Starting phenix.real_space_refine on Fri Apr 5 13:14:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owj_17238/04_2024/8owj_17238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owj_17238/04_2024/8owj_17238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owj_17238/04_2024/8owj_17238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owj_17238/04_2024/8owj_17238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owj_17238/04_2024/8owj_17238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8owj_17238/04_2024/8owj_17238.pdb" } resolution = 3.75 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= 0.001 sd= 0.005 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 S 10 5.16 5 C 1730 2.51 5 N 490 2.21 5 O 490 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-5288/modules/chem_data/mon_lib" Total number of atoms: 2720 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "A" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "B" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "D" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "F" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "H" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "I" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "J" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 272 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Time building chain proxies: 1.63, per 1000 atoms: 0.60 Number of scatterers: 2720 At special positions: 0 Unit cell: (84, 116.55, 45.15, 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) S 10 16.00 O 490 8.00 N 490 7.00 C 1730 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: 0.86 Conformation dependent library (CDL) restraints added in 361.2 milliseconds 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.294A pdb=" N TYR A 10 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR G 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 23 removed outlier: 6.558A pdb=" N LYS E 16 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE C 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL E 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ALA C 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE E 20 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP C 23 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU E 22 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 35 removed outlier: 6.809A pdb=" N LEU A 34 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET C 35 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY E 29 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE C 32 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE E 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 34 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY E 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET G 35 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA I 30 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE G 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE I 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY G 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.272A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR H 10 " --> pdb=" O GLU J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 23 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 35 removed outlier: 6.763A pdb=" N LEU B 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET D 35 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 34 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET F 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU F 34 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N MET H 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU H 34 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET J 35 " --> pdb=" O LEU H 34 " (cutoff:3.500A) 79 hydrogen bonds defined for protein. 234 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: 0.64 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 817 1.34 - 1.46: 433 1.46 - 1.58: 1500 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 2770 Sorted by residual: bond pdb=" N SER E 8 " pdb=" CA SER E 8 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.35e+00 bond pdb=" N SER H 8 " pdb=" CA SER H 8 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.23e-02 6.61e+03 7.20e+00 bond pdb=" N SER J 8 " pdb=" CA SER J 8 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.14e+00 bond pdb=" N SER D 8 " pdb=" CA SER D 8 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.97e+00 bond pdb=" N SER A 8 " pdb=" CA SER A 8 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.97e+00 ... (remaining 2765 not shown) Histogram of bond angle deviations from ideal: 102.82 - 108.32: 313 108.32 - 113.82: 1137 113.82 - 119.32: 947 119.32 - 124.82: 1217 124.82 - 130.32: 96 Bond angle restraints: 3710 Sorted by residual: angle pdb=" C VAL C 24 " pdb=" N GLY C 25 " pdb=" CA GLY C 25 " ideal model delta sigma weight residual 119.92 126.56 -6.64 9.60e-01 1.09e+00 4.78e+01 angle pdb=" C VAL F 24 " pdb=" N GLY F 25 " pdb=" CA GLY F 25 " ideal model delta sigma weight residual 119.92 126.52 -6.60 9.60e-01 1.09e+00 4.72e+01 angle pdb=" C VAL A 24 " pdb=" N GLY A 25 " pdb=" CA GLY A 25 " ideal model delta sigma weight residual 119.92 126.51 -6.59 9.60e-01 1.09e+00 4.71e+01 angle pdb=" C