Starting phenix.real_space_refine on Sun Mar 10 16:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/03_2024/7zh3_14720.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/03_2024/7zh3_14720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/03_2024/7zh3_14720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/03_2024/7zh3_14720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/03_2024/7zh3_14720.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh3_14720/03_2024/7zh3_14720.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.186 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 14 5.16 5 C 2082 2.51 5 N 538 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 452": "OD1" <-> "OD2" Residue "D PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 574": "OD1" <-> "OD2" Residue "D PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 759": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3301 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2656 Unusual residues: {' ZN': 1} Inner-chain residues flagged as termini: ['pdbres="LEU D 785 "'] Classifications: {'peptide': 330, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 316, None: 1} Not linked: pdbres="LEU D 785 " pdbres=" ZN D1000 " Chain breaks: 5 Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1793 SG CYS D 440 37.260 78.151 22.375 1.00 6.35 S ATOM 1816 SG CYS D 443 38.958 78.902 19.208 1.00 6.36 S ATOM 2191 SG CYS D 506 40.949 77.487 22.051 1.00 6.09 S ATOM 2214 SG CYS D 509 39.607 81.273 22.115 1.00 6.77 S Time building chain proxies: 2.25, per 1000 atoms: 0.68 Number of scatterers: 3301 At special positions: 0 Unit cell: (69.96, 92.22, 58.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 14 16.00 O 666 8.00 N 538 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 543.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " Number of angles added : 6 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 8 sheets defined 39.1% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'D' and resid 89 through 101 removed outlier: 3.717A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 Processing helix chain 'D' and resid 143 through 166 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 200 through 222 Processing helix chain 'D' and resid 424 through 431 removed outlier: 3.542A pdb=" N GLN D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 494 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.763A pdb=" N LYS D 503 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 568 Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.867A pdb=" N GLU D 742 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 768 removed outlier: 3.649A pdb=" N SER D 768 " --> pdb=" O LEU D 764 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 17 Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'D' and resid 82 through 83 removed outlier: 6.505A pdb=" N GLY D 82 " --> pdb=" O THR D 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 446 through 453 Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 459 removed outlier: 5.876A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 456 through 459 removed outlier: 5.876A pdb=" N TYR D 778 " --> pdb=" O LEU D 532 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL D 582 " --> pdb=" O TYR D 778 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU D 780 " --> pdb=" O ALA D 580 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA D 580 " --> pdb=" O LEU D 780 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR D 782 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 578 " --> pdb=" O TYR D 782 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS D 784 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 576 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE D 579 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AA8, first strand: chain 'D' and resid 535 through 536 187 hydrogen bonds defined for protein. 