Starting phenix.real_space_refine on Fri Aug 2 13:50:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwk_60530/08_2024/8zwk_60530.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwk_60530/08_2024/8zwk_60530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwk_60530/08_2024/8zwk_60530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwk_60530/08_2024/8zwk_60530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwk_60530/08_2024/8zwk_60530.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwk_60530/08_2024/8zwk_60530.cif" } resolution = 3.4 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: 4 Type Number sf(0) Gaussians P 6 5.49 5 C 1704 2.51 5 N 486 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2760 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 2.83, per 1000 atoms: 1.03 Number of scatterers: 2760 At special positions: 0 Unit cell: (104.58, 97.11, 32.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 6 15.00 O 564 8.00 N 486 7.00 C 1704 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: 0.89 Conformation dependent library (CDL) restraints added in 498.7 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 28.6% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 49 removed outlier: 6.803A pdb=" N GLU D 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLU A 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL E 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL A 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54 removed outlier: 6.518A pdb=" N ALA A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.541A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.884A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL A 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 74 through 82 removed outlier: 6.933A pdb=" N THR D 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL E 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 49 removed outlier: 6.804A pdb=" N GLU C 46 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU B 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N VAL F 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.518A pdb=" N ALA B 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.541A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.885A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.932A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N THR B 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ALA F 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL B 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS F 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN B 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL F 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR B 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.30: 462 1.30 - 1.38: 516 1.38 - 1.46: 365 1.46 - 1.53: 1315 1.53 - 1.61: 130 Bond restraints: 2788 Sorted by residual: bond pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta sigma weight residual 1.445 1.450 -0.006 8.30e-03 1.45e+04 4.68e-01 bond pdb=" N GLY E 68 " pdb=" CA GLY E 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.84e-01 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.445 1.450 -0.005 8.30e-03 1.45e+04 3.63e-01 bond pdb=" N GLY C 68 " pdb=" CA GLY C 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.47e-01 bond pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta sigma weight residual 1.445 1.449 -0.005 8.30e-03 1.45e+04 3.27e-01 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 101.44 - 107.69: 113 107.69 - 113.95: 1709 113.95 - 120.20: 718 120.20 - 126.45: 1220 126.45 - 132.71: 36 Bond angle restraints: 3796 Sorted by residual: angle pdb=" N SER D 42 " pdb=" CA SER D 42 " pdb=" C SER D 42 " ideal model delta sigma weight residual 110.80 114.75 -3.95 2.13e+00 2.20e-01 3.44e+00 angle pdb=" N SER C 42 " pdb=" CA SER C 42 " pdb=" C SER C 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER B 42 " pdb=" CA SER B 42 " pdb=" C SER B 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.42e+00 angle pdb=" N SER A 42 " pdb=" CA SER A 42 " pdb=" C SER A 42 " ideal model delta sigma weight residual 110.80 114.74 -3.94 2.13e+00 2.20e-01 