VAL B 24 " pdb=" N GLY B 25 " pdb=" CA GLY B 25 " ideal model delta sigma weight residual 119.92 126.50 -6.58 9.60e-01 1.09e+00 4.70e+01 angle pdb=" C VAL J 24 " pdb=" N GLY J 25 " pdb=" CA GLY J 25 " ideal model delta sigma weight residual 119.92 126.50 -6.58 9.60e-01 1.09e+00 4.70e+01 ... (remaining 3705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 1408 17.79 - 35.57: 102 35.57 - 53.35: 30 53.35 - 71.14: 0 71.14 - 88.92: 10 Dihedral angle restraints: 1550 sinusoidal: 590 harmonic: 960 Sorted by residual: dihedral pdb=" C HIS G 13 " pdb=" N HIS G 13 " pdb=" CA HIS G 13 " pdb=" CB HIS G 13 " ideal model delta harmonic sigma weight residual -122.60 -131.42 8.82 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" C HIS A 13 " pdb=" N HIS A 13 " pdb=" CA HIS A 13 " pdb=" CB HIS A 13 " ideal model delta harmonic sigma weight residual -122.60 -131.40 8.80 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C HIS E 13 " pdb=" N HIS E 13 " pdb=" CA HIS E 13 " pdb=" CB HIS E 13 " ideal model delta harmonic sigma weight residual -122.60 -131.37 8.77 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 1547 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.050: 83 0.050 - 0.100: 153 0.100 - 0.150: 93 0.150 - 0.200: 41 0.200 - 0.250: 30 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA HIS G 13 " pdb=" N HIS G 13 " pdb=" C HIS G 13 " pdb=" CB HIS G 13 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA HIS A 13 " pdb=" N HIS A 13 " pdb=" C HIS A 13 " pdb=" CB HIS A 13 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA HIS D 13 " pdb=" N HIS D 13 " pdb=" C HIS D 13 " pdb=" CB HIS D 13 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 397 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 13 " 0.045 2.00e-02 2.50e+03 3.52e-02 1.86e+01 pdb=" CG HIS C 13 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS C 13 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS C 13 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS C 13 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 13 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 13 " 0.045 2.00e-02 2.50e+03 3.50e-02 1.84e+01 pdb=" CG HIS H 13 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS H 13 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS H 13 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS H 13 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS H 13 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 13 " 0.045 2.00e-02 2.50e+03 3.49e-02 1.83e+01 pdb=" CG HIS G 13 " -0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS G 13 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS G 13 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 HIS G 13 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS G 13 " 0.022 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1682 3.07 - 3.53: 2845 3.53 - 3.98: 4140 3.98 - 4.44: 4971 4.44 - 4.90: 9197 Nonbonded interactions: 22835 Sorted by model distance: nonbonded pdb=" OD2 ASP G 23 " pdb=" NZ LYS G 28 " model vdw 2.610 2.520 nonbonded pdb=" OD2 ASP F 23 " pdb=" NZ LYS F 28 " model vdw 2.610 2.520 nonbonded pdb=" OD2 ASP B 23 " pdb=" NZ LYS B 28 " model vdw 2.610 2.520 nonbonded pdb=" OD2 ASP C 23 " pdb=" NZ LYS C 28 " model vdw 2.610 2.520 nonbonded pdb=" OD2 ASP H 23 " pdb=" NZ LYS H 28 " model vdw 2.610 2.520 ... (remaining 22830 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 0.790 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: 3.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.180 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 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 : 0.012 0.033 2770 Z= 0.834 Angle : 2.256 8.813 3710 Z= 1.604 Chirality : 0.112 0.250 400 Planarity : 0.015 0.048 480 Dihedral : 15.837 88.923 950 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.57 % Allowed : 14.29 % 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: -1.73 (0.36), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.010 HIS D 14 PHE 0.041 0.014 PHE B 20 TYR 0.004 0.001 TYR E 10 ARG 0.001 0.000 ARG F 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.6681 (ptpt) cc_final: 0.6209 (tptp) REVERT: G 11 GLU cc_start: 0.6215 (tt0) cc_final: 0.5480 (tm-30) REVERT: G 35 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.7026 (ptp) REVERT: H 11 GLU cc_start: 0.6450 (tt0) cc_final: 0.6104 (tm-30) REVERT: J 35 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7718 (ptp) outliers start: 10 outliers final: 0 residues processed: 110 average time/residue: 0.1107 time to fit residues: 14.7871 Evaluate side-chains 61 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 MET Chi-restraints excluded: chain J residue 35 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 HIS E 27 ASN A 6 HIS D 14 HIS H 27 ASN I 14 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2770 Z= 0.305 Angle : 0.753 7.454 3710 Z= 0.415 Chirality : 0.047 0.127 400 Planarity : 0.003 0.011 480 Dihedral : 6.814 18.035 376 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.64 % Allowed : 20.36 % Favored : 75.00 % 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: -2.42 (0.37), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.28), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 6 PHE 0.009 0.002 PHE B 19 TYR 0.009 0.002 