Starting phenix.real_space_refine on Sun Oct 13 13:54:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/10_2024/7pf6_13369.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/10_2024/7pf6_13369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/10_2024/7pf6_13369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/10_2024/7pf6_13369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/10_2024/7pf6_13369.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf6_13369/10_2024/7pf6_13369.cif" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 8.39, per 1000 atoms: 0.62 Number of scatterers: 13470 At special positions: 0 Unit cell: (118.65, 149.1, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.9% alpha, 2.8% beta 167 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 7.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.681A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.815A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.759A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.144A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.621A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.514A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.619A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.834A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 101 removed outlier: 3.513A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.856A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.835A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.884A pdb=" N GLY U 90 " --> pdb=" O LEU U 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.789A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.492A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.023A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.367A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 431 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 852 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 4932 1.45 - 1.57: 6305 1.57 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 610 " pdb=" O3' DG J 610 " ideal model delta sigma weight residual 1.422 1.524 -0.102 3.00e-02 1.11e+03 1.15e+01 bond pdb=" C3' DT I 167 " pdb=" O3' DT I 167 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C3' DG J 675 " pdb=" O3' DG J 675 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" C ASN C 110 " pdb=" N ILE C 111 " ideal model delta sigma weight residual 1.331 1.307 0.023 1.27e-02 6.20e+03 3.40e+00 bond pdb=" CG1 ILE E 130 " pdb=" CD1 ILE E 130 " ideal model delta sigma weight residual 1.513 1.444 0.069 3.90e-02 6.57e+02 3.09e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 20808 5.95 - 11.89: 42 11.89 - 17.84: 0 17.84 - 23.79: 2 23.79 - 29.73: 1 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 108.00 78.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP1 DG J 611 " ideal model delta sigma weight residual 108.00 85.49 22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" OP1 DG J 611 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 120.00 141.43 -21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb=" N ILE G 79 " pdb=" CA ILE G 79 " pdb=" C ILE G 79 " ideal model delta sigma weight residual 108.45 102.43 6.02 1.20e+00 6.94e-01 2.52e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 119.47 -8.45 1.86e+00 2.89e-01 2.07e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 6024 34.71 - 69.42: 1725 69.42 - 104.13: 44 104.13 - 138.84: 3 138.84 - 173.55: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLN G 24 " pdb=" C GLN G 24 " pdb=" N PHE G 25 " pdb=" CA PHE G 25 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ILE H 54 " pdb=" C ILE H 54 " pdb=" N SER H 55 " pdb=" CA SER H 55 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 2375 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.535: 0 1.535 - 1.919: 1 Chirality restraints: 2376 Sorted by residual: chirality pdb=" P DG J 611 " pdb=" OP1 DG J 611 " pdb=" OP2 DG J 611 " pdb=" O5' DG J 611 " both_signs ideal model delta sigma weight residual True 2.35 0.43 1.92 2.00e-01 2.50e+01 9.21e+01 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO G 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.034 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC I 30 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 103 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2943 2.79 - 3.32: 12785 3.32 - 3.85: 29386 3.85 - 4.37: 32078 4.37 - 4.90: 44329 Nonbonded interactions: 121521 Sorted by model distance: nonbonded pdb=" NZ LYS A 37 " pdb=" OP1 DC J 726 " model vdw 2.268 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.291 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.309 3.040 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 92 " model vdw 2.313 3.120 nonbonded pdb=" OG SER F 47 " pdb=" OP1 DC J 662 " model vdw 2.314 3.040 ... (remaining 121516 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.970 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 38.