Starting phenix.real_space_refine on Thu Nov 14 02:34:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2024/8hed_34688.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2024/8hed_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_2024/8hed_34688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2024/8hed_34688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2024/8hed_34688.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hed_34688/11_2024/8hed_34688.cif" } 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. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.52, per 1000 atoms: 1.66 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 356.7 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: 0.58 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: 0.97 Time building geometry restraints manager: 1.02 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: 0.00 - 1.27: 4338 1.27 - 2.55: 222 2.55 - 3.82: 55 3.82 - 5.09: 7 5.09 - 6.37: 3 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: 1740 14.74 - 29.48: 203 29.48 - 44.21: 64 44.21 - 58.95: 12 58.95 - 73.69: 3 Dihedral angle restraints: 2022 sinusoidal: 802 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 2019 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 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.247 3.040 nonbonded pdb=" N GLU B 340 " pdb=" OE1 GLU B 340 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR F 35 " pdb=" O VAL G 103 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP G 52 " pdb=" N SER G 53 " model vdw 2.360 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.670 Find NCS groups from input model: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 : 13.888 73.689 1232 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 61 HIS 0.001 0.001 HIS G 55 PHE 0.007 0.001 PHE B 342 TYR 0.007 0.001 TYR B 495 ARG 0.002 0.000 ARG G 30 *********************** 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 to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2810 time to fit residues: 21.8453 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 chunk 24 optimal weight: 0.0000 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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: 0.8164 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3399 Z= 0.160 Angle : 0.579 7.929 4625 Z= 0.301 Chirality : 0.043 0.151 518 Planarity : 0.003 0.022 592 Dihedral : 5.111 34.527 529 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.41 % Favored : 93.35 % Rotamer: Outliers : 3.64 % Allowed : 17.09 % Favored : 79.27 % 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: -0.38 (0.42), residues: 421 helix: -1.89 (1.40), residues: 15 sheet: 1.15 (0.46), residues: 148 loop : -1.07 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS G 55 PHE 0.007 0.001 PHE B 342 TYR 0.009 0.001 TYR B 453 ARG 0.003 0.000 ARG B 403 *********************** 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 85 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4175 (t0) cc_final: 0.3967 (t0) REVERT: G 52 ASP cc_start: 0.8895 (p0) cc_final: 0.8675 (p0) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.1967 time to fit residues: 18.2303 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8234 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3399 Z= 0.268 Angle : 0.594 5.381 4625 Z= 0.312 Chirality : 0.044 0.156 518 Planarity : 0.003 0.024 592 Dihedral : 5.489 35.565 529 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 3.36 % Allowed : 20.17 % Favored : 76.47 % 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: -0.45 (0.42), residues: 421 helix: -1.63 (1.42), residues: 15 sheet: 1.23 (0.48), residues: 137 loop : -1.11 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 PHE 0.010 0.001 PHE B 342 TYR 0.012 0.001 TYR B 453 ARG 0.002 0.000 ARG B 403 *********************** 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 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7833 (tm-30) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.2037 time to fit residues: 17.5616 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8287 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3399 Z= 0.390 Angle : 0.666 7.208 4625 Z= 0.349 Chirality : 0.047 0.154 518 Planarity : 0.004 0.031 592 Dihedral : 6.276 38.815 529 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.26 % Favored : 90.50 % Rotamer: Outliers : 5.60 % Allowed : 19.05 % Favored : 75.35 % 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: -0.70 (0.42), residues: 421 helix: -1.48 (1.45), residues: 15 sheet: 1.19 (0.48), residues: 137 loop : -1.40 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 46 HIS 0.003 0.002 HIS G 55 PHE 0.013 0.002 PHE G 91 TYR 0.015 0.002 TYR B 495 ARG 0.002 0.000 ARG B 454 *********************** 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 88 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7867 (tm-30) REVERT: F 35 TYR cc_start: 0.9233 (m-80) cc_final: 0.8996 (m-80) REVERT: F 97 ASP cc_start: 0.8817 (m-30) cc_final: 0.8540 (m-30) outliers start: 20 outliers final: 13 residues processed: 82 average time/residue: 0.1936 time to fit residues: 18.7002 Evaluate side-chains 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3399 Z= 0.234 Angle : 0.621 6.643 4625 Z= 0.321 Chirality : 0.044 0.159 518 Planarity : 0.003 0.029 592 Dihedral : 5.785 35.408 529 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 4.20 % Allowed : 20.17 % 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: -0.59 (0.42), residues: 421 helix: -1.63 (1.41), residues: 15 sheet: 1.16 (0.47), residues: 142 loop : -1.29 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 PHE 0.010 0.001 PHE B 342 TYR 0.011 0.001 TYR B 453 ARG 0.002 0.000 ARG B 403 *********************** 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 88 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.3509 (t0) cc_final: 0.3164 (t0) REVERT: F 75 ARG cc_start: 0.7918 (ttm110) cc_final: 0.7554 (mtm-85) REVERT: F 97 ASP cc_start: 0.8782 (m-30) cc_final: 0.8482 (m-30) outliers start: 15 outliers final: 10 residues processed: 82 average time/residue: 0.1885 time to fit residues: 18.2430 Evaluate side-chains 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3399 Z= 0.198 Angle : 0.594 8.359 4625 Z= 0.307 Chirality : 0.044 0.159 518 Planarity : 0.003 0.032 592 Dihedral : 5.394 33.408 529 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 4.20 % Allowed : 21.01 % 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: -0.58 (0.42), residues: 421 helix: -1.58 (1.46), residues: 15 sheet: 1.13 (0.47), residues: 140 loop : -1.23 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 