Starting phenix.real_space_refine on Wed Jul 23 12:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh3_14720/07_2025/7zh3_14720.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh3_14720/07_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_14720/07_2025/7zh3_14720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh3_14720/07_2025/7zh3_14720.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh3_14720/07_2025/7zh3_14720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh3_14720/07_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-5711/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: 3.15, per 1000 atoms: 0.95 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: 0.77 Conformation dependent library (CDL) restraints added in 407.9 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: 0.46 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: 0.94 Time building geometry restraints manager: 0.93 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: 2.290 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.050 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 0.103 3321 Z= 0.424 Angle : 0.846 8.273 4483 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 Details of bonding type rmsd hydrogen bonds : bond 0.13752 ( 175) hydrogen bonds : angle 6.01219 ( 489) metal coordination : bond 0.06860 ( 4) metal coordination : angle 2.39840 ( 6) covalent geometry : bond 0.00990 ( 3317) covalent geometry : angle 0.84196 ( 4477) *********************** 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 : 0.380 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: 1.6410 time to fit residues: 114.0065 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 : 0.403 ------------------------------------------------------------------------------- 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: 0.0000 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: 0.5584 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.129465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.103802 restraints weight = 2987.027| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.34 r_work: 0.2929 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3321 Z= 0.108 Angle : 0.487 5.122 4483 Z= 0.258 Chirality : 0.038 0.130 519 Planarity : 0.004 0.034 566 Dihedral : 5.131 33.397 432 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.60 % Allowed : 6.68 % 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: 1.51 (0.46), residues: 130 sheet: -0.35 (0.44), residues: 104 loop : -0.44 (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 0.007 0.001 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 175) hydrogen bonds : angle 4.14576 ( 489) metal coordination : bond 0.00441 ( 4) metal coordination : angle 2.40533 ( 6) covalent geometry : bond 0.00235 ( 3317) covalent geometry : angle 0.47925 ( 4477) *********************** 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 73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: D 158 GLN cc_start: 0.8336 (mt0) cc_final: 0.7971 (mt0) REVERT: D 424 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: D 565 GLU cc_start: 0.8554 (tt0) cc_final: 0.8234 (tt0) outliers start: 6 outliers final: 3 residues processed: 67 average time/residue: 1.5286 time to fit residues: 104.8318 Evaluate side-chains 64 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 772 SER 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: 1.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.127970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.102525 restraints weight = 2998.180| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.31 r_work: 0.2930 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3321 Z= 0.129 Angle : 0.490 4.739 4483 Z= 0.257 Chirality : 0.038 0.127 519 Planarity : 0.004 0.033 566 Dihedral : 4.940 31.089 432 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.87 % Allowed : 8.82 % Favored : 89.30 % 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: 0.80 (0.42), residues: 393 helix: 2.13 (0.46), residues: 130 sheet: -0.17 (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 0.009 0.002 TYR D 195 ARG 0.006 0.001 ARG D 450 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 175) hydrogen bonds : angle 4.02762 ( 489) metal coordination : bond 0.00387 ( 4) metal coordination : angle 2.07427 ( 6) covalent geometry : bond 0.00290 ( 3317) covalent geometry : angle 0.48492 ( 4477) *********************** 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 72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: D 565 GLU cc_start: 0.8489 (tt0) cc_final: 0.8090 (tt0) REVERT: D 764 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7391 (mm) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 1.5372 time to fit residues: 103.9241 Evaluate side-chains 71 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN C 62 GLN D 177 GLN D 216 GLN D 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.128984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103306 restraints weight = 3021.118| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.33 r_work: 0.2919 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3321 Z= 0.117 Angle : 0.471 5.082 4483 Z= 0.246 Chirality : 0.037 0.128 519 Planarity : 0.003 0.031 566 Dihedral : 4.505 24.946 430 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.94 % Allowed : 9.09 % 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: 1.05 (0.42), residues: 393 helix: 2.42 (0.45), residues: 130 sheet: -0.06 (0.44), residues: 104 loop : -0.16 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 487 HIS 0.002 0.001 HIS D 511 PHE 0.011 0.001 PHE D 505 TYR 0.008 0.001 TYR D 195 ARG 0.008 0.001 ARG D 450 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 175) hydrogen bonds : angle 3.90686 ( 489) metal coordination : bond 0.00359 ( 4) metal coordination : angle 2.08327 ( 6) covalent