3.41e+00 angle pdb=" N SER E 42 " pdb=" CA SER E 42 " pdb=" C SER E 42 " ideal model delta sigma weight residual 110.80 114.72 -3.92 2.13e+00 2.20e-01 3.39e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 1550 24.43 - 48.86: 46 48.86 - 73.29: 12 73.29 - 97.71: 0 97.71 - 122.14: 6 Dihedral angle restraints: 1614 sinusoidal: 588 harmonic: 1026 Sorted by residual: dihedral pdb=" CA GLY A 41 " pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY F 41 " pdb=" C GLY F 41 " pdb=" N SER F 42 " pdb=" CA SER F 42 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLY E 41 " pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 263 0.027 - 0.054: 112 0.054 - 0.081: 51 0.081 - 0.108: 37 0.108 - 0.135: 35 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 495 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 43 " -0.003 2.00e-02 2.50e+03 6.65e-03 4.42e-01 pdb=" C LYS F 43 " 0.012 2.00e-02 2.50e+03 pdb=" O LYS F 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR F 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 43 " -0.003 2.00e-02 2.50e+03 6.62e-03 4.38e-01 pdb=" C LYS B 43 " 0.011 2.00e-02 2.50e+03 pdb=" O LYS B 43 " -0.004 2.00e-02 2.50e+03 pdb=" N THR B 44 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 43 " 0.003 2.00e-02 2.50e+03 6.61e-03 4.37e-01 pdb=" C LYS A 43 " -0.011 2.00e-02 2.50e+03 pdb=" O LYS A 43 " 0.004 2.00e-02 2.50e+03 pdb=" N THR A 44 " 0.004 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 527 2.78 - 3.31: 2457 3.31 - 3.84: 4297 3.84 - 4.37: 4504 4.37 - 4.90: 9330 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.254 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.254 3.120 ... (remaining 21110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.100 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.003 0.016 2788 Z= 0.219 Angle : 0.602 3.950 3796 Z= 0.340 Chirality : 0.052 0.135 498 Planarity : 0.002 0.007 450 Dihedral : 16.324 122.139 966 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.27), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.21), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.003 0.001 PHE F 94 TYR 0.011 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.281 Fit side-chains REVERT: A 83 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7257 (tp30) REVERT: D 83 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7523 (tp30) REVERT: E 83 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7494 (tp30) REVERT: B 37 VAL cc_start: 0.6552 (m) cc_final: 0.6225 (m) REVERT: B 43 LYS cc_start: 0.6199 (ptpt) cc_final: 0.5442 (tttp) REVERT: B 83 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7353 (tp30) REVERT: F 83 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7593 (tp30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1745 time to fit residues: 7.5048 Evaluate side-chains 26 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 overall best weight: 2.2044 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2788 Z= 0.233 Angle : 0.613 4.803 3796 Z= 0.335 Chirality : 0.052 0.128 498 Planarity : 0.002 0.009 450 Dihedral : 15.369 112.539 444 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.56 % Allowed : 7.41 % Favored : 87.04 % 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: -4.66 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.011 0.003 PHE A 94 TYR 0.013 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 19 time to evaluate : 0.260 Fit side-chains REVERT: A 83 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7349 (tp30) REVERT: D 83 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7632 (tp30) REVERT: E 60 LYS cc_start: 0.7093 (mttt) cc_final: 0.6640 (mtpt) REVERT: E 83 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7545 (tp30) REVERT: B 37 VAL cc_start: 0.6655 (OUTLIER) cc_final: 0.6309 (m) REVERT: F 60 LYS cc_start: 0.7073 (mttt) cc_final: 0.6644 (mtpt) REVERT: F 83 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7804 (tp30) outliers start: 15 outliers final: 14 residues processed: 33 average time/residue: 0.1664 time to fit residues: 6.6074 Evaluate side-chains 34 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 19 