Starting phenix.real_space_refine on Wed Mar 5 18:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v4b_31706/03_2025/7v4b_31706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v4b_31706/03_2025/7v4b_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_2025/7v4b_31706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2025/7v4b_31706.map" model { file = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2025/7v4b_31706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v4b_31706/03_2025/7v4b_31706.cif" } resolution = 3.1 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= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3336 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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, B, E, D, F Time building chain proxies: 2.89, per 1000 atoms: 0.87 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: 0.81 Conformation dependent library (CDL) restraints added in 459.9 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: 0.55 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: 0.78 Time building geometry restraints manager: 0.97 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 4.530 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- 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= 0.379 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 (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: -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 HIS 0.001 0.001 HIS C 50 PHE 0.008 0.003 PHE D 94 TYR 0.007 0.002 TYR C 39 *********************** 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 : 0.426 Fit side-chains REVERT: C 46 GLU cc_start: 0.6649 (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: 0.0917 time to fit residues: 7.5925 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.5072 r_free = 0.5072 target = 0.226195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.197654 restraints weight = 4911.325| |-----------------------------------------------------------------------------| r_work (start): 0.4827 rms_B_bonded: 3.93 r_work: 0.4717 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3342 Z= 0.225 Angle : 0.499 5.590 4488 Z= 0.286 Chirality : 0.046 0.129 576 Planarity : 0.002 0.008 558 Dihedral : 5.260 19.905 474 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.89 % Allowed : 13.99 % Favored : 85.12 % 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: -5.56 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.008 0.002 PHE A 94 TYR 0.010 0.002 TYR E 39 *********************** 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 52 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.378 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.0885 time to fit residues: 6.4336 Evaluate side-chains 48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain A residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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 = 0.5052 r_free = 0.5052 target = 0.222729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.193986 restraints weight = 4868.295| |-----------------------------------------------------------------------------| r_work (start): 0.4795 rms_B_bonded: 3.98 r_work: 0.4686 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3342 Z= 0.314 Angle : 0.560 3.403 4488 Z= 0.324 Chirality : 0.046 0.136 576 Planarity : 0.002 0.007 558 Dihedral : 5.646 20.421 474 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % Rotamer: Outliers : 3.87 % Allowed : 18.45 % Favored : 77.68 % 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: -5.37 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.016 0.003 PHE A 94 TYR 0.009 0.002 TYR F 39 *********************** 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 64 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.403 Fit side-chains outliers start: 13 outliers final: 13 residues processed: 61 average time/residue: 0.0862 time to fit residues: 7.6142 Evaluate side-chains 60 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 THR 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 D residue 37 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 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 11 optimal weight: 9.9990 chunk 16 optimal weight: 0.0770 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9498 ------------------------------------------------------------------------------- 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 = 0.5136 r_free = 0.5136 target = 0.230910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.202408 restraints weight = 4907.150| |-----------------------------------------------------------------------------| r_work (start): 0.4888 rms_B_bonded: 3.96 r_work: 0.4772 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3342 Z= 0.158 Angle : 0.433 3.068 4488 Z= 0.254 Chirality : 0.045 0.124 576 Planarity : 0.002 0.011 558 Dihedral : 4.880 18.347 474 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.17 % Allowed : 19.35 % Favored : 76.49 % 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: -5.23 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.010 0.002 PHE A 94 TYR 0.006 0.001 TYR E 39 *********************** 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 62 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.381 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.0798 time to fit residues: 6.7725 Evaluate side-chains 56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 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 5 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- 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 = 0.5138 r_free = 0.5138 target = 0.229974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.201353 restraints weight = 4921.197| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 4.01 r_work: 0.4760 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3342 Z= 0.178 Angle : 0.436 3.623 4488 Z= 0.254 Chirality : 0.045 0.128 576 Planarity : 0.002 0.008 558 Dihedral : 4.803 17.311 474 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 5.36 % Allowed : 19.94 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.26), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.011 0.002 PHE A 94 TYR 0.007 0.001 TYR F 39 *********************** 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 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.360 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 64 average time/residue: 0.1004 time to fit residues: 9.1296 Evaluate side-chains 61 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 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 44 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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 = 0.5100 r_free = 0.5100 target = 0.225425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.196874 restraints weight = 4978.134| |-----------------------------------------------------------------------------| r_work (start): 0.4807 rms_B_bonded: 3.97 r_work: 0.4701 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3342 Z= 0.316 Angle : 0.558 4.800 4488 Z= 0.321 Chirality : 0.046 0.141 576 Planarity : 0.002 0.008 558 Dihedral : 5.468 19.643 474 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 7.44 % Allowed : 19.05 % 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 (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: -5.12 (0.26), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.018 0.004 PHE A 94 TYR 0.009 0.002 TYR E 39 *********************** 