PHE 0.009 0.001 PHE B 342 TYR 0.010 0.001 TYR B 453 ARG 0.004 0.000 ARG F 62 *********************** 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 85 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.3792 (t0) cc_final: 0.3364 (t0) REVERT: F 23 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7818 (tm-30) REVERT: F 35 TYR cc_start: 0.9171 (m-80) cc_final: 0.8945 (m-80) REVERT: F 75 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7510 (mtm-85) REVERT: F 97 ASP cc_start: 0.8756 (m-30) cc_final: 0.8442 (m-30) outliers start: 15 outliers final: 11 residues processed: 79 average time/residue: 0.2194 time to fit residues: 20.7100 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3399 Z= 0.199 Angle : 0.593 7.767 4625 Z= 0.304 Chirality : 0.043 0.156 518 Planarity : 0.003 0.036 592 Dihedral : 5.187 32.561 529 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.36 % Allowed : 22.41 % Favored : 74.23 % 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: -1.64 (1.43), residues: 15 sheet: 1.06 (0.47), residues: 140 loop : -1.20 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 PHE 0.009 0.001 PHE B 342 TYR 0.010 0.001 TYR B 453 ARG 0.002 0.000 ARG B 403 *********************** 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 81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.3767 (t0) cc_final: 0.3558 (t0) REVERT: B 518 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7978 (pp) REVERT: F 62 ARG cc_start: 0.7998 (tmm-80) cc_final: 0.7660 (mtp180) REVERT: F 97 ASP cc_start: 0.8752 (m-30) cc_final: 0.8446 (m-30) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.2038 time to fit residues: 18.1105 Evaluate side-chains 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.1980 chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8209 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3399 Z= 0.203 Angle : 0.595 7.441 4625 Z= 0.305 Chirality : 0.043 0.156 518 Planarity : 0.003 0.035 592 Dihedral : 5.105 31.858 529 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.76 % Allowed : 21.01 % Favored : 74.23 % 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: -0.63 (0.42), residues: 421 helix: -2.64 (1.06), residues: 21 sheet: 1.04 (0.47), residues: 140 loop : -1.11 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 46 HIS 0.001 0.001 HIS G 55 PHE 0.009 0.001 PHE B 342 TYR 0.009 0.001 TYR B 453 ARG 0.002 0.000 ARG B 403 *********************** 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 87 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.3838 (t0) cc_final: 0.3609 (t0) REVERT: B 518 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7983 (pp) REVERT: F 23 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7795 (tm-30) REVERT: F 62 ARG cc_start: 0.7982 (tmm-80) cc_final: 0.7690 (mtp180) REVERT: F 97 ASP cc_start: 0.8767 (m-30) cc_final: 0.8470 (m-30) outliers start: 17 outliers final: 15 residues processed: 79 average time/residue: 0.2020 time to fit residues: 18.8690 Evaluate side-chains 84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 1 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 39 optimal weight: 0.3980 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.2948 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3399 Z= 0.169 Angle : 0.595 7.558 4625 Z= 0.302 Chirality : 0.043 0.156 518 Planarity : 0.003 0.032 592 Dihedral : 4.798 29.111 529 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.92 % Allowed : 21.01 % 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: -0.63 (0.42), residues: 421 helix: -2.69 (1.06), residues: 21 sheet: 0.94 (0.47), residues: 140 loop : -1.04 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 61 HIS 0.001 0.000 HIS G 55 PHE 0.007 0.001 PHE B 342 TYR 0.008 0.001 TYR F 35 ARG 0.002 0.000 ARG B 454 *********************** 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 91 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4040 (t0) cc_final: 0.3608 (t0) REVERT: B 518 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7987 (pp) REVERT: F 23 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7718 (tm-30) REVERT: F 62 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7669 (mtp180) REVERT: F 97 ASP cc_start: 0.8704 (m-30) cc_final: 0.8411 (m-30) outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.1825 time to fit residues: 18.0452 Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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: 0.8176 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3399 Z= 0.176 Angle : 0.628 8.687 4625 Z= 0.321 Chirality : 0.044 0.171 518 Planarity : 0.003 0.031 592 Dihedral : 4.855 28.572 529 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.36 % Allowed : 22.97 % Favored : 73.67 % 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: -0.57 (0.42), residues: 421 helix: -2.64 (1.08), residues: 21 sheet: 0.96 (0.47), residues: 140 loop : -0.98 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 61 HIS 0.001 0.000 HIS G 55 PHE 0.007 0.001 PHE G 106 TYR 0.013 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 ********************** 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 83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: B 518 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.8007 (pp) REVERT: F 23 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7714 (tm-30) REVERT: F 62 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7696 (mtp180) REVERT: F 97 ASP cc_start: 0.8681 (m-30) cc_final: 0.8411 (m-30) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.1972 time to fit residues: 18.0981 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.078469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068900 restraints weight = 9915.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.071200 restraints weight = 4550.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.072720 restraints weight = 2665.140| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3399 Z= 0.216 Angle : 0.672 8.392 4625 Z= 0.345 Chirality : 0.045 0.155 518 Planarity : 0.003 0.034 592 Dihedral : 4.999 29.166 529 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.48 % Allowed : 21.29 % Favored : 74.23 % 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: -0.61 (0.42), residues: 421 helix: -2.64 (1.08), residues: 21 sheet: 1.04 (0.47), residues: 136 loop : -1.05 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 436 HIS 0.001 0.000 HIS G 55 PHE 0.011 0.001 PHE B 486 TYR 0.010 0.001 TYR B 453 ARG 0.002 0.000 ARG G 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.13 seconds wall clock time: 30 minutes 31.42 seconds (1831.42 seconds total)