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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: 0.7510 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2788 Z= 0.275 Angle : 0.619 4.823 3796 Z= 0.339 Chirality : 0.051 0.130 498 Planarity : 0.002 0.008 450 Dihedral : 13.997 102.688 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 6.67 % Allowed : 7.41 % Favored : 85.93 % 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: -4.41 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.013 0.003 PHE B 94 TYR 0.011 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 27 time to evaluate : 0.258 Fit side-chains REVERT: A 37 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.6312 (m) REVERT: A 60 LYS cc_start: 0.6408 (mttt) cc_final: 0.5993 (mtpt) REVERT: D 60 LYS cc_start: 0.6512 (mttt) cc_final: 0.6125 (mtpt) REVERT: D 83 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7714 (tp30) REVERT: E 60 LYS cc_start: 0.7051 (mttt) cc_final: 0.6557 (mtpt) REVERT: E 83 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7763 (tp30) REVERT: B 37 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6482 (m) REVERT: B 60 LYS cc_start: 0.6263 (mttt) cc_final: 0.5939 (mtpt) REVERT: C 60 LYS cc_start: 0.6380 (mttt) cc_final: 0.5975 (mtpt) REVERT: F 60 LYS cc_start: 0.7128 (mttt) cc_final: 0.6646 (mtpt) REVERT: F 83 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7874 (tp30) outliers start: 18 outliers final: 15 residues processed: 40 average time/residue: 0.2080 time to fit residues: 9.6470 Evaluate side-chains 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 27 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.7468 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.163 Angle : 0.518 4.371 3796 Z= 0.283 Chirality : 0.050 0.127 498 Planarity : 0.002 0.007 450 Dihedral : 13.489 100.190 444 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.67 % Allowed : 8.89 % Favored : 84.44 % 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: -4.11 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.010 0.002 PHE A 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 22 time to evaluate : 0.252 Fit side-chains REVERT: A 37 VAL cc_start: 0.6600 (OUTLIER) cc_final: 0.6203 (m) REVERT: A 60 LYS cc_start: 0.6400 (mttt) cc_final: 0.6008 (mtpt) REVERT: D 83 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7793 (tp30) REVERT: E 60 LYS cc_start: 0.6992 (mttt) cc_final: 0.6532 (mtpt) REVERT: E 83 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7777 (tp30) REVERT: B 37 VAL cc_start: 0.6721 (OUTLIER) cc_final: 0.6384 (m) REVERT: B 60 LYS cc_start: 0.6232 (mttt) cc_final: 0.5889 (mtpt) REVERT: F 60 LYS cc_start: 0.7101 (mttt) cc_final: 0.6592 (mtpt) REVERT: F 83 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7893 (tp30) outliers start: 18 outliers final: 15 residues processed: 37 average time/residue: 0.1890 time to fit residues: 8.1960 Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 22 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2788 Z= 0.357 Angle : 0.656 4.429 3796 Z= 0.363 Chirality : 0.051 0.129 498 Planarity : 0.003 0.010 450 Dihedral : 13.412 97.207 444 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 8.52 % Allowed : 8.89 % Favored : 82.59 % 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: -4.06 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS A 50 PHE 0.014 0.004 PHE A 94 TYR 0.014 0.004 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 30 time to evaluate : 0.276 Fit side-chains REVERT: A 37 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6381 (m) REVERT: A 60 LYS cc_start: 0.6548 (mttt) cc_final: 0.6090 (mtpt) REVERT: D 60 LYS cc_start: 0.6422 (mttt) cc_final: 0.6015 (mtpt) REVERT: D 83 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7775 (tp30) REVERT: E 60 LYS cc_start: 0.6997 (mttt) cc_final: 0.6570 (mtpt) REVERT: E 83 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7816 (tp30) REVERT: B 37 VAL cc_start: 0.6850 (OUTLIER) cc_final: 0.6461 (m) REVERT: B 60 LYS cc_start: 0.6411 (mttt) cc_final: 0.6053 (mtpt) REVERT: C 37 VAL cc_start: 0.7145 (OUTLIER) cc_final: 0.6899 (m) REVERT: C 60 LYS cc_start: 0.6542 (mttt) cc_final: 0.6167 (mtpt) REVERT: F 60 