TYR A 10 ARG 0.003 0.001 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.310 Fit side-chains REVERT: E 11 GLU cc_start: 0.6410 (tm-30) cc_final: 0.5255 (tm-30) REVERT: E 22 GLU cc_start: 0.7620 (tm-30) cc_final: 0.6908 (tm-30) REVERT: A 28 LYS cc_start: 0.7137 (ptpt) cc_final: 0.6471 (tptp) REVERT: B 19 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: C 11 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5784 (tm-30) REVERT: C 35 MET cc_start: 0.8003 (ptp) cc_final: 0.7791 (ptp) REVERT: D 11 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6659 (tm-30) REVERT: F 11 GLU cc_start: 0.6767 (tm-30) cc_final: 0.5571 (tm-30) REVERT: G 19 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6083 (m-80) REVERT: G 22 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6868 (tm-30) REVERT: I 35 MET cc_start: 0.7896 (ptp) cc_final: 0.7529 (ptt) REVERT: J 11 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6025 (tm-30) REVERT: J 22 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7434 (tm-30) REVERT: J 35 MET cc_start: 0.7735 (ptp) cc_final: 0.7479 (ptt) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.1122 time to fit residues: 8.4909 Evaluate side-chains 39 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 29 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2770 Z= 0.390 Angle : 0.765 7.265 3710 Z= 0.431 Chirality : 0.048 0.127 400 Planarity : 0.004 0.018 480 Dihedral : 6.699 19.184 370 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.29 % Allowed : 21.43 % Favored : 74.29 % 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: -2.52 (0.38), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 6 PHE 0.021 0.003 PHE G 20 TYR 0.021 0.004 TYR H 10 ARG 0.002 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.337 Fit side-chains REVERT: E 11 GLU cc_start: 0.6229 (tm-30) cc_final: 0.5639 (tm-30) REVERT: E 22 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 19 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: C 11 GLU cc_start: 0.6989 (tm-30) cc_final: 0.5786 (tm-30) REVERT: D 11 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6547 (tm-30) REVERT: F 11 GLU cc_start: 0.6712 (tm-30) cc_final: 0.6101 (tm-30) REVERT: G 11 GLU cc_start: 0.5769 (tm-30) cc_final: 0.5260 (tm-30) REVERT: G 19 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: G 22 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7164 (tm-30) REVERT: I 15 GLN cc_start: 0.8381 (mt0) cc_final: 0.7522 (mp10) REVERT: I 35 MET cc_start: 0.7773 (ptp) cc_final: 0.7378 (ptt) REVERT: J 11 GLU cc_start: 0.6128 (tm-30) cc_final: 0.5525 (tm-30) REVERT: J 35 MET cc_start: 0.7750 (ptp) cc_final: 0.7345 (ptt) outliers start: 12 outliers final: 9 residues processed: 50 average time/residue: 0.1015 time to fit residues: 6.5410 Evaluate side-chains 37 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 26 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.6483 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2770 Z= 0.365 Angle : 0.715 5.281 3710 Z= 0.407 Chirality : 0.049 0.135 400 Planarity : 0.003 0.015 480 Dihedral : 6.492 18.777 370 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.36 % Allowed : 20.00 % Favored : 74.64 % 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: -2.50 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 6 PHE 0.019 0.002 PHE G 20 TYR 0.015 0.003 TYR H 10 ARG 0.002 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.315 Fit side-chains REVERT: E 11 GLU cc_start: 0.6358 (tm-30) cc_final: 0.6010 (tm-30) REVERT: E 22 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 19 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: B 22 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7168 (tm-30) REVERT: C 11 GLU cc_start: 0.6808 (tm-30) cc_final: 0.5809 (tm-30) REVERT: C 39 VAL cc_start: 0.8369 (t) cc_final: 0.8141 (t) REVERT: D 11 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6521 (tm-30) REVERT: D 22 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6900 (tm-30) REVERT: D 35 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6966 (ttm) REVERT: F 11 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6187 (tm-30) REVERT: G 11 GLU cc_start: 0.6034 (tm-30) cc_final: 0.5805 (tm-30) REVERT: G 19 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6449 (m-80) REVERT: G 22 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7189 (tm-30) REVERT: I 22 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7420 (tm-30) REVERT: I 35 MET cc_start: 0.8161 (ptp) cc_final: 0.7685 (ptt) REVERT: J 11 GLU cc_start: 0.5894 (tm-30) cc_final: 0.5604 (tm-30) REVERT: J 35 MET cc_start: 0.7746 (ptp) cc_final: 0.7350 (ptt) outliers start: 15 outliers final: 8 residues processed: 56 average time/residue: 0.0990 time to fit residues: 7.2273 Evaluate side-chains 48 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN D 15 GLN H 15 GLN I 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2770 Z= 0.414 Angle : 0.736 6.665 3710 Z= 0.422 Chirality : 0.049 0.134 400 Planarity : 0.003 0.015 480 Dihedral : 6.646 18.553 370 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.71 % Allowed : 23.21 % Favored : 71.07 % 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: -2.52 (0.40), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 6 PHE 0.021 0.003 PHE G 20 TYR 