Starting phenix.real_space_refine on Sun Mar 10 16:52:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4b_31706/03_2024/7v4b_31706.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4b_31706/03_2024/7v4b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4b_31706/03_2024/7v4b_31706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4b_31706/03_2024/7v4b_31706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4b_31706/03_2024/7v4b_31706.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v4b_31706/03_2024/7v4b_31706.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3336 Number of models: 1 Model: "" Number of chains: 6 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 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 Chain: "B" 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 Time building chain proxies: 2.21, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 667.8 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: 0.57 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: 0.91 Time building geometry restraints manager: 1.24 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: 106.11 - 111.13: 1419 111.13 - 116.14: 1045 116.14 - 121.15: 981 121.15 - 126.17: 1037 126.17 - 131.18: 6 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 2.440 nonbonded pdb=" O THR A 81 " pdb=" OG1 THR B 81 " model vdw 2.382 2.440 nonbonded pdb=" O THR E 81 " pdb=" OG1 THR A 81 " model vdw 2.417 2.440 nonbonded pdb=" O THR F 81 " pdb=" OG1 THR C 81 " model vdw 2.428 2.440 nonbonded pdb=" OG1 THR C 81 " pdb=" N VAL C 82 " model vdw 2.473 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 2.590 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: 12.000 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.353 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: 0.0946 time to fit residues: 7.7619 Evaluate side-chains 48 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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: 8.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1627 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= 0.259 Angle : 0.511 5.167 4488 Z= 0.293 Chirality : 0.046 0.132 576 Planarity : 0.002 0.008 558 Dihedral : 5.330 20.360 474 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 1.49 % Allowed : 16.37 % Favored : 82.14 % 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: -5.58 (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 HIS 0.002 0.001 HIS E 50 PHE 0.011 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 55 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.392 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.0882 time to fit residues: 6.7650 Evaluate side-chains 52 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3342 Z= 0.252 Angle : 0.488 2.839 4488 Z= 0.285 Chirality : 0.045 0.129 576 Planarity : 0.002 0.006 558 Dihedral : 5.302 19.703 474 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.57 % Allowed : 18.75 % 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: -5.36 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.014 0.003 PHE A 94 TYR 0.008 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 60 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.421 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 56 average time/residue: 0.0902 time to fit residues: 7.1580 Evaluate side-chains 54 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 E residue 16 VAL 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 22 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2214 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= 0.307 Angle : 0.537 3.274 4488 Z= 0.312 Chirality : 0.045 0.126 576 Planarity : 0.002 0.007 558 Dihedral : 5.580 20.295 474 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 8.93 % Allowed : 15.77 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.25), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.19), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.015 0.003 PHE A 94 TYR 0.009 0.002 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 80 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 50 time to evaluate : 0.394 Fit side-chains REVERT: B 57 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 61 GLU cc_start: 0.7438 (mp0) cc_final: 0.6315 (mp0) outliers start: 30 outliers final: 24 residues processed: 73 average time/residue: 0.0794 time to fit residues: 8.3483 Evaluate side-chains 70 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 46 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 E residue 81 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 37 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 34 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 0.0670 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3342 Z= 0.439 Angle : 0.672 4.168 4488 Z= 0.389 Chirality : 0.047 0.144 576 Planarity : 0.003 0.010 558 Dihedral : 6.254 22.060 474 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.13 % Favored : 84.87 % Rotamer: Outliers : 10.12 % Allowed : 16.07 % Favored : 73.81 % 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 (0.26), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.022 0.005 PHE A 94 TYR 0.011 0.003 TYR E 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 80 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 46 time to evaluate : 0.332 Fit side-chains REVERT: B 61 GLU cc_start: 0.7405 (mp0) cc_final: 0.6395 (mp0) outliers start: 34 outliers final: 29 residues processed: 75 average time/residue: 0.0877 time to fit residues: 9.0609 Evaluate side-chains 71 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 42 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 77 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 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3342 Z= 0.433 Angle : 0.675 4.385 4488 Z= 0.389 Chirality : 0.047 0.133 576 Planarity : 0.003 0.010 558 Dihedral : 6.311 22.598 474 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.69 % Favored : 85.31 % Rotamer: Outliers : 8.93 % Allowed : 18.45 % Favored : 72.62 % 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: -5.18 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.021 0.005 PHE D 94 TYR 0.010 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 71 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 41 time to evaluate : 0.443 Fit side-chains REVERT: B 61 GLU cc_start: 0.7404 (mp0) cc_final: 0.6418 (mp0) outliers start: 30 outliers final: 28 residues processed: 68 average time/residue: 0.0747 time to fit residues: 7.3858 Evaluate side-chains 70 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 42 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 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 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3342 Z= 0.345 Angle : 0.604 3.895 4488 Z= 0.349 Chirality : 0.046 0.126 576 Planarity : 0.002 0.008 558 Dihedral : 6.063 21.765 474 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 8.33 % Allowed : 19.35 % Favored : 72.32 % 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: -5.13 (0.28), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.017 0.004 PHE A 94 TYR 0.010 0.002 TYR E 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 71 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 43 time to evaluate : 0.411 Fit side-chains REVERT: A 61 GLU cc_start: 0.7947 (mp0) cc_final: 0.6688 (mp0) REVERT: B 61 GLU cc_start: 0.7374 (mp0) cc_final: 0.6494 (mp0) outliers start: 28 outliers final: 28 residues processed: 67 average time/residue: 0.0764 time to fit residues: 7.5068 Evaluate side-chains 69 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 41 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 81 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 0.0370 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3342 Z= 0.130 Angle : 0.432 3.625 4488 Z= 0.252 Chirality : 0.045 0.122 576 Planarity : 0.002 0.008 558 Dihedral : 4.785 15.979 474 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.46 % Allowed : 22.62 % 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: -5.09 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.20), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 50 PHE 0.008 0.002 PHE A 94 TYR 0.006 0.001 TYR A 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 59 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.414 Fit side-chains REVERT: B 61 GLU cc_start: 0.7370 (mp0) cc_final: 0.6390 (mp0) outliers start: 15 outliers final: 13 residues processed: 55 average time/residue: 0.0796 time to fit residues: 6.4955 Evaluate side-chains 53 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 81 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 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 33 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.0070 chunk 45 optimal weight: 0.2980 chunk 27 optimal weight: 0.0570 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3060 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= 0.224 Angle : 0.499 8.602 4488 Z= 0.280 Chirality : 0.045 0.132 576 Planarity : 0.002 0.007 558 Dihedral : 5.160 18.175 474 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 4.17 % Allowed : 22.32 % 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: -5.05 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.012 0.003 PHE C 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 52 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 0.381 Fit side-chains REVERT: B 61 GLU cc_start: 0.7394 (mp0) cc_final: 0.6393 (mp0) outliers start: 14 outliers final: 14 residues processed: 49 average time/residue: 0.0807 time to fit residues: 5.8225 Evaluate side-chains 51 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 37 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 81 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 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 44 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3342 Z= 0.141 Angle : 0.433 7.665 4488 Z= 0.246 Chirality : 0.045 0.122 576 Planarity : 0.002 0.007 558 Dihedral : 4.631 16.029 474 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.17 % Allowed : 22.92 % 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: -4.94 (0.27), residues: 456 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.010 0.002 PHE A 94 TYR 0.008 0.001 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 56 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 42 time to evaluate : 0.398 Fit side-chains REVERT: B 61 GLU cc_start: 0.7363 (mp0) cc_final: 0.6393 (mp0) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.0772 time to fit residues: 6.2209 Evaluate side-chains 52 residues out of total 336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 40 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 44 THR 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 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 38 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 27 optimal weight: 0.0170 chunk 43 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 = 0.5113 r_free = 0.5113 target = 0.222468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.194470 restraints weight = 4975.520| |-----------------------------------------------------------------------------| r_work (start): 0.4816 rms_B_bonded: 3.82 r_work: 0.4701 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3342 Z= 0.309 Angle : 0.555 7.067 4488 Z= 0.316 Chirality : 0.045 0.135 576 Planarity : 0.002 0.009 558 Dihedral : 5.462 19.737 474 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.47 % Favored : 85.53 % Rotamer: Outliers : 3.57 % Allowed : 23.21 % 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 : -3.77 (0.21), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.020 0.004 PHE B 94 TYR 0.011 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1289.78 seconds wall clock time: 24 minutes 1.12 seconds (1441.12 seconds total)