489 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: 1.00 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 803 1.33 - 1.45: 598 1.45 - 1.57: 1897 1.57 - 1.69: 0 1.69 - 1.81: 19 Bond restraints: 3317 Sorted by residual: bond pdb=" C SER D 775 " pdb=" N THR D 776 " ideal model delta sigma weight residual 1.331 1.286 0.045 1.63e-02 3.76e+03 7.78e+00 bond pdb=" CB ARG D 186 " pdb=" CG ARG D 186 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.14e+00 bond pdb=" CB LEU D 159 " pdb=" CG LEU D 159 " ideal model delta sigma weight residual 1.530 1.495 0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" CG LYS D 551 " pdb=" CD LYS D 551 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" CA ASP D 751 " pdb=" CB ASP D 751 " ideal model delta sigma weight residual 1.536 1.474 0.062 4.10e-02 5.95e+02 2.31e+00 ... (remaining 3312 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.10: 51 105.10 - 112.35: 1709 112.35 - 119.60: 1127 119.60 - 126.85: 1560 126.85 - 134.10: 30 Bond angle restraints: 4477 Sorted by residual: angle pdb=" CA LEU C 15 " pdb=" CB LEU C 15 " pdb=" CG LEU C 15 " ideal model delta sigma weight residual 116.30 124.57 -8.27 3.50e+00 8.16e-02 5.59e+00 angle pdb=" C PHE D 535 " pdb=" CA PHE D 535 " pdb=" CB PHE D 535 " ideal model delta sigma weight residual 110.16 114.38 -4.22 1.83e+00 2.99e-01 5.32e+00 angle pdb=" CA GLN D 433 " pdb=" CB GLN D 433 " pdb=" CG GLN D 433 " ideal model delta sigma weight residual 114.10 118.69 -4.59 2.00e+00 2.50e-01 5.28e+00 angle pdb=" C GLU D 424 " pdb=" CA GLU D 424 " pdb=" CB GLU D 424 " ideal model delta sigma weight residual 110.42 114.98 -4.56 1.99e+00 2.53e-01 5.26e+00 angle pdb=" N ASP D 172 " pdb=" CA ASP D 172 " pdb=" C ASP D 172 " ideal model delta sigma weight residual 111.24 114.11 -2.87 1.29e+00 6.01e-01 4.94e+00 ... (remaining 4472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 1819 15.58 - 31.16: 158 31.16 - 46.74: 34 46.74 - 62.32: 11 62.32 - 77.89: 4 Dihedral angle restraints: 2026 sinusoidal: 838 harmonic: 1188 Sorted by residual: dihedral pdb=" CA PRO D 555 " pdb=" C PRO D 555 " pdb=" N LEU D 556 " pdb=" CA LEU D 556 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG D 486 " pdb=" CD ARG D 486 " pdb=" NE ARG D 486 " pdb=" CZ ARG D 486 " ideal model delta sinusoidal sigma weight residual -90.00 -46.72 -43.28 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CB LYS D 428 " pdb=" CG LYS D 428 " pdb=" CD LYS D 428 " pdb=" CE LYS D 428 " ideal model delta sinusoidal sigma weight residual 60.00 118.40 -58.40 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 434 0.074 - 0.149: 83 0.149 - 0.223: 1 0.223 - 0.297: 0 0.297 - 0.371: 1 Chirality restraints: 519 Sorted by residual: chirality pdb=" CG LEU D 519 " pdb=" CB LEU D 519 " pdb=" CD1 LEU D 519 " pdb=" CD2 LEU D 519 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB VAL D 755 " pdb=" CA VAL D 755 " pdb=" CG1 VAL D 755 " pdb=" CG2 VAL D 755 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA PHE D 535 " pdb=" N PHE D 535 " pdb=" C PHE D 535 " pdb=" CB PHE D 535 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 516 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 189 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO D 190 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 190 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 190 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 177 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO D 178 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 178 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 178 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 505 " -0.020 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE D 505 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE D 505 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 505 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 505 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 505 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 505 " -0.005 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 451 2.75 - 3.29: 2912 3.29 - 3.82: 5767 3.82 - 4.36: 7330 4.36 - 4.90: 11851 Nonbonded interactions: 28311 Sorted by model distance: nonbonded pdb=" OE1 GLN D 454 " pdb=" O HOH D1101 " model vdw 2.209 2.440 nonbonded pdb=" O ALA C 46 " pdb=" O HOH C 101 " model vdw 2.270 2.440 nonbonded pdb=" NZ LYS C 33 " pdb=" OD1 ASP D 502 " model vdw 2.298 2.520 nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.306 2.440 nonbonded pdb=" O HOH D1131 " pdb=" O HOH D1132 " model vdw 2.329 2.440 ... (remaining 28306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 7.100 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.970 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: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.010 0.062 3317 Z= 0.655 Angle : 0.842 8.273 4477 Z= 0.451 Chirality : 0.055 0.371 519 Planarity : 0.007 0.060 566 Dihedral : 13.327 77.893 1252 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.37), residues: 