Starting phenix.real_space_refine on Mon Feb 10 23:56:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh3_14720/02_2025/7zh3_14720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh3_14720/02_2025/7zh3_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/cci-nas-00/data/ceres_data/7zh3_14720/02_2025/7zh3_14720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh3_14720/02_2025/7zh3_14720.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh3_14720/02_2025/7zh3_14720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh3_14720/02_2025/7zh3_14720.cif" } 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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3301 Number of models: 1 Model: "" Number of chains: 5 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: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2655 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 5 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: 3.44, per 1000 atoms: 1.04 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 - 3.00 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 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 353.7 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: 0.50 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: 1.05 Time building geometry restraints manager: 0.88 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: 0.00 - 1.65: 4226 1.65 - 3.31: 214 3.31 - 4.96: 29 4.96 - 6.62: 6 6.62 - 8.27: 2 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 3.040 nonbonded pdb=" O ALA C 46 " pdb=" O HOH C 101 " model vdw 2.270 3.040 nonbonded pdb=" NZ LYS C 33 " pdb=" OD1 ASP D 502 " model vdw 2.298 3.120 nonbonded pdb=" O LEU C 73 " pdb=" OH TYR D 594 " model vdw 2.306 3.040 nonbonded pdb=" O HOH D1131 " pdb=" O HOH D1132 " model vdw 2.329 3.040 ... (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 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 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: 1.560 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.730 Find NCS groups from input model: 0.030 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:11.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.389 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: 1.6982 time to fit residues: 117.9963 Evaluate side-chains 62 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.102706 restraints weight = 2998.464| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.35 r_work: 0.2920 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3317 Z= 0.159 Angle : 0.483 5.098 4477 Z= 0.260 Chirality : 0.038 0.131 519 Planarity : 0.004 0.034 566 Dihedral : 5.153 33.409 432 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 0.28 (0.41), residues: 393 helix: 1.50 (0.46), residues: 130 sheet: -0.35 (0.44), residues: 104 loop : -0.43 (0.50), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.003 0.001 HIS C 68 PHE 0.009 0.001 PHE D 453 TYR 0.010 0.002 TYR D 195 ARG 0.007 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 72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: D 424 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: D 565 GLU cc_start: 0.8569 (tt0) cc_final: 0.8247 (tt0) outliers start: 5 outliers final: 2 residues processed: 67 average time/residue: 1.7196 time to fit residues: 117.9540 Evaluate side-chains 66 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 424 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.102038 restraints weight = 3001.794| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.31 r_work: 0.2921 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3317 Z= 0.205 Angle : 0.497 4.923 4477 Z= 0.263 Chirality : 0.038 0.127 519 Planarity : 0.004 0.034 566 Dihedral : 4.995 31.448 432 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.14 % Allowed : 8.29 % 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: 0.79 (0.42), residues: 393 helix: 2.12 (0.46), residues: 130 sheet: -0.17 (0.44), residues: 104 loop : -0.23 (0.51), residues: 159 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 0.009 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 73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: D 158 GLN cc_start: 0.8361 (mt0) cc_final: 0.7996 (mt0) REVERT: D 565 GLU cc_start: 0.8515 (tt0) cc_final: 0.8108 (tt0) REVERT: D 764 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7364 (mm) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 1.5989 time to fit residues: 109.7046 Evaluate side-chains 70 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 772 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.130081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.104348 restraints weight = 3008.945| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.35 r_work: 0.2938 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3317 Z= 0.146 Angle : 0.443 5.074 4477 Z= 0.235 Chirality : 0.037 0.129 519 Planarity : 0.003 0.030 566 Dihedral : 4.371 24.076 430 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.67 % Allowed : 9.36 % Favored : 87.97 % 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: 1.12 (0.43), residues: 393 helix: 2.52 (0.46), residues: 130 sheet: 0.01 (0.44), residues: 102 loop : -0.17 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 511 PHE 