geometry : bond 0.00265 ( 3317) covalent geometry : angle 0.46496 ( 4477) *********************** 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 73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.422 Fit side-chains REVERT: D 158 GLN cc_start: 0.8337 (mt0) cc_final: 0.7978 (mt0) REVERT: D 565 GLU cc_start: 0.8521 (tt0) cc_final: 0.8119 (tt0) REVERT: D 756 LYS cc_start: 0.8225 (mmpt) cc_final: 0.7434 (mtmm) REVERT: D 758 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7203 (p) REVERT: D 764 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7278 (mm) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 1.7185 time to fit residues: 116.5469 Evaluate side-chains 71 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 495 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.125334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.099669 restraints weight = 3145.114| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.33 r_work: 0.2901 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3321 Z= 0.189 Angle : 0.540 5.745 4483 Z= 0.279 Chirality : 0.040 0.126 519 Planarity : 0.004 0.033 566 Dihedral : 4.812 25.922 430 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.94 % Allowed : 9.89 % 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: 0.95 (0.42), residues: 393 helix: 2.26 (0.45), residues: 130 sheet: -0.04 (0.44), residues: 102 loop : -0.18 (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 0.017 0.002 PHE D 505 TYR 0.013 0.002 TYR D 195 ARG 0.008 0.001 ARG D 450 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 175) hydrogen bonds : angle 4.12472 ( 489) metal coordination : bond 0.00464 ( 4) metal coordination : angle 2.19306 ( 6) covalent geometry : bond 0.00438 ( 3317) covalent geometry : angle 0.53431 ( 4477) *********************** 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 76 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.400 Fit side-chains REVERT: D 756 LYS cc_start: 0.8185 (mmpt) cc_final: 0.7373 (mtmm) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 2.1909 time to fit residues: 152.4691 Evaluate side-chains 75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.125814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.100164 restraints weight = 3196.934| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.34 r_work: 0.2902 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3321 Z= 0.175 Angle : 0.527 5.607 4483 Z= 0.273 Chirality : 0.039 0.125 519 Planarity : 0.004 0.033 566 Dihedral : 4.791 26.227 430 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.01 % Allowed : 9.36 % 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: 1.02 (0.42), residues: 393 helix: 2.30 (0.45), residues: 130 sheet: -0.07 (0.44), residues: 104 loop : -0.07 (0.52), residues: 159 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 0.013 0.002 TYR D 195 ARG 0.010 0.001 ARG D 450 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 175) hydrogen bonds : angle 4.10490 ( 489) metal coordination : bond 0.00449 ( 4) metal coordination : angle 2.24535 ( 6) covalent geometry : bond 0.00404 ( 3317) covalent geometry : angle 0.52067 ( 4477) *********************** 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 80 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.421 Fit side-chains REVERT: C 54 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8572 (mmm-85) REVERT: D 450 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7763 (mtp85) REVERT: D 756 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7378 (mtmm) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 2.1431 time to fit residues: 153.8506 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 : 0.697 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.126843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.101171 restraints weight = 3100.639| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.34 r_work: 0.2913 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3321 Z= 0.151 Angle : 0.501 5.017 4483 Z= 0.261 Chirality : 0.038 0.125 519 Planarity : 0.004 0.032 566 Dihedral : 4.684 25.424 430 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.89 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: 1.08 (0.42), residues: 393 helix: 2.41 (0.45), residues: 130 sheet: -0.09 (0.44), residues: 104 loop : -0.05 (0.52), 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 0.011 0.002 TYR D 195 ARG 0.007 0.001 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 175) hydrogen bonds : angle 4.03053 ( 489) metal coordination : bond 0.00409 ( 4) metal coordination : angle 2.13267 ( 6) covalent geometry : bond 0.00344 ( 3317) covalent geometry : angle 0.49531 ( 4477) *********************** 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 77 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.802 Fit side-chains REVERT: C 54 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8538 (mmm-85) REVERT: D 450 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7702 (mtp85) REVERT: D 526 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8136 (mm-30) REVERT: D 565 GLU cc_start: 0.8539 (tt0) cc_final: 0.8262 (tt0) REVERT: D 756 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7348 (mtmm) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 2.7268 time to fit residues: 193.3529 Evaluate side-chains 75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 = 0.128323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.102812 restraints weight = 3065.814| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.32 r_work: 0.2923 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3321 Z= 0.115 Angle : 0.462 4.374 4483 Z= 0.243 Chirality : 0.037 0.127 519 Planarity : 0.003 0.031 566 Dihedral : 4.443 22.555 430 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.48 % Allowed : 9.89 % 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: 1.22 (0.43), residues: 