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 14386 Z= 0.360 Angle : 0.986 29.733 20853 Z= 0.539 Chirality : 0.064 1.919 2376 Planarity : 0.008 0.084 1478 Dihedral : 29.581 173.553 6233 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.75 (0.26), residues: 825 helix: -0.26 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 75 PHE 0.032 0.003 PHE E 104 TYR 0.034 0.004 TYR E 54 ARG 0.014 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.6986 (mm) cc_final: 0.5837 (mm) REVERT: A 90 MET cc_start: 0.8665 (mmp) cc_final: 0.8320 (mmp) REVERT: A 93 GLN cc_start: 0.8953 (tt0) cc_final: 0.8694 (tp40) REVERT: A 94 GLU cc_start: 0.8981 (mp0) cc_final: 0.8595 (pm20) REVERT: B 68 ASP cc_start: 0.9022 (m-30) cc_final: 0.8784 (m-30) REVERT: C 62 ILE cc_start: 0.9108 (pt) cc_final: 0.8908 (pt) REVERT: C 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8361 (p0) REVERT: D 108 LYS cc_start: 0.9237 (mppt) cc_final: 0.8997 (mtmm) REVERT: E 104 PHE cc_start: 0.8634 (m-80) cc_final: 0.8386 (m-80) REVERT: F 62 LEU cc_start: 0.9648 (mt) cc_final: 0.9444 (mt) REVERT: F 63 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7914 (tm-30) REVERT: G 36 LYS cc_start: 0.9070 (mppt) cc_final: 0.8656 (mppt) REVERT: G 64 GLU cc_start: 0.8945 (tp30) cc_final: 0.8717 (tp30) REVERT: G 95 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8448 (mmmt) REVERT: H 47 GLN cc_start: 0.9116 (mt0) cc_final: 0.8805 (mt0) REVERT: H 85 LYS cc_start: 0.9417 (mppt) cc_final: 0.9120 (tptp) REVERT: H 106 LEU cc_start: 0.9607 (tp) cc_final: 0.9403 (tp) REVERT: H 113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2900 time to fit residues: 72.5817 Evaluate side-chains 120 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14386 Z= 0.311 Angle : 0.754 27.281 20853 Z= 0.424 Chirality : 0.057 2.060 2376 Planarity : 0.006 0.066 1478 Dihedral : 32.734 171.525 4581 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.88 % Allowed : 10.53 % Favored : 87.59 % 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: 0.61 (0.28), residues: 825 helix: 0.86 (0.21), residues: 579 sheet: None (None), residues: 0 loop : -0.49 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.012 0.002 PHE G 25 TYR 0.028 0.003 TYR F 88 ARG 0.009 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8873 (m-80) cc_final: 0.8637 (m-80) REVERT: A 93 GLN cc_start: 0.9166 (tt0) cc_final: 0.8821 (tp40) REVERT: B 68 ASP cc_start: 0.9101 (m-30) cc_final: 0.8878 (m-30) REVERT: B 85 ASP cc_start: 0.8370 (m-30) cc_final: 0.8091 (m-30) REVERT: D 46 LYS cc_start: 0.8652 (mmtt) cc_final: 0.7881 (mmmt) REVERT: D 108 LYS cc_start: 0.9171 (mppt) cc_final: 0.8726 (mmtm) REVERT: E 77 ASP cc_start: 0.9185 (m-30) cc_final: 0.8705 (t0) REVERT: E 108 ASN cc_start: 0.8861 (m-40) cc_final: 0.8602 (m110) REVERT: F 63 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7923 (tm-30) REVERT: G 36 LYS cc_start: 0.8839 (mppt) cc_final: 0.8588 (mmtm) REVERT: G 64 GLU cc_start: 0.8743 (tp30) cc_final: 0.8503 (tp30) REVERT: G 95 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8597 (mmmt) REVERT: H 47 GLN cc_start: 0.9168 (mt0) cc_final: 0.8735 (mt0) REVERT: H 85 LYS cc_start: 0.9378 (mppt) cc_final: 0.8938 (tptp) outliers start: 13 outliers final: 7 residues processed: 146 average time/residue: 0.2372 time to fit residues: 51.5055 Evaluate side-chains 116 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14386 Z= 0.329 Angle : 0.756 27.336 20853 Z= 0.426 Chirality : 0.058 2.051 2376 Planarity : 0.006 0.056 1478 Dihedral : 32.896 172.430 4581 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 14.72 % Favored : 83.41 % 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: 0.69 (0.28), residues: 825 helix: 0.91 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.51 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 49 