbonded pdb=" O ASN B 501 " pdb=" NE2 GLN B 506 " model vdw 2.568 2.520 nonbonded pdb=" O5 NAG C 1 " pdb=" O6 NAG C 1 " model vdw 2.569 2.432 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.574 2.560 ... (remaining 16278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.260 Check model and map are aligned: 0.030 Convert atoms to be neutral: 0.020 Process input model: 12.480 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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= 0.935 Angle : 1.368 12.810 2830 Z= 0.938 Chirality : 0.082 0.409 318 Planarity : 0.005 0.026 363 Dihedral : 9.253 71.478 736 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.52), residues: 254 helix: 0.21 (0.51), residues: 85 sheet: 0.78 (0.76), residues: 52 loop : 0.82 (0.60), residues: 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.238 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1681 time to fit residues: 12.5502 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 0.0770 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 19 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.0170 chunk 14 optimal weight: 0.0370 chunk 22 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 overall best weight: 0.0630 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 2082 Z= 0.151 Angle : 0.604 7.912 2830 Z= 0.308 Chirality : 0.042 0.141 318 Planarity : 0.004 0.039 363 Dihedral : 4.353 17.312 306 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 2.49 % 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: 1.10 (0.53), residues: 254 helix: 1.13 (0.58), residues: 87 sheet: 0.62 (0.78), residues: 49 loop : 0.66 (0.57), residues: 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.244 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1612 time to fit residues: 7.8267 Evaluate side-chains 42 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.241 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0234 time to fit residues: 0.4793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.0670 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.0000 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.0030 chunk 15 optimal weight: 0.3980 overall best weight: 0.0730 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 2082 Z= 0.129 Angle : 0.542 6.320 2830 Z= 0.273 Chirality : 0.040 0.135 318 Planarity : 0.003 0.038 363 Dihedral : 4.055 17.450 306 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 0.50 % 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: 1.02 (0.53), residues: 254 helix: 1.26 (0.58), residues: 88 sheet: 0.45 (0.74), residues: 49 loop : 0.49 (0.57), residues: 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.260 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1338 time to fit residues: 5.4851 Evaluate side-chains 31 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.0270 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.0020 chunk 6 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 0 optimal weight: 0.0980 chunk 17 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.0924 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 2082 Z= 0.130 Angle : 0.511 6.344 2830 Z= 0.259 Chirality : 0.040 0.135 318 Planarity : 0.003 0.040 363 Dihedral : 3.935 16.582 306 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 1.49 % 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: 0.95 (0.53), residues: 254 helix: 1.25 (0.57), residues: 88 sheet: 0.29 (0.71), residues: 49 loop : 0.48 (0.58), residues: 117 *********************** 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 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.251 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 35 average time/residue: 0.1365 time to fit residues: 5.7541 Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 14 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 overall best weight: 0.1016 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.135 2082 Z= 0.273 Angle : 0.724 14.555 2830 Z= 0.374 Chirality : 0.041 0.133 318 Planarity : 0.003 0.040 363 Dihedral : 3.904 16.195 306 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 1.00 % 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: 0.93 (0.53), residues: 254 helix: 1.29 (0.57), residues: 88 sheet: 0.26 (0.72), residues: 49 loop : 0.43 (0.59), residues: 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.247 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.1427 time to fit residues: 6.1136 Evaluate side-chains 33 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.252 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0243 time to fit residues: 0.3789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.0980 chunk 8 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 13 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 11 optimal weight: 0.0060 overall best weight: 0.0750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 2082 Z= 0.128 Angle : 0.601 12.126 2830 Z= 0.290 Chirality : 0.040 0.132 318 Planarity : 0.003 0.039 363 Dihedral : 3.867 16.170 306 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.00 % 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: 0.94 (0.54), residues: 254 helix: 1.30 (0.57), residues: 88 sheet: 0.26 (0.73), residues: 49 loop : 0.42 (0.59), residues: 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1461 time to fit residues: 5.9016 Evaluate side-chains 32 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.238 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.0030 chunk 9 optimal weight: 0.0170 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 overall best weight: 0.0806 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.3636 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= 0.122 Angle : 0.557 9.490 2830 Z= 0.272 Chirality : 0.040 0.131 318 Planarity : 0.003 0.040 363 Dihedral : 3.807 16.729 306 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.00 % 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: 0.95 (0.54), residues: 254 helix: 1.25 (0.57), residues: 88 sheet: 0.36 (0.76), residues: 49 loop : 0.43 (0.60), residues: 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 508 Ramachandran restraints generated. 254 Oldfield, 0 Emsley, 254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1297 time to fit residues: 5.8087 Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.236 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.4980 chunk 22 optimal weight: 0.0770 chunk 23 optimal weight: 0.0870 chunk 13 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.0670 overall best weight: 0.1192 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 2082 Z= 0.146 Angle : 0.564 8.253 2830 Z= 0.279 Chirality : 0.041 0.131 318 Planarity : 0.003 0.042 363 Dihedral : 3.848 16.977 306 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 1.00 % 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 (0.54), residues: 254 helix: 1.18 (0.58), residues: 88 sheet: 0.36 (0.77), residues: 49 loop : 0.46 (0.60), residues: 117 *********************** 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 39 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.281 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 38 average time/residue: 0.1401 time to fit residues: 6.5606 Evaluate side-chains 38 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0377 time to fit residues: 0.5188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 21 optimal weight: 0.0980 chunk 6 optimal weight: 0.0970 chunk 18 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.0470 overall best weight: 0.0876 ------------------------------------------------------------------------------- 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: 0.7827 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 2082 Z= 0.131 Angle : 0.620 11.970 2830 Z= 0.290 Chirality : 0.041 0.130 318 Planarity : 0.003 0.042 363 Dihedral : 3.842 17.118 306 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.50 % 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: 0.89 (0.54), residues: 254 helix: 1.12 (0.57), residues: 88 sheet: 0.49 (0.80), residues: 47 loop : 0.39 (0.59), residues: 119 *********************** 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: 1 poor density : 35 time to evaluate : 0.259 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.1367 time to fit residues: 5.9240 Evaluate side-chains 36 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0226 time to fit residues: 0.3733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.0570 chunk 3 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.0060 chunk 0 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 0.3980 overall best weight: 0.1914 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 2082 Z= 0.195 Angle : 0.630 10.820 2830 Z= 0.304 Chirality : 0.042 0.132 318 Planarity : 0.003 0.044 363 Dihedral : 3.992 15.793 306 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.54), residues: 254 helix: 1.13 (0.58), residues: 88 sheet: 0.40 (0.80), residues: 47 loop : 0.24 (0.58), residues: 119 ********************** 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 38 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1261 time to fit residues: 5.8168 Evaluate side-chains 37 residues out of total 227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 0.0980 chunk 24 optimal weight: 0.0470 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.0856 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.132378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116289 restraints weight = 2908.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119053 restraints weight = 1661.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121006 restraints weight = 1144.851| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 2082 Z= 0.143 Angle : 0.621 10.858 2830 Z= 0.294 Chirality : 0.041 0.130 318 Planarity : 0.003 0.044 363 Dihedral : 4.074 18.398 306 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.00 % 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: 0.70 (0.54), residues: 254 helix: 0.98 (0.58), residues: 87 sheet: 0.44 (0.81), residues: 47 loop : 0.24 (0.58), residues: 120 =============================================================================== Job complete usr+sys time: 1224.80 seconds wall clock time: 23 minutes 59.12 seconds (1439.12 seconds total)