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 76 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.405 Fit side-chains REVERT: D 80 LYS cc_start: 0.7822 (mttp) cc_final: 0.7554 (tmtt) REVERT: E 57 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7942 (mp0) REVERT: B 61 GLU cc_start: 0.7530 (mp0) cc_final: 0.6303 (mp0) outliers start: 25 outliers final: 23 residues processed: 72 average time/residue: 0.1039 time to fit residues: 10.4471 Evaluate side-chains 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 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 71 VAL Chi-restraints excluded: chain A residue 74 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.5162 r_free = 0.5162 target = 0.228715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.199922 restraints weight = 4869.644| |-----------------------------------------------------------------------------| r_work (start): 0.4880 rms_B_bonded: 3.97 r_work: 0.4763 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2767 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= 0.196 Angle : 0.464 4.435 4488 Z= 0.269 Chirality : 0.045 0.131 576 Planarity : 0.002 0.011 558 Dihedral : 4.989 17.305 474 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 6.55 % Allowed : 20.24 % 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 (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: -5.02 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.014 0.003 PHE A 94 TYR 0.007 0.001 TYR F 39 *********************** 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 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.353 Fit side-chains REVERT: E 57 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7868 (mp0) REVERT: B 61 GLU cc_start: 0.7461 (mp0) cc_final: 0.6317 (mp0) outliers start: 22 outliers final: 19 residues processed: 67 average time/residue: 0.0829 time to fit residues: 7.7960 Evaluate side-chains 69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 44 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 E residue 74 VAL 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 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 22 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 0.0070 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- 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 = 0.5115 r_free = 0.5115 target = 0.222641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.194224 restraints weight = 4975.207| |-----------------------------------------------------------------------------| r_work (start): 0.4815 rms_B_bonded: 3.98 r_work: 0.4703 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3342 Z= 0.392 Angle : 0.646 5.360 4488 Z= 0.367 Chirality : 0.047 0.153 576 Planarity : 0.003 0.024 558 Dihedral : 5.803 21.651 474 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 7.14 % Allowed : 19.94 % 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 (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: -5.03 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.023 0.004 PHE A 94 TYR 0.009 0.002 TYR E 39 *********************** 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 79 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.396 Fit side-chains REVERT: E 57 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8128 (mp0) REVERT: B 61 GLU cc_start: 0.7454 (mp0) cc_final: 0.6393 (mp0) REVERT: B 80 LYS cc_start: 0.7990 (mttp) cc_final: 0.7750 (tmtt) outliers start: 24 outliers final: 24 residues processed: 76 average time/residue: 0.1095 time to fit residues: 10.8232 Evaluate side-chains 76 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 C residue 16 VAL Chi-restraints excluded: chain C residue 37 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.5149 r_free = 0.5149 target = 0.227329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.198833 restraints weight = 4913.075| |-----------------------------------------------------------------------------| r_work (start): 0.4873 rms_B_bonded: 3.95 r_work: 0.4760 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3342 Z= 0.261 Angle : 0.548 7.380 4488 Z= 0.313 Chirality : 0.045 0.135 576 Planarity : 0.002 0.028 558 Dihedral : 5.301 19.554 474 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 7.74 % Allowed : 19.05 % 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 (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: -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 HIS 0.002 0.001 HIS C 50 PHE 0.017 0.003 PHE A 94 TYR 0.010 0.002 TYR F 39 *********************** 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 77 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.388 Fit side-chains REVERT: E 57 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7913 (mp0) REVERT: B 43 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8320 (tppt) REVERT: B 45 LYS cc_start: 0.7656 (ttpt) cc_final: 0.7395 (tptp) REVERT: B 61 GLU cc_start: 0.7430 (mp0) cc_final: 0.6319 (mp0) outliers start: 26 outliers final: 23 residues processed: 72 average time/residue: 0.1190 time to fit residues: 11.0354 Evaluate side-chains 68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 37 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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 = 0.5082 r_free = 0.5082 target = 0.219246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.190909 restraints weight = 4967.241| |-----------------------------------------------------------------------------| r_work (start): 0.4791 rms_B_bonded: 3.97 r_work: 0.4673 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 3342 Z= 0.499 Angle : 0.777 9.459 4488 Z= 0.437 Chirality : 0.049 0.164 576 Planarity : 0.003 0.028 558 Dihedral : 6.161 24.342 474 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 7.74 % Allowed : 20.24 % Favored : 72.02 % 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: -4.97 (0.28), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.031 0.006 PHE A 94 TYR 0.009 0.002 TYR F 39 ********************** 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 72 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.385 Fit side-chains REVERT: E 57 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8095 (mp0) REVERT: A 61 GLU cc_start: 0.8084 (mp0) cc_final: 0.6818 (mp0) REVERT: B 61 GLU cc_start: 0.7518 (mp0) cc_final: 0.6613 (mp0) outliers start: 26 outliers final: 25 residues processed: 67 average time/residue: 0.0796 time to fit residues: 7.7352 Evaluate side-chains 71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 46 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 37 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 E residue 92 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.232910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.204797 restraints weight = 4860.180| |-----------------------------------------------------------------------------| r_work (start): 0.4944 rms_B_bonded: 3.83 r_work: 0.4823 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3342 Z= 0.187 Angle : 0.531 10.744 4488 Z= 0.299 Chirality : 0.046 0.123 576 Planarity : 0.002 0.018 558 Dihedral : 4.927 18.146 474 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.25 % Allowed : 22.02 % 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 (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: -4.87 (0.28), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.013 0.003 PHE A 94 TYR 0.008 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.64 seconds wall clock time: 41 minutes 32.84 seconds (2492.84 seconds total)