0.015 0.004 TYR H 10 ARG 0.002 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.300 Fit side-chains REVERT: E 11 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6256 (tm-30) REVERT: E 22 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7486 (tm-30) REVERT: B 19 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: C 11 GLU cc_start: 0.6726 (tm-30) cc_final: 0.5793 (tm-30) REVERT: C 19 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: D 11 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6509 (tm-30) REVERT: D 22 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7094 (tm-30) REVERT: D 35 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7084 (ttm) REVERT: F 11 GLU cc_start: 0.6443 (tm-30) cc_final: 0.5966 (tm-30) REVERT: G 11 GLU cc_start: 0.6192 (tm-30) cc_final: 0.5712 (tm-30) REVERT: G 19 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: G 22 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7236 (tm-30) REVERT: H 11 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6495 (tm-30) REVERT: H 19 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7053 (m-10) REVERT: I 22 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6991 (tm-30) REVERT: J 11 GLU cc_start: 0.6027 (tm-30) cc_final: 0.5682 (tm-30) outliers start: 16 outliers final: 8 residues processed: 56 average time/residue: 0.0895 time to fit residues: 6.5594 Evaluate side-chains 50 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2770 Z= 0.415 Angle : 0.731 4.836 3710 Z= 0.422 Chirality : 0.049 0.136 400 Planarity : 0.003 0.010 480 Dihedral : 6.587 20.035 370 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 6.79 % Allowed : 22.50 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.40), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 6 PHE 0.020 0.003 PHE G 20 TYR 0.015 0.004 TYR H 10 ARG 0.003 0.001 ARG D 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.309 Fit side-chains REVERT: B 19 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: C 11 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6526 (tm-30) REVERT: C 19 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6470 (m-10) REVERT: D 11 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6545 (tm-30) REVERT: D 22 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 35 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7002 (ttm) REVERT: F 11 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5831 (tm-30) REVERT: G 19 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: G 22 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7456 (tm-30) REVERT: H 11 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6525 (tm-30) REVERT: H 19 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: I 11 GLU cc_start: 0.6250 (tm-30) cc_final: 0.5655 (tm-30) REVERT: I 22 GLU cc_start: 0.7760 (tm-30) cc_final: 0.6636 (tm-30) REVERT: J 11 GLU cc_start: 0.6125 (tm-30) cc_final: 0.5861 (tm-30) outliers start: 19 outliers final: 11 residues processed: 63 average time/residue: 0.0933 time to fit residues: 7.6956 Evaluate side-chains 59 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 19 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.7720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2770 Z= 0.310 Angle : 0.688 8.015 3710 Z= 0.391 Chirality : 0.049 0.135 400 Planarity : 0.003 0.013 480 Dihedral : 6.005 18.416 370 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.64 % Allowed : 26.79 % Favored : 68.57 % 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: -2.69 (0.40), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 6 PHE 0.019 0.002 PHE C 20 TYR 0.012 0.003 TYR H 10 ARG 0.001 0.000 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.331 Fit side-chains REVERT: C 11 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6414 (tm-30) REVERT: C 35 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7376 (ptm) REVERT: D 11 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6513 (tm-30) REVERT: D 35 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7070 (ttm) REVERT: F 11 GLU cc_start: 0.6343 (tm-30) cc_final: 0.5754 (tm-30) REVERT: G 19 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: G 22 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7404 (tm-30) REVERT: G 35 MET cc_start: 0.6692 (ttm) cc_final: 0.6325 (ttt) REVERT: H 11 GLU cc_start: 0.6693 (tm-30) cc_final: 0.6459 (tm-30) REVERT: I 22 GLU cc_start: 0.7792 (tm-30) cc_final: 0.6843 (tm-30) REVERT: J 11 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5842 (tm-30) outliers start: 13 outliers final: 7 residues processed: 58 average time/residue: 0.0973 time to fit residues: 7.6237 Evaluate side-chains 51 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 20.0000 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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: 0.6549 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2770 Z= 0.325 Angle : 0.735 7.649 3710 Z= 0.413 Chirality : 0.049 0.136 400 Planarity : 0.003 0.012 480 Dihedral : 5.975 18.644 370 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.29 % Allowed : 30.00 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.40), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 6 PHE 0.018 0.003 PHE C 20 TYR 0.012 0.003 TYR H 10 ARG 0.001 