Starting phenix.real_space_refine on Mon Nov 13 17:17:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2023/8hed_34688.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2023/8hed_34688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2023/8hed_34688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2023/8hed_34688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2023/8hed_34688.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2023/8hed_34688.pdb" } resolution = 3.59 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= -0.002 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 18 5.16 5 C 2102 2.51 5 N 547 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 95": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1578 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.73 Number of scatterers: 3318 At special positions: 0 Unit cell: (79.54, 62.32, 102.5, 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 18 16.00 O 651 8.00 N 547 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " 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 O 1 " - " NAG O 2 " NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 615.7 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.666A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.546A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.506A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.765A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.820A pdb=" N ASP F 81 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 82' Processing helix chain 'G' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.192A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.692A pdb=" N VAL F 18 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR F 71 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.569A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.569A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 89 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA F 100 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.196A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.981A pdb=" N PHE G 106 " --> pdb=" O ARG G 94 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 252 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: 0.89 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1054 1.35 - 1.47: 906 1.47 - 1.59: 1418 1.59 - 1.71: 0 1.71 - 1.83: 21 Bond restraints: 3399 Sorted by residual: bond pdb=" N ASN B 501 " pdb=" CA ASN B 501 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.22e-02 6.72e+03 6.06e+00 bond pdb=" N CYS F 98 " pdb=" CA CYS F 98 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" N GLU F 90 " pdb=" CA GLU F 90 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.34e-02 5.57e+03 5.97e+00 bond pdb=" N THR F 99 " pdb=" CA THR F 99 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.78e+00 bond pdb=" N CYS F 93 " pdb=" CA CYS F 93 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.47e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 93 106.88 - 113.66: 1813 113.66 - 120.44: 1238 120.44 - 127.22: 1448 127.22 - 134.00: 33 Bond angle restraints: 4625 Sorted by residual: angle pdb=" CA ASP F 97 " pdb=" C ASP F 97 " pdb=" O ASP F 97 " ideal model delta sigma weight residual 121.78 118.20 3.58 1.12e+00 7.97e-01 1.02e+01 angle pdb=" CA LYS G 63 " pdb=" CB LYS G 63 " pdb=" CG LYS G 63 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" CA GLU F 90 " pdb=" C GLU F 90 " pdb=" O GLU F 90 " ideal model delta sigma weight residual 121.87 118.35 3.52 1.16e+00 7.43e-01 9.22e+00 angle pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" O ARG B 403 " ideal model delta sigma weight residual 121.87 118.71 3.16 1.10e+00 8.26e-01 8.23e+00 angle pdb=" CA PHE F 91 " pdb=" C PHE F 91 " pdb=" O PHE F 91 " ideal model delta sigma weight residual 122.31 118.61 3.70 1.31e+00 5.83e-01 7.98e+00 ... (remaining 4620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1685 14.74 - 29.48: 199 29.48 - 44.21: 60 44.21 - 58.95: 12 58.95 - 73.69: 3 Dihedral angle restraints: 1959 sinusoidal: 739 harmonic: 1220 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 -86.00 -37.18 -48.82 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 54.96 38.04 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.20 34.80 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 1956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 302 0.029 - 0.058: 129 0.058 - 0.087: 39 0.087 - 0.116: 41 0.116 - 0.146: 7 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA LEU G 28 " pdb=" N LEU G 28 " pdb=" C LEU G 28 " pdb=" CB LEU G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA PHE F 91 " pdb=" N PHE F 91 " pdb=" C PHE F 91 " pdb=" CB PHE F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA PRO B 337 " pdb=" N PRO B 337 " pdb=" C PRO B 337 " pdb=" CB PRO B 337 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 515 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 63 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS G 63 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS G 63 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY G 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ILE B 468 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE B 468 " -0.007 2.00e-02 2.50e+03 pdb=" N SER B 469 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 89 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C GLY F 89 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY F 89 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU F 90 " -0.006 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 698 2.78 - 3.31: 2933 3.31 - 3.84: 5034 3.84 - 4.37: 5680 4.37 - 4.90: 10270 Nonbonded interactions: 24615 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.247 2.440 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.247 2.440 nonbonded pdb=" N GLU B 340 " pdb=" OE1 GLU B 340 " model vdw 2.254 2.520 nonbonded pdb=" OH TYR F 35 " pdb=" O VAL G 103 " model vdw 2.318 2.440 nonbonded pdb=" OD1 ASP G 52 " pdb=" N SER G 53 " model vdw 2.360 2.520 ... (remaining 24610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 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: 26.340 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.004 0.033 3399 Z= 0.250 Angle : 0.670 6.368 4625 Z= 0.375 Chirality : 0.044 0.146 518 Planarity : 0.003 0.026 592 Dihedral : 13.945 73.689 1169 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.65 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.42), residues: 421 helix: -2.38 (1.25), residues: 15 sheet: 1.03 (0.49), residues: 136 loop : -0.94 (0.38), residues: 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.370 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2562 time to fit residues: 19.8394 Evaluate side-chains 63 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 24 optimal weight: 0.0060 chunk 38 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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: 0.8159 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3399 Z= 0.150 Angle : 0.563 7.943 4625 Z= 0.294 Chirality : 0.043 0.150 518 Planarity : 0.003 0.022 592 Dihedral : 4.163 15.417 466 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.65 % Favored : 93.11 % Rotamer: Outliers : 3.08 % Allowed : 18.21 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.43), residues: 421 helix: -1.75 (1.47), residues: 15 sheet: 1.12 (0.46), residues: 148 loop : -1.04 (0.39), residues: 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.347 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.2063 time to fit residues: 17.3696 Evaluate side-chains 68 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0395 time to fit residues: 0.9790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.8225 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3399 Z= 0.268 Angle : 0.586 5.427 4625 Z= 0.308 Chirality : 0.044 0.155 518 Planarity : 0.003 0.026 592 Dihedral : 4.481 17.739 466 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 2.24 % Allowed : 19.33 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.42), residues: 421 helix: -1.36 (1.57), residues: 15 sheet: 1.27 (0.48), residues: 137 loop : -1.10 (0.38), residues: 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.397 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.2043 time to fit residues: 16.5614 Evaluate side-chains 67 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0354 time to fit residues: 0.8216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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: 0.8233 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3399 Z= 0.269 Angle : 0.592 7.708 4625 Z= 0.305 Chirality : 0.044 0.154 518 Planarity : 0.003 0.027 592 Dihedral : 4.465 17.900 466 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 2.80 % Allowed : 21.29 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.42), residues: 421 helix: -1.40 (1.52), residues: 15 sheet: 1.18 (0.46), residues: 147 loop : -1.37 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.392 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.1999 time to fit residues: 17.3510 Evaluate side-chains 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0406 time to fit residues: 0.9156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.0040 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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: 0.8219 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3399 Z= 0.223 Angle : 0.578 6.732 4625 Z= 0.296 Chirality : 0.043 0.156 518 Planarity : 0.003 0.024 592 Dihedral : 4.430 17.586 466 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 1.96 % Allowed : 20.45 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.42), residues: 421 helix: -1.53 (1.47), residues: 15 sheet: 1.23 (0.46), residues: 146 loop : -1.38 (0.37), residues: 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.2081 time to fit residues: 17.5589 Evaluate side-chains 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0428 time to fit residues: 0.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.0010 chunk 39 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4104 ------------------------------------------------------------------------------- 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: 0.8193 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3399 Z= 0.172 Angle : 0.575 6.940 4625 Z= 0.293 Chirality : 0.043 0.157 518 Planarity : 0.003 0.022 592 Dihedral : 4.296 20.231 466 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 1.40 % Allowed : 20.73 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.42), residues: 421 helix: -1.69 (1.44), residues: 15 sheet: 1.09 (0.46), residues: 148 loop : -1.37 (0.38), residues: 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.2097 time to fit residues: 17.2693 Evaluate side-chains 69 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0467 time to fit residues: 0.6749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3399 Z= 0.273 Angle : 0.604 6.050 4625 Z= 0.313 Chirality : 0.044 0.157 518 Planarity : 0.003 0.024 592 Dihedral : 4.491 18.877 466 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.03 % Favored : 90.74 % Rotamer: Outliers : 2.52 % Allowed : 20.45 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.42), residues: 421 helix: -1.63 (1.42), residues: 15 sheet: 1.06 (0.46), residues: 147 loop : -1.49 (0.37), residues: 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.369 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 70 average time/residue: 0.2191 time to fit residues: 18.1000 Evaluate side-chains 72 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0353 time to fit residues: 0.9140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3399 Z= 0.221 Angle : 0.616 8.053 4625 Z= 0.312 Chirality : 0.043 0.156 518 Planarity : 0.003 0.035 592 Dihedral : 4.493 20.770 466 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 0.84 % Allowed : 22.41 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.42), residues: 421 helix: -1.66 (1.44), residues: 15 sheet: 1.03 (0.46), residues: 147 loop : -1.37 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.378 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 69 average time/residue: 0.1885 time to fit residues: 15.3404 Evaluate side-chains 67 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0432 time to fit residues: 0.5668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3399 Z= 0.188 Angle : 0.617 8.749 4625 Z= 0.307 Chirality : 0.043 0.156 518 Planarity : 0.003 0.039 592 Dihedral : 4.407 17.915 466 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.65 % Favored : 93.11 % Rotamer: Outliers : 0.28 % Allowed : 24.09 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.68 (0.42), residues: 421 helix: -1.69 (1.44), residues: 15 sheet: 1.02 (0.46), residues: 147 loop : -1.34 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.386 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.1983 time to fit residues: 15.9473 Evaluate side-chains 67 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0360 time to fit residues: 0.5736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0170 chunk 26 optimal weight: 0.0980 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3399 Z= 0.174 Angle : 0.615 8.970 4625 Z= 0.304 Chirality : 0.042 0.155 518 Planarity : 0.003 0.042 592 Dihedral : 4.173 18.919 466 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 1.12 % Allowed : 24.09 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.42), residues: 421 helix: -2.73 (1.05), residues: 21 sheet: 1.02 (0.46), residues: 147 loop : -1.31 (0.39), residues: 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1944 time to fit residues: 17.0584 Evaluate side-chains 73 residues out of total 358 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0468 time to fit residues: 0.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.078981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069336 restraints weight = 10061.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071578 restraints weight = 4699.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073114 restraints weight = 2798.457| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3399 Z= 0.175 Angle : 0.612 9.125 4625 Z= 0.301 Chirality : 0.042 0.154 518 Planarity : 0.003 0.039 592 Dihedral : 4.063 17.242 466 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 24.93 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.42), residues: 421 helix: -2.69 (1.06), residues: 21 sheet: 1.16 (0.46), residues: 144 loop : -1.33 (0.38), residues: 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1552.33 seconds wall clock time: 28 minutes 35.44 seconds (1715.44 seconds total)