393 helix: -0.49 (0.40), residues: 130 sheet: -0.68 (0.44), residues: 100 loop : -1.31 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.004 TRP D 487 HIS 0.006 0.002 HIS D 593 PHE 0.027 0.005 PHE D 505 TYR 0.021 0.004 TYR D 195 ARG 0.010 0.002 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.340 Fit side-chains REVERT: D 455 ASP cc_start: 0.8188 (p0) cc_final: 0.7885 (p0) REVERT: D 524 MET cc_start: 0.8540 (mmm) cc_final: 0.8316 (tpt) outliers start: 0 outliers final: 1 residues processed: 68 average time/residue: 1.5964 time to fit residues: 110.9817 Evaluate side-chains 62 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3317 Z= 0.150 Angle : 0.476 5.170 4477 Z= 0.257 Chirality : 0.037 0.129 519 Planarity : 0.004 0.035 566 Dihedral : 5.124 33.295 432 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.34 % Allowed : 6.95 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.41), residues: 393 helix: 1.51 (0.45), residues: 130 sheet: -0.35 (0.44), residues: 104 loop : -0.45 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 747 HIS 0.002 0.001 HIS C 68 PHE 0.009 0.001 PHE D 453 TYR 0.009 0.001 TYR D 195 ARG 0.006 0.001 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: C 21 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: C 32 ASP cc_start: 0.7611 (m-30) cc_final: 0.7392 (m-30) REVERT: D 523 LYS cc_start: 0.8051 (tttt) cc_final: 0.7848 (tttt) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 1.5778 time to fit residues: 106.5515 Evaluate side-chains 66 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 115 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0170 chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 210 ASN D 216 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3317 Z= 0.185 Angle : 0.482 4.722 4477 Z= 0.255 Chirality : 0.037 0.124 519 Planarity : 0.004 0.034 566 Dihedral : 4.923 32.485 432 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.87 % Allowed : 8.56 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.42), residues: 393 helix: 2.21 (0.46), residues: 130 sheet: -0.16 (0.44), residues: 104 loop : -0.25 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.013 0.002 PHE D 505 TYR 0.010 0.002 TYR D 195 ARG 0.006 0.001 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: D 158 GLN cc_start: 0.7874 (mt0) cc_final: 0.7552 (mt0) REVERT: D 764 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7470 (mm) outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 1.5544 time to fit residues: 105.0189 Evaluate side-chains 65 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 764 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3317 Z= 0.463 Angle : 0.647 7.924 4477 Z= 0.332 Chirality : 0.045 0.126 519 Planarity : 0.005 0.038 566 Dihedral : 5.463 30.152 432 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.74 % Allowed : 8.56 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.42), residues: 393 helix: 1.81 (0.45), residues: 130 sheet: -0.06 (0.44), residues: 102 loop : -0.23 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP D 487 HIS 0.003 0.001 HIS C 68 PHE 0.023 0.003 PHE D 505 TYR 0.017 0.003 TYR D 195 ARG 0.007 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.427 Fit side-chains REVERT: C 64 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8525 (mt-10) REVERT: D 158 GLN cc_start: 0.7951 (mt0) cc_final: 0.7661 (mt0) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 1.6034 time to fit residues: 109.9412 Evaluate side-chains 72 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3317 Z= 0.167 Angle : 0.459 4.734 4477 Z= 0.245 Chirality : 0.037 0.123 519 Planarity : 0.004 0.032 566 Dihedral : 4.603 26.104 430 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.21 % Allowed : 9.63 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.42), residues: 393 helix: 2.39 (0.45), residues: 130 sheet: 0.02 (0.45), residues: 104 loop : -0.08 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 487 HIS 0.002 0.001 HIS D 511 PHE 0.010 0.002 PHE D 505 TYR 0.010 0.002 TYR D 195 ARG 0.008 0.001 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.385 Fit side-chains REVERT: D 158 GLN cc_start: 0.7955 (mt0) cc_final: 0.7632 (mt0) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 1.4418 time to fit residues: 100.4223 Evaluate side-chains 72 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3317 Z= 0.297 Angle : 0.545 6.245 4477 Z= 0.283 Chirality : 0.040 0.128 519 Planarity : 0.004 0.035 566 