Starting phenix.real_space_refine on Tue Mar 3 11:32:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4b_31706/03_2026/7v4b_31706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4b_31706/03_2026/7v4b_31706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2026/7v4b_31706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2026/7v4b_31706.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2026/7v4b_31706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2026/7v4b_31706.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 3 Type Number sf(0) Gaussians C 2076 2.51 5 N 588 2.21 5 O 672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3336 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 556 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Restraints were copied for chains: C, D, E, A, B Time building chain proxies: 0.54, per 1000 atoms: 0.16 Number of scatterers: 3336 At special positions: 0 Unit cell: (75.26, 160.06, 33.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 672 8.00 N 588 7.00 C 2076 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: 0.26 Conformation dependent library (CDL) restraints added in 157.4 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 19 through 20 removed outlier: 6.737A pdb=" N ALA F 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'F' and resid 46 through 55 removed outlier: 6.988A pdb=" N VAL C 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA F 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR C 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL F 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 61 through 62 Processing sheet with id=AA5, first strand: chain 'F' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 70 through 72 removed outlier: 6.050A pdb=" N VAL F 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 75 through 79 removed outlier: 6.333A pdb=" N THR F 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA C 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL F 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 85 through 88 removed outlier: 6.182A pdb=" N ALA C 85 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE D 88 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 91 through 93 removed outlier: 6.491A pdb=" N ALA F 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 19 through 20 removed outlier: 6.741A pdb=" N ALA E 19 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'E' and resid 46 through 55 removed outlier: 6.982A pdb=" N VAL A 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA E 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N THR A 54 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL E 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA A 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 61 through 62 Processing sheet with id=AB5, first strand: chain 'E' and resid 65 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.042A pdb=" N VAL E 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.343A pdb=" N THR E 75 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ALA A 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL E 77 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR A 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA B 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.195A pdb=" N ALA E 85 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 87 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A 85 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE B 88 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A 87 " --> pdb=" O ILE B 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 93 removed outlier: 6.486A pdb=" N ALA E 91 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 35 hydrogen bonds defined for protein. 105 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: 0.44 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 594 1.29 - 1.35: 512 1.35 - 1.42: 106 1.42 - 1.48: 540 1.48 - 1.55: 1590 Bond restraints: 3342 Sorted by residual: bond pdb=" CA GLN D 62 " pdb=" CB GLN D 62 " ideal model delta sigma weight residual 1.532 1.516 0.016 1.62e-02 3.81e+03 1.03e+00 bond pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " ideal model delta sigma weight residual 1.532 1.516 0.016 1.62e-02 3.81e+03 1.02e+00 bond pdb=" CA GLN A 62 " pdb=" CB GLN A 62 " ideal model delta sigma weight residual 1.532 1.516 0.016 1.62e-02 3.81e+03 9.59e-01 bond pdb=" CA GLN B 62 " pdb=" CB GLN B 62 " ideal model delta sigma weight residual 1.532 1.516 0.016 1.62e-02 3.81e+03 9.52e-01 bond pdb=" CA GLN E 62 " pdb=" CB GLN E 62 " ideal model delta sigma weight residual 1.532 1.517 0.015 1.62e-02 3.81e+03 9.13e-01 ... (remaining 3337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.66: 3598 0.66 - 1.32: 668 1.32 - 1.98: 174 1.98 - 2.64: 34 2.64 - 3.30: 14 Bond angle restraints: 4488 Sorted by residual: angle pdb=" N GLU A 83 " pdb=" CA GLU A 83 " pdb=" C GLU A 83 " ideal model delta sigma weight residual 109.86 107.49 2.37 1.55e+00 4.16e-01 2.34e+00 angle pdb=" N GLU C 83 " pdb=" CA GLU C 83 " pdb=" C GLU C 83 " ideal model delta sigma weight residual 109.86 107.53 2.33 1.55e+00 4.16e-01 2.27e+00 angle pdb=" N GLU E 83 " pdb=" CA GLU E 83 " pdb=" C GLU E 83 " ideal model delta sigma weight residual 109.86 107.54 2.32 1.55e+00 4.16e-01 2.25e+00 angle pdb=" N GLU F 83 " pdb=" CA GLU F 83 " pdb=" C GLU F 83 " ideal model delta sigma weight residual 109.86 107.54 2.32 1.55e+00 4.16e-01 2.24e+00 angle pdb=" N GLU B 83 " pdb=" CA GLU B 83 " pdb=" C GLU B 83 " ideal model