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.336 Fit side-chains REVERT: C 11 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6483 (tm-30) REVERT: D 11 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6537 (tm-30) REVERT: D 35 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7159 (ttm) REVERT: F 11 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5872 (tm-30) REVERT: F 19 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: G 19 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: G 22 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7417 (tm-30) REVERT: H 11 GLU cc_start: 0.6604 (tm-30) cc_final: 0.6322 (tm-30) REVERT: I 22 GLU cc_start: 0.7778 (tm-30) cc_final: 0.6840 (tm-30) REVERT: J 11 GLU cc_start: 0.6105 (tm-30) cc_final: 0.5875 (tm-30) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.0929 time to fit residues: 7.1601 Evaluate side-chains 54 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain J residue 7 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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: 0.6534 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2770 Z= 0.284 Angle : 0.721 8.275 3710 Z= 0.400 Chirality : 0.049 0.135 400 Planarity : 0.003 0.015 480 Dihedral : 5.751 17.896 370 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.79 % Allowed : 32.86 % Favored : 65.36 % 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: -2.99 (0.40), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 6 PHE 0.017 0.002 PHE C 20 TYR 0.010 0.002 TYR H 10 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.327 Fit side-chains REVERT: C 11 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6479 (tm-30) REVERT: D 11 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6472 (tm-30) REVERT: D 35 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7215 (ttm) REVERT: F 11 GLU cc_start: 0.6371 (OUTLIER) cc_final: 0.5784 (tm-30) REVERT: F 19 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: F 22 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7493 (tm-30) REVERT: G 22 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7284 (tm-30) REVERT: G 35 MET cc_start: 0.6503 (ttt) cc_final: 0.5746 (ttt) REVERT: H 11 GLU cc_start: 0.6561 (tm-30) cc_final: 0.6277 (tm-30) REVERT: I 22 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6810 (tm-30) REVERT: J 11 GLU cc_start: 0.6137 (tm-30) cc_final: 0.5901 (tm-30) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.0921 time to fit residues: 6.6492 Evaluate side-chains 54 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 19 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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: 0.6595 moved from start: 0.8348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2770 Z= 0.437 Angle : 0.813 7.194 3710 Z= 0.453 Chirality : 0.050 0.132 400 Planarity : 0.003 0.012 480 Dihedral : 6.329 19.804 370 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 24.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.50 % Allowed : 33.57 % Favored : 63.93 % 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: -3.17 (0.40), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 6 PHE 0.018 0.004 PHE C 20 TYR 0.017 0.004 TYR C 10 ARG 0.002 0.001 ARG C 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.342 Fit side-chains REVERT: E 11 GLU cc_start: 0.6232 (tm-30) cc_final: 0.5937 (tm-30) REVERT: C 11 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6533 (tm-30) REVERT: D 11 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6342 (tm-30) REVERT: D 35 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7221 (ttm) REVERT: F 11 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5736 (tm-30) REVERT: F 19 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: F 22 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7488 (tm-30) REVERT: G 22 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7410 (tm-30) REVERT: H 11 GLU cc_start: 0.6384 (tm-30) cc_final: 0.6109 (tm-30) REVERT: I 22 GLU cc_start: 0.7724 (tm-30) cc_final: 0.6815 (tm-30) REVERT: J 11 GLU cc_start: 0.6081 (tm-30) cc_final: 0.5708 (tm-30) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0897 time to fit residues: 7.0155 Evaluate side-chains 58 residues out of total 280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain I residue 7 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.094230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.086282 restraints weight = 10061.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.087362 restraints weight = 5479.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.088113 restraints weight = 3775.133| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.8393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2770 Z= 0.311 Angle : 0.758 8.154 3710 Z= 0.416 Chirality : 0.049 0.136 400 Planarity : 0.003 0.013 480 Dihedral : 5.870 18.862 370 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.86 % Allowed : 35.00 % Favored : 62.14 % 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: -3.23 (0.39), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 6 PHE 0.018 0.003 PHE G 20 TYR 0.011 0.003 TYR C 10 ARG 0.002 0.000 ARG C 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 796.60 seconds wall clock time: 14 minutes 59.86 seconds (899.86 seconds total)