393 helix: 2.60 (0.45), residues: 130 sheet: -0.04 (0.44), residues: 104 loop : -0.03 (0.52), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 0.008 0.001 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 175) hydrogen bonds : angle 3.88087 ( 489) metal coordination : bond 0.00366 ( 4) metal coordination : angle 2.06198 ( 6) covalent geometry : bond 0.00260 ( 3317) covalent geometry : angle 0.45634 ( 4477) *********************** 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: 13 poor density : 65 time to evaluate : 0.387 Fit side-chains REVERT: D 450 ARG cc_start: 0.8247 (mtt90) cc_final: 0.7705 (mtp85) REVERT: D 523 LYS cc_start: 0.8475 (tttt) cc_final: 0.8267 (tttt) REVERT: D 565 GLU cc_start: 0.8567 (tt0) cc_final: 0.8336 (tt0) REVERT: D 756 LYS cc_start: 0.8188 (mmpt) cc_final: 0.7375 (mtmm) REVERT: D 758 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7214 (p) outliers start: 13 outliers final: 10 residues processed: 70 average time/residue: 1.5993 time to fit residues: 114.6600 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 : 0.430 ------------------------------------------------------------------------------- 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 115 ILE Chi-restraints excluded: chain D residue 424 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 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: 8.9990 chunk 11 optimal weight: 0.0050 chunk 4 optimal weight: 3.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.127991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102402 restraints weight = 3087.875| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.32 r_work: 0.2935 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3321 Z= 0.121 Angle : 0.471 4.316 4483 Z= 0.248 Chirality : 0.037 0.126 519 Planarity : 0.004 0.034 566 Dihedral : 4.428 21.242 430 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 : 2.67 % Allowed : 11.76 % Favored : 85.56 % 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: 1.23 (0.42), residues: 393 helix: 2.58 (0.45), residues: 130 sheet: -0.02 (0.45), residues: 104 loop : -0.00 (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 0.012 0.002 PHE D 505 TYR 0.009 0.001 TYR D 195 ARG 0.008 0.001 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 175) hydrogen bonds : angle 3.90290 ( 489) metal coordination : bond 0.00352 ( 4) metal coordination : angle 2.01780 ( 6) covalent geometry : bond 0.00274 ( 3317) covalent geometry : angle 0.46534 ( 4477) *********************** 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 75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.448 Fit side-chains REVERT: C 51 GLU cc_start: 0.8341 (mt-10) cc_final: 0.6851 (mm-30) REVERT: D 450 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7673 (mtp85) REVERT: D 565 GLU cc_start: 0.8564 (tt0) cc_final: 0.8321 (tt0) REVERT: D 756 LYS cc_start: 0.8174 (mmpt) cc_final: 0.7335 (mtmm) REVERT: D 758 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7232 (p) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 1.6883 time to fit residues: 117.7321 Evaluate side-chains 75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.128543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.103112 restraints weight = 3030.621| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.31 r_work: 0.2943 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3321 Z= 0.115 Angle : 0.477 6.168 4483 Z= 0.249 Chirality : 0.037 0.127 519 Planarity : 0.003 0.034 566 Dihedral : 4.367 19.788 430 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.41 % Allowed : 12.03 % Favored : 85.56 % 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: 2.55 (0.45), residues: 130 sheet: 0.09 (0.45), residues: 102 loop : -0.02 (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 0.011 0.001 PHE D 505 TYR 0.009 0.001 TYR D 195 ARG 0.008 0.001 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 175) hydrogen bonds : angle 3.88086 ( 489) metal coordination : bond 0.00346 ( 4) metal coordination : angle 2.00678 ( 6) covalent geometry : bond 0.00261 ( 3317) covalent geometry : angle 0.47149 ( 4477) ********************** 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 : 1.225 Fit side-chains REVERT: C 51 GLU cc_start: 0.8235 (mt-10) cc_final: 0.6754 (mm-30) REVERT: D 450 ARG cc_start: 0.8276 (mtt90) cc_final: 0.7683 (mtp85) REVERT: D 526 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8129 (mm-30) REVERT: D 565 GLU cc_start: 0.8556 (tt0) cc_final: 0.8307 (tt0) REVERT: D 756 LYS cc_start: 0.8163 (mmpt) cc_final: 0.7334 (mtmm) REVERT: D 758 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7205 (p) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 2.7442 time to fit residues: 191.9270 Evaluate side-chains 72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.127235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101584 restraints weight = 3090.547| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.33 r_work: 0.2919 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3321 Z= 0.145 Angle : 0.517 5.161 4483 Z= 0.272 Chirality : 0.038 0.125 519 Planarity : 0.004 0.035 566 Dihedral : 4.520 20.401 430 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 12.03 % Favored : 85.56 % 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: 2.36 (0.45), residues: 130 sheet: 0.05 (0.45), residues: 102 loop : -0.03 (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 C 68 PHE 0.014 0.002 PHE D 505 TYR 0.010 0.002 TYR D 195 ARG 0.008 0.001 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 175) hydrogen bonds : angle 4.00829 ( 489) metal coordination : bond 0.00379 ( 4) metal coordination : angle 1.99794 ( 6) covalent geometry : bond 0.00330 ( 3317) covalent geometry : angle 0.51265 ( 4477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.67 seconds wall clock time: 73 minutes 58.12 seconds (4438.12 seconds total)