delta sigma weight residual 109.86 107.55 2.31 1.55e+00 4.16e-01 2.22e+00 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1788 17.91 - 35.81: 180 35.81 - 53.72: 6 53.72 - 71.62: 6 71.62 - 89.53: 6 Dihedral angle restraints: 1986 sinusoidal: 696 harmonic: 1290 Sorted by residual: dihedral pdb=" CA ILE B 88 " pdb=" C ILE B 88 " pdb=" N ALA B 89 " pdb=" CA ALA B 89 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE F 88 " pdb=" C ILE F 88 " pdb=" N ALA F 89 " pdb=" CA ALA F 89 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " pdb=" CA ALA A 89 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 1983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 267 0.027 - 0.053: 161 0.053 - 0.079: 64 0.079 - 0.105: 69 0.105 - 0.132: 15 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA VAL F 48 " pdb=" N VAL F 48 " pdb=" C VAL F 48 " pdb=" CB VAL F 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL D 48 " pdb=" N VAL D 48 " pdb=" C VAL D 48 " pdb=" CB VAL D 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA VAL B 48 " pdb=" N VAL B 48 " pdb=" C VAL B 48 " pdb=" CB VAL B 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 573 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 58 " -0.004 2.00e-02 2.50e+03 7.60e-03 5.77e-01 pdb=" C LYS C 58 " 0.013 2.00e-02 2.50e+03 pdb=" O LYS C 58 " -0.005 2.00e-02 2.50e+03 pdb=" N THR C 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 58 " -0.004 2.00e-02 2.50e+03 7.51e-03 5.64e-01 pdb=" C LYS D 58 " 0.013 2.00e-02 2.50e+03 pdb=" O LYS D 58 " -0.005 2.00e-02 2.50e+03 pdb=" N THR D 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 58 " 0.004 2.00e-02 2.50e+03 7.42e-03 5.50e-01 pdb=" C LYS B 58 " -0.013 2.00e-02 2.50e+03 pdb=" O LYS B 58 " 0.005 2.00e-02 2.50e+03 pdb=" N THR B 59 " 0.004 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1279 2.88 - 3.38: 3017 3.38 - 3.89: 5374 3.89 - 4.39: 5238 4.39 - 4.90: 10909 Nonbonded interactions: 25817 Sorted by model distance: nonbonded pdb=" O THR C 81 " pdb=" OG1 THR D 81 " model vdw 2.375 3.040 nonbonded pdb=" O THR A 81 " pdb=" OG1 THR B 81 " model vdw 2.382 3.040 nonbonded pdb=" O THR E 81 " pdb=" OG1 THR A 81 " model vdw 2.417 3.040 nonbonded pdb=" O THR F 81 " pdb=" OG1 THR C 81 " model vdw 2.428 3.040 nonbonded pdb=" OG1 THR C 81 " pdb=" N VAL C 82 " model vdw 2.473 3.120 ... (remaining 25812 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: 0.01 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'A' selection = chain 'B' } 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: 7.440 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.380 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 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 : 0.006 0.029 3342 Z= 0.271 Angle : 0.597 3.295 4488 Z= 0.350 Chirality : 0.049 0.132 576 Planarity : 0.002 0.008 558 Dihedral : 14.552 89.530 1170 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.99 (0.24), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.18), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR C 39 PHE 0.008 0.003 PHE D 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00561 ( 3342) covalent geometry : angle 0.59675 ( 4488) hydrogen bonds : bond 0.19030 ( 35) hydrogen bonds : angle 7.47754 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.112 Fit side-chains REVERT: C 46 GLU cc_start: 0.6650 (pm20) cc_final: 0.6310 (pm20) REVERT: E 44 THR cc_start: 0.8074 (p) cc_final: 0.7846 (p) REVERT: A 46 GLU cc_start: 0.7258 (pm20) cc_final: 0.6981 (pm20) REVERT: B 57 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7965 (mt-10) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0336 time to fit residues: 2.8030 Evaluate side-chains 48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN C 50 HIS C 79 GLN D 50 HIS D 79 GLN E 79 GLN A 50 HIS A 79 GLN B 50 HIS B 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.222668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.193553 restraints weight = 4998.535| |-----------------------------------------------------------------------------| r_work (start): 0.4793 rms_B_bonded: 4.02 r_work: 0.4682 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3342 Z= 0.202 Angle : 0.551 5.094 4488 Z= 0.316 Chirality : 0.046 0.133 576 Planarity : 0.002 0.008 558 Dihedral : 5.568 20.510 474 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 2.08 % Allowed : 15.18 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.57 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR E 39 PHE 0.010 0.002 PHE A 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 3342) covalent geometry : angle 0.55084 ( 4488) hydrogen bonds : bond 0.02746 ( 35) hydrogen bonds : angle 5.33654 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.128 Fit side-chains REVERT: B 57 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8414 (mt-10) outliers start: 7 outliers final: 7 residues processed: 54 average time/residue: 0.0355 time to fit residues: 2.8434 Evaluate side-chains 52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 47 optimal weight: 0.0020 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5112 r_free = 0.5112 target = 0.229445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.200962 restraints weight = 4893.960| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 3.94 r_work: 0.4749 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3342 Z= 0.124 Angle : 0.454 3.083 4488 Z= 0.265 Chirality : 0.045 0.124 576 Planarity : 0.002 0.006 558 Dihedral : 5.002 18.854 474 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.79 % Allowed : 19.05 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 39 PHE 0.007 0.002 PHE A 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3342) covalent geometry : angle 0.45421 ( 4488) hydrogen bonds : bond 0.02542 ( 35) hydrogen bonds : angle 5.06973 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.089 Fit side-chains REVERT: B 57 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8362 (mt-10) outliers start: 6 outliers final: 5 residues processed: 53 average time/residue: 0.0323 time to fit residues: 2.3707 Evaluate side-chains 49 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.227553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.198562 restraints weight = 4855.945| |-----------------------------------------------------------------------------| r_work (start): 0.4853 rms_B_bonded: 3.95 r_work: 0.4741 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3342 Z= 0.140 Angle : 0.464 4.442 4488 Z= 0.270 Chirality : 0.045 0.130 576 Planarity : 0.002 0.011 558 Dihedral : 4.998 17.988 474 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 4.76 % Allowed : 18.45 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.24 (0.26), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR F 39 PHE 0.009 0.002 PHE C 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 3342) covalent geometry : angle 0.46442 ( 4488) hydrogen bonds : bond 0.02380 ( 35) hydrogen bonds : angle 5.04394 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.131 Fit side-chains REVERT: B 57 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8379 (mt-10) outliers start: 16 outliers final: 15 residues processed: 61 average time/residue: 0.0338 time to fit residues: 3.0316 Evaluate side-chains 60 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 41 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.219385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.190687 restraints weight = 4932.437| |-----------------------------------------------------------------------------| r_work (start): 0.4769 rms_B_bonded: 3.91 r_work: 0.4660 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3342 Z= 0.346 Angle : 0.722 4.500 4488 Z= 0.414 Chirality : 0.048 0.175 576 Planarity : 0.003 0.011 558 Dihedral : 6.228 23.225 474 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.89 % Favored : 83.11 % Rotamer: Outliers : 9.23 % Allowed : 16.67 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.26), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.97 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR E 39 PHE 0.025 0.005 PHE A 94 HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 3342) covalent geometry : angle 0.72235 ( 4488) hydrogen bonds : bond 0.03285 ( 35) hydrogen bonds : angle 6.10944 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.109 Fit side-chains REVERT: E 57 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8089 (mp0) REVERT: B 57 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8400 (mt-10) REVERT: B 61 GLU cc_start: 0.7561 (mp0) cc_final: 0.6336 (mp0) outliers start: 31 outliers final: 27 residues processed: 74 average time/residue: 0.0329 time to fit residues: 3.4736 Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5166 r_free = 0.5166 target = 0.229293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.201129 restraints weight = 4861.266| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 3.84 r_work: 0.4784 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3342 Z= 0.124 Angle : 0.476 4.956 4488 Z= 0.277 Chirality : 0.045 0.127 576 Planarity : 0.002 0.007 558 Dihedral : 5.135 17.697 474 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 6.85 % Allowed : 19.64 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.12 (0.26), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR F 39 PHE 0.008 0.002 PHE D 94 HIS 0.001 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3342) covalent geometry : angle 0.47585 ( 4488) hydrogen bonds : bond 0.03009 ( 35) hydrogen bonds : angle 5.40042 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.127 Fit side-chains REVERT: D 80 LYS cc_start: 0.7825 (mttp) cc_final: 0.7597 (tmtt) REVERT: E 57 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7795 (mp0) REVERT: B 57 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8368 (mt-10) REVERT: B 61 GLU cc_start: 0.7492 (mp0) cc_final: 0.6363 (mp0) outliers start: 23 outliers final: 19 residues processed: 65 average time/residue: 0.0317 time to fit residues: 2.9588 Evaluate side-chains 65 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.233434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.204565 restraints weight = 5001.018| |-----------------------------------------------------------------------------| r_work (start): 0.4933 rms_B_bonded: 4.02 r_work: 0.4820 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3342 Z= 0.093 Angle : 0.423 4.805 4488 Z= 0.246 Chirality : 0.045 0.124 576 Planarity : 0.002 0.010 558 Dihedral : 4.427 15.060 474 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 4.76 % Allowed : 22.02 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.03 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR F 39 PHE 0.009 0.002 PHE A 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 3342) covalent geometry : angle 0.42287 ( 4488) hydrogen bonds : bond 0.02833 ( 35) hydrogen bonds : angle 4.91618 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.149 Fit side-chains REVERT: E 57 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7651 (mp0) REVERT: B 57 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8338 (mt-10) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.0263 time to fit residues: 2.3761 Evaluate side-chains 64 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 45 optimal weight: 0.0470 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.227541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.198498 restraints weight = 4989.024| |-----------------------------------------------------------------------------| r_work (start): 0.4858 rms_B_bonded: 3.96 r_work: 0.4741 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3342 Z= 0.157 Angle : 0.490 4.631 4488 Z= 0.281 Chirality : 0.045 0.137 576 Planarity : 0.002 0.006 558 Dihedral : 4.964 17.536 474 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 5.65 % Allowed : 21.43 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.96 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR F 39 PHE 0.011 0.003 PHE D 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3342) covalent geometry : angle 0.48989 ( 4488) hydrogen bonds : bond 0.02882 ( 35) hydrogen bonds : angle 5.34477 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.113 Fit side-chains REVERT: C 57 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8050 (mp0) REVERT: E 57 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7854 (mp0) REVERT: B 57 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 61 GLU cc_start: 0.7496 (mp0) cc_final: 0.6347 (mp0) outliers start: 19 outliers final: 18 residues processed: 66 average time/residue: 0.0432 time to fit residues: 3.7828 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5179 r_free = 0.5179 target = 0.226814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.198742 restraints weight = 5107.677| |-----------------------------------------------------------------------------| r_work (start): 0.4915 rms_B_bonded: 3.89 r_work: 0.4805 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3342 Z= 0.180 Angle : 0.543 6.171 4488 Z= 0.307 Chirality : 0.046 0.138 576 Planarity : 0.002 0.026 558 Dihedral : 5.146 19.009 474 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 5.65 % Allowed : 21.43 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.95 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR F 39 PHE 0.022 0.004 PHE A 94 HIS 0.002 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3342) covalent geometry : angle 0.54297 ( 4488) hydrogen bonds : bond 0.03234 ( 35) hydrogen bonds : angle 5.57631 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.139 Fit side-chains REVERT: E 57 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7910 (mp0) REVERT: B 43 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8345 (tppt) REVERT: B 57 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 61 GLU cc_start: 0.7460 (mp0) cc_final: 0.6296 (mp0) outliers start: 19 outliers final: 18 residues processed: 69 average time/residue: 0.0482 time to fit residues: 4.3722 Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 45 optimal weight: 0.0040 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.229189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.200760 restraints weight = 5065.014| |-----------------------------------------------------------------------------| r_work (start): 0.4936 rms_B_bonded: 3.93 r_work: 0.4829 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3342 Z= 0.140 Angle : 0.528 8.680 4488 Z= 0.293 Chirality : 0.045 0.129 576 Planarity : 0.002 0.026 558 Dihedral : 4.784 17.261 474 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 5.36 % Allowed : 22.92 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR F 39 PHE 0.019 0.003 PHE A 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3342) covalent geometry : angle 0.52850 ( 4488) hydrogen bonds : bond 0.03069 ( 35) hydrogen bonds : angle 5.33591 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.140 Fit side-chains REVERT: C 57 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8075 (mp0) REVERT: E 57 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7848 (mp0) REVERT: B 43 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8321 (tppt) REVERT: B 57 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8290 (mt-10) REVERT: B 61 GLU cc_start: 0.7450 (mp0) cc_final: 0.6305 (mp0) outliers start: 18 outliers final: 18 residues processed: 64 average time/residue: 0.0425 time to fit residues: 3.7364 Evaluate side-chains 65 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 0.0060 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 overall best weight: 1.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5199 r_free = 0.5199 target = 0.228479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.200776 restraints weight = 5148.045| |-----------------------------------------------------------------------------| r_work (start): 0.4931 rms_B_bonded: 3.97 r_work: 0.4822 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3342 Z= 0.154 Angle : 0.543 8.523 4488 Z= 0.297 Chirality : 0.046 0.133 576 Planarity : 0.002 0.027 558 Dihedral : 4.854 17.167 474 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 5.36 % Allowed : 22.92 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.85 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR F 39 PHE 0.019 0.003 PHE A 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3342) covalent geometry : angle 0.54266 ( 4488) hydrogen bonds : bond 0.03218 ( 35) hydrogen bonds : angle 5.36668 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1170.26 seconds wall clock time: 20 minutes 41.12 seconds (1241.12 seconds total)