Dihedral : 4.904 26.652 430 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.21 % Allowed : 10.43 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.42), residues: 393 helix: 2.27 (0.45), residues: 130 sheet: -0.01 (0.44), residues: 102 loop : -0.04 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 487 HIS 0.003 0.001 HIS C 68 PHE 0.019 0.003 PHE D 505 TYR 0.013 0.002 TYR D 195 ARG 0.006 0.001 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.452 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 1.5094 time to fit residues: 105.1572 Evaluate side-chains 72 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 0.028 3317 Z= 0.251 Angle : 0.513 5.444 4477 Z= 0.269 Chirality : 0.039 0.126 519 Planarity : 0.004 0.032 566 Dihedral : 4.791 26.225 430 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.74 % Allowed : 9.63 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.42), residues: 393 helix: 2.38 (0.45), residues: 130 sheet: -0.00 (0.44), residues: 102 loop : -0.00 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.015 0.002 PHE D 505 TYR 0.013 0.002 TYR D 195 ARG 0.009 0.001 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.416 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 71 average time/residue: 1.5261 time to fit residues: 110.8693 Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3317 Z= 0.252 Angle : 0.517 5.529 4477 Z= 0.271 Chirality : 0.039 0.127 519 Planarity : 0.004 0.033 566 Dihedral : 4.777 25.914 430 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.01 % Allowed : 9.89 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.42), residues: 393 helix: 2.38 (0.45), residues: 130 sheet: -0.02 (0.44), residues: 102 loop : 0.02 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.016 0.002 PHE D 505 TYR 0.012 0.002 TYR D 195 ARG 0.009 0.001 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.429 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 1.5058 time to fit residues: 107.9441 Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3317 Z= 0.201 Angle : 0.484 4.826 4477 Z= 0.256 Chirality : 0.038 0.125 519 Planarity : 0.004 0.032 566 Dihedral : 4.584 23.968 430 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.21 % Allowed : 10.70 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.42), residues: 393 helix: 2.54 (0.45), residues: 130 sheet: 0.03 (0.45), residues: 102 loop : 0.04 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.012 0.002 PHE D 505 TYR 0.011 0.002 TYR D 195 ARG 0.009 0.001 ARG D 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.432 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 1.5045 time to fit residues: 103.2446 Evaluate side-chains 69 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3317 Z= 0.348 Angle : 0.582 7.167 4477 Z= 0.302 Chirality : 0.041 0.130 519 Planarity : 0.004 0.034 566 Dihedral : 4.969 25.906 430 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.94 % Allowed : 10.96 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.42), residues: 393 helix: 2.17 (0.44), residues: 130 sheet: -0.08 (0.44), residues: 102 loop : 0.01 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 487 HIS 0.003 0.001 HIS D 511 PHE 0.020 0.003 PHE D 505 TYR 0.015 0.002 TYR D 195 ARG 0.010 0.001 ARG D 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.442 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 1.6018 time to fit residues: 109.8506 Evaluate side-chains 72 residues out of total 374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 768 SER Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 ASN C 60 ASN C 62 GLN D 177 GLN D 216 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.100814 restraints weight = 3057.992| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.33 r_work: 0.2899 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3317 Z= 0.222 Angle : 0.506 5.184 4477 Z= 0.267 Chirality : 0.038 0.125 519 Planarity : 0.004 0.031 566 Dihedral : 4.688 24.657 430 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.94 % Allowed : 10.70 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.42), residues: 393 helix: 2.37 (0.45), residues: 130 sheet: -0.02 (0.45), residues: 102 loop : 0.04 (0.52), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 487 HIS 0.002 0.001 HIS C 68 PHE 0.014 0.002 PHE D 505 TYR 0.012 0.002 TYR D 195 ARG 0.010 0.001 ARG D 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.34 seconds wall clock time: 38 minutes 24.32 seconds (2304.32 seconds total)