0.008 0.001 PHE D 505 TYR 0.007 0.001 TYR D 504 ARG 0.008 0.001 ARG D 450 *********************** 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 72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.323 Fit side-chains REVERT: D 158 GLN cc_start: 0.8398 (mt0) cc_final: 0.8039 (mt0) REVERT: D 424 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: D 565 GLU cc_start: 0.8499 (tt0) cc_final: 0.8107 (tt0) REVERT: D 756 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7442 (mtmm) REVERT: D 758 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7326 (p) REVERT: D 764 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7235 (mm) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 1.5585 time to fit residues: 105.2569 Evaluate side-chains 68 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 424 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.100301 restraints weight = 3128.851| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.34 r_work: 0.2895 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3317 Z= 0.290 Angle : 0.535 5.886 4477 Z= 0.279 Chirality : 0.040 0.126 519 Planarity : 0.004 0.033 566 Dihedral : 4.794 25.600 430 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.94 % Allowed : 10.16 % Favored : 86.90 % 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: 2.31 (0.46), residues: 130 sheet: -0.03 (0.44), residues: 102 loop : -0.17 (0.51), 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 0.017 0.002 PHE D 505 TYR 0.013 0.002 TYR D 195 ARG 0.007 0.001 ARG D 486 *********************** 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 77 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.386 Fit side-chains REVERT: C 54 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8546 (mmm-85) REVERT: D 450 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7710 (mtp85) REVERT: D 756 LYS cc_start: 0.8199 (mmpt) cc_final: 0.7397 (mtmm) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 1.5438 time to fit residues: 110.6114 Evaluate side-chains 75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 424 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.126757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100913 restraints weight = 3187.676| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.35 r_work: 0.2910 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3317 Z= 0.231 Angle : 0.497 5.039 4477 Z= 0.262 Chirality : 0.038 0.126 519 Planarity : 0.004 0.032 566 Dihedral : 4.679 25.258 430 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.48 % Allowed : 10.16 % 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: 1.08 (0.42), residues: 393 helix: 2.42 (0.45), residues: 130 sheet: -0.06 (0.44), residues: 104 loop : -0.10 (0.51), residues: 159 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 0.007 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 78 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.426 Fit side-chains REVERT: C 54 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8422 (mmm-85) REVERT: D 158 GLN cc_start: 0.8345 (mt0) cc_final: 0.7973 (mt0) REVERT: D 450 ARG cc_start: 0.8291 (mtt90) cc_final: 0.7717 (mtp85) REVERT: D 565 GLU cc_start: 0.8535 (tt0) cc_final: 0.8192 (tt0) REVERT: D 756 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7372 (mtmm) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 1.5823 time to fit residues: 111.7284 Evaluate side-chains 75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 115 ILE Chi-restraints excluded: chain D residue 424 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.128504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.102983 restraints weight = 3081.946| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.32 r_work: 0.2932 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3317 Z= 0.165 Angle : 0.450 4.314 4477 Z= 0.239 Chirality : 0.037 0.128 519 Planarity : 0.003 0.032 566 Dihedral : 4.413 22.407 430 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.21 % Allowed : 10.16 % 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: 1.25 (0.43), residues: 393 helix: 2.66 (0.45), residues: 130 sheet: 0.01 (0.45), residues: 104 loop : -0.07 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 511 PHE 0.010 0.001 PHE D 505 TYR 0.009 0.001 TYR D 504 ARG 0.007 0.001 ARG D 486 *********************** 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 76 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.403 Fit side-chains REVERT: D 450 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7728 (mtp85) REVERT: D 523 LYS cc_start: 0.8452 (tttt) cc_final: 0.8217 (tttt) REVERT: D 565 GLU cc_start: 0.8557 (tt0) cc_final: 0.8200 (tt0) REVERT: D 756 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7385 (mtmm) REVERT: D 758 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (p) outliers start: 12 outliers final: 9 residues processed: 70 average time/residue: 1.5776 time to fit residues: 112.9979 Evaluate side-chains 73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 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 115 ILE Chi-restraints excluded: chain D residue 424 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 11 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.102165 restraints weight = 