LYS cc_start: 0.7187 (mttt) cc_final: 0.6680 (mtpt) REVERT: F 83 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7890 (tp30) outliers start: 23 outliers final: 20 residues processed: 46 average time/residue: 0.1829 time to fit residues: 9.7882 Evaluate side-chains 53 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 30 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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: 0.7509 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2788 Z= 0.321 Angle : 0.616 4.395 3796 Z= 0.340 Chirality : 0.051 0.131 498 Planarity : 0.002 0.009 450 Dihedral : 13.184 94.830 444 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 8.15 % Allowed : 10.00 % Favored : 81.85 % 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: -3.96 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS A 50 PHE 0.015 0.004 PHE A 94 TYR 0.014 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 30 time to evaluate : 0.219 Fit side-chains REVERT: A 37 VAL cc_start: 0.6592 (OUTLIER) cc_final: 0.6205 (m) REVERT: A 60 LYS cc_start: 0.6518 (mttt) cc_final: 0.6084 (mtpt) REVERT: D 60 LYS cc_start: 0.6523 (mttt) cc_final: 0.6121 (mtpt) REVERT: E 60 LYS cc_start: 0.6996 (mttt) cc_final: 0.6619 (mtpt) REVERT: E 83 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7916 (tp30) REVERT: B 37 VAL cc_start: 0.6795 (OUTLIER) cc_final: 0.6451 (m) REVERT: B 60 LYS cc_start: 0.6411 (mttt) cc_final: 0.6048 (mtpt) REVERT: C 60 LYS cc_start: 0.6664 (mttt) cc_final: 0.6264 (mtpt) REVERT: F 60 LYS cc_start: 0.7217 (mttt) cc_final: 0.6731 (mtpt) REVERT: F 83 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7888 (tp30) outliers start: 22 outliers final: 20 residues processed: 45 average time/residue: 0.1929 time to fit residues: 10.0823 Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 30 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7456 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2788 Z= 0.146 Angle : 0.516 4.399 3796 Z= 0.281 Chirality : 0.049 0.129 498 Planarity : 0.002 0.007 450 Dihedral : 12.834 95.328 444 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 6.67 % Allowed : 11.48 % Favored : 81.85 % 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: -3.77 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.011 0.003 PHE A 94 TYR 0.010 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 25 time to evaluate : 0.288 Fit side-chains REVERT: A 37 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6268 (m) REVERT: A 60 LYS cc_start: 0.6465 (mttt) cc_final: 0.6059 (mtpt) REVERT: D 60 LYS cc_start: 0.6474 (mttt) cc_final: 0.6056 (mtpt) REVERT: E 60 LYS cc_start: 0.7019 (mttt) cc_final: 0.6633 (mtpt) REVERT: E 83 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7915 (tp30) REVERT: B 37 VAL cc_start: 0.6773 (OUTLIER) cc_final: 0.6429 (m) REVERT: B 60 LYS cc_start: 0.6379 (mttt) cc_final: 0.6057 (mtpt) REVERT: C 60 LYS cc_start: 0.6563 (mttt) cc_final: 0.6188 (mtpt) REVERT: F 60 LYS cc_start: 0.7137 (mttt) cc_final: 0.6741 (mtpt) REVERT: F 83 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7890 (tp30) outliers start: 18 outliers final: 15 residues processed: 40 average time/residue: 0.2191 time to fit residues: 10.1351 Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 25 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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: 0.7483 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2788 Z= 0.238 Angle : 0.574 4.294 3796 Z= 0.315 Chirality : 0.049 0.127 498 Planarity : 0.002 0.008 450 Dihedral : 12.779 93.261 444 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 7.41 % Allowed : 10.74 % Favored : 81.85 % 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: -3.77 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.013 0.003 PHE A 94 TYR 0.012 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 29 time to evaluate : 0.244 Fit side-chains REVERT: A 37 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6277 (m) REVERT: A 60 LYS cc_start: 0.6525 (mttt) cc_final: 0.6105 (mtpt) REVERT: D 60 LYS cc_start: 0.6559 (mttt) cc_final: 0.6147 (mtpt) REVERT: E 60 LYS cc_start: 0.7053 (mttt) cc_final: 