3059.299| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.32 r_work: 0.2924 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1689 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= 0.197 Angle : 0.474 4.514 4477 Z= 0.251 Chirality : 0.037 0.128 519 Planarity : 0.003 0.031 566 Dihedral : 4.472 21.791 430 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.34 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: 1.25 (0.42), residues: 393 helix: 2.60 (0.45), residues: 130 sheet: 0.04 (0.45), residues: 104 loop : -0.04 (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 D 511 PHE 0.013 0.002 PHE D 505 TYR 0.010 0.002 TYR D 195 ARG 0.007 0.001 ARG D 486 *********************** 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 78 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.328 Fit side-chains REVERT: D 756 LYS cc_start: 0.8168 (mmpt) cc_final: 0.7363 (mtmm) REVERT: D 758 THR cc_start: 0.7615 (OUTLIER) cc_final: 0.7213 (p) outliers start: 12 outliers final: 9 residues processed: 70 average time/residue: 1.5599 time to fit residues: 111.6689 Evaluate side-chains 74 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 115 ILE Chi-restraints excluded: chain D residue 424 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 0.0060 chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.0020 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7006 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.102585 restraints weight = 3090.679| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.32 r_work: 0.2943 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3317 Z= 0.168 Angle : 0.467 6.619 4477 Z= 0.245 Chirality : 0.037 0.128 519 Planarity : 0.003 0.034 566 Dihedral : 4.342 20.249 430 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.67 % Allowed : 12.30 % Favored : 85.03 % 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: 1.31 (0.42), residues: 393 helix: 2.66 (0.45), residues: 130 sheet: 0.15 (0.46), residues: 102 loop : -0.08 (0.51), residues: 161 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 0.001 PHE D 505 TYR 0.009 0.001 TYR D 195 ARG 0.008 0.001 ARG D 486 *********************** 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 to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.311 Fit side-chains REVERT: C 51 GLU cc_start: 0.8147 (mt-10) cc_final: 0.6681 (mm-30) REVERT: D 450 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7879 (mtp85) REVERT: D 565 GLU cc_start: 0.8605 (tt0) cc_final: 0.8349 (tt0) REVERT: D 756 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7346 (mtmm) REVERT: D 758 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7322 (p) outliers start: 10 outliers final: 8 residues processed: 67 average time/residue: 1.5730 time to fit residues: 107.7240 Evaluate side-chains 72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 424 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.127883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.102285 restraints weight = 3045.104| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.32 r_work: 0.2925 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3317 Z= 0.200 Angle : 0.494 5.934 4477 Z= 0.259 Chirality : 0.038 0.127 519 Planarity : 0.003 0.034 566 Dihedral : 4.439 20.249 430 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.41 % Allowed : 12.30 % Favored : 85.29 % 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: 1.21 (0.42), residues: 393 helix: 2.51 (0.45), residues: 130 sheet: 0.09 (0.45), residues: 102 loop : -0.07 (0.50), residues: 161 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 0.008 0.001 ARG D 486 ********************** 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 73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.414 Fit side-chains REVERT: C 51 GLU cc_start: 0.8178 (mt-10) cc_final: 0.6699 (mm-30) REVERT: D 450 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7676 (mtp85) REVERT: D 526 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8131 (mm-30) REVERT: D 756 LYS cc_start: 0.8156 (mmpt) cc_final: 0.7333 (mtmm) REVERT: D 758 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.7202 (p) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 1.6330 time to fit residues: 111.9609 Evaluate side-chains 73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 424 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 D 454 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.102932 restraints weight = 3077.502| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.37 r_work: 0.2944 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3317 Z= 0.155 Angle : 0.464 5.808 4477 Z= 0.245 Chirality : 0.037 0.128 519 Planarity : 0.003 0.035 566 Dihedral : 4.261 18.253 430 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.67 % Allowed : 12.30 % Favored : 85.03 % 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: 1.30 (0.42), residues: 393 helix: 2.59 (0.45), residues: 130 sheet: 0.17 (0.46), residues: 102 loop : -0.04 (0.50), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 747 HIS 0.002 0.001 HIS D 511 PHE 0.009 0.001 PHE D 505 TYR 0.009 0.001 TYR D 504 ARG 0.008 0.001 ARG D 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.46 seconds wall clock time: 60 minutes 34.86 seconds (3634.86 seconds total)