0.6666 (mtpt) REVERT: B 37 VAL cc_start: 0.6759 (OUTLIER) cc_final: 0.6414 (m) REVERT: B 60 LYS cc_start: 0.6426 (mttt) cc_final: 0.6097 (mtpt) REVERT: C 60 LYS cc_start: 0.6666 (mttt) cc_final: 0.6285 (mtpt) REVERT: F 60 LYS cc_start: 0.7189 (mttt) cc_final: 0.6711 (mtpt) REVERT: F 83 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7860 (tp30) outliers start: 20 outliers final: 18 residues processed: 43 average time/residue: 0.1963 time to fit residues: 9.8087 Evaluate side-chains 49 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 29 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 0.0050 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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: 0.7432 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.123 Angle : 0.480 3.994 3796 Z= 0.262 Chirality : 0.049 0.130 498 Planarity : 0.001 0.007 450 Dihedral : 12.440 93.320 444 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 6.67 % Allowed : 11.48 % Favored : 81.85 % 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: -3.61 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.007 0.002 PHE A 94 TYR 0.006 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 24 time to evaluate : 0.292 Fit side-chains REVERT: A 37 VAL cc_start: 0.6601 (OUTLIER) cc_final: 0.6207 (m) REVERT: A 60 LYS cc_start: 0.6494 (mttt) cc_final: 0.6089 (mtpt) REVERT: D 60 LYS cc_start: 0.6524 (mttt) cc_final: 0.6072 (mtpt) REVERT: E 60 LYS cc_start: 0.7034 (mttt) cc_final: 0.6639 (mtpt) REVERT: B 60 LYS cc_start: 0.6386 (mttt) cc_final: 0.6033 (mtpt) REVERT: C 37 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6942 (m) REVERT: C 60 LYS cc_start: 0.6586 (mttt) cc_final: 0.6207 (mtpt) REVERT: F 60 LYS cc_start: 0.7103 (mttt) cc_final: 0.6699 (mtpt) REVERT: F 83 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7880 (tp30) outliers start: 18 outliers final: 12 residues processed: 38 average time/residue: 0.2124 time to fit residues: 9.3289 Evaluate side-chains 37 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 23 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2788 Z= 0.276 Angle : 0.590 4.260 3796 Z= 0.325 Chirality : 0.049 0.127 498 Planarity : 0.002 0.009 450 Dihedral : 12.500 91.583 444 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 5.56 % Allowed : 12.22 % Favored : 82.22 % 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: -3.74 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.015 0.004 PHE A 94 TYR 0.014 0.003 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 0.287 Fit side-chains REVERT: A 37 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6333 (m) REVERT: A 60 LYS cc_start: 0.6562 (mttt) cc_final: 0.6144 (mtpt) REVERT: D 60 LYS cc_start: 0.6645 (mttt) cc_final: 0.6191 (mtpt) REVERT: E 60 LYS cc_start: 0.7068 (mttt) cc_final: 0.6682 (mtpt) REVERT: B 37 VAL cc_start: 0.6806 (OUTLIER) cc_final: 0.6456 (m) REVERT: B 60 LYS cc_start: 0.6459 (mttt) cc_final: 0.6133 (mtpt) REVERT: C 60 LYS cc_start: 0.6698 (mttt) cc_final: 0.6335 (mtpt) REVERT: F 60 LYS cc_start: 0.7196 (mttt) cc_final: 0.6793 (mtpt) REVERT: F 83 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7856 (tp30) outliers start: 15 outliers final: 13 residues processed: 39 average time/residue: 0.2104 time to fit residues: 9.5087 Evaluate side-chains 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 29 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4627 r_free = 0.4627 target = 0.194201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.146027 restraints weight = 2546.601| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.48 r_work: 0.4040 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2788 Z= 0.154 Angle : 0.503 4.011 3796 Z= 0.274 Chirality : 0.049 0.128 498 Planarity : 0.002 0.007 450 Dihedral : 12.267 91.709 444 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 6.30 % Allowed : 11.48 % Favored : 82.22 % 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: -3.65 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.010 0.002 PHE A 94 TYR 0.007 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1125.77 seconds wall clock time: 20 minutes 45.62 seconds (1245.62 seconds total)