PHE 0.025 0.002 PHE E 104 TYR 0.039 0.003 TYR F 88 ARG 0.006 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8891 (m-80) cc_final: 0.8589 (m-80) REVERT: A 55 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9122 (mp10) REVERT: A 93 GLN cc_start: 0.9070 (tt0) cc_final: 0.8717 (tp40) REVERT: B 44 LYS cc_start: 0.7751 (pttt) cc_final: 0.7385 (pttp) REVERT: B 68 ASP cc_start: 0.9084 (m-30) cc_final: 0.8864 (m-30) REVERT: B 85 ASP cc_start: 0.8402 (m-30) cc_final: 0.8098 (m-30) REVERT: C 25 PHE cc_start: 0.8523 (m-80) cc_final: 0.8231 (m-80) REVERT: D 46 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7979 (mmmt) REVERT: D 108 LYS cc_start: 0.9217 (mppt) cc_final: 0.8789 (mmtm) REVERT: E 77 ASP cc_start: 0.9216 (m-30) cc_final: 0.8710 (t70) REVERT: E 108 ASN cc_start: 0.8905 (m-40) cc_final: 0.8583 (m110) REVERT: F 63 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7915 (tm-30) REVERT: G 36 LYS cc_start: 0.8803 (mppt) cc_final: 0.8566 (mmtm) REVERT: G 64 GLU cc_start: 0.8767 (tp30) cc_final: 0.8160 (tp30) REVERT: G 68 ASN cc_start: 0.9192 (m-40) cc_final: 0.8794 (m-40) REVERT: G 95 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8684 (mmmt) REVERT: H 113 GLU cc_start: 0.9026 (tp30) cc_final: 0.8762 (tp30) outliers start: 13 outliers final: 9 residues processed: 134 average time/residue: 0.2876 time to fit residues: 57.2690 Evaluate side-chains 119 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14386 Z= 0.256 Angle : 0.726 27.096 20853 Z= 0.408 Chirality : 0.056 2.003 2376 Planarity : 0.005 0.055 1478 Dihedral : 32.706 171.986 4581 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.88 % Allowed : 17.89 % Favored : 80.23 % 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: 0.91 (0.28), residues: 825 helix: 1.11 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.56 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 49 PHE 0.020 0.002 PHE E 104 TYR 0.039 0.002 TYR F 88 ARG 0.003 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8889 (m-80) cc_final: 0.8558 (m-80) REVERT: A 93 GLN cc_start: 0.8989 (tt0) cc_final: 0.8633 (tp-100) REVERT: A 105 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8545 (mt-10) REVERT: B 44 LYS cc_start: 0.7759 (pttt) cc_final: 0.7393 (pttp) REVERT: B 68 ASP cc_start: 0.9089 (m-30) cc_final: 0.8875 (m-30) REVERT: B 85 ASP cc_start: 0.8351 (m-30) cc_final: 0.8040 (m-30) REVERT: C 25 PHE cc_start: 0.8497 (m-80) cc_final: 0.8150 (m-80) REVERT: D 46 LYS cc_start: 0.8684 (mmtt) cc_final: 0.7922 (mmmt) REVERT: E 77 ASP cc_start: 0.9219 (m-30) cc_final: 0.8677 (t0) REVERT: E 79 LYS cc_start: 0.8007 (tmtt) cc_final: 0.7408 (tmtt) REVERT: E 108 ASN cc_start: 0.8845 (m-40) cc_final: 0.8539 (m-40) REVERT: F 63 GLU cc_start: 0.8453 (tm-30) cc_final: 0.7866 (tm-30) REVERT: F 74 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8530 (tm-30) REVERT: G 36 LYS cc_start: 0.8800 (mppt) cc_final: 0.8558 (mmtm) REVERT: G 64 GLU cc_start: 0.8747 (tp30) cc_final: 0.8024 (tp30) REVERT: G 68 ASN cc_start: 0.9200 (m-40) cc_final: 0.8735 (m-40) REVERT: G 95 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8725 (mmmt) REVERT: H 113 GLU cc_start: 0.8979 (tp30) cc_final: 0.8719 (tp30) outliers start: 13 outliers final: 11 residues processed: 137 average time/residue: 0.2949 time to fit residues: 58.3638 Evaluate side-chains 127 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN D 109 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 14386 Z= 0.447 Angle : 0.845 29.531 20853 Z= 0.472 Chirality : 0.059 1.959 2376 Planarity : 0.006 0.064 1478 Dihedral : 33.312 172.538 4581 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.32 % Allowed : 20.35 % Favored : 76.33 % 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: 0.19 (0.28), residues: 825 helix: 0.62 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.86 (0.35), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS D 109 PHE 0.034 0.002 PHE E 104 TYR 0.045 0.003 TYR F 88 ARG 0.007 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8903 (m-80) cc_final: 0.8578 (m-80) REVERT: A 105 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8472 (mt-10) REVERT: B 85 ASP cc_start: 0.8355 (m-30) cc_final: 0.7994 (m-30) REVERT: D 42 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7834 (t80) REVERT: E 79 LYS cc_start: 0.8241 (tmtt) cc_final: 0.7630 (tmtt) REVERT: E 108 ASN cc_start: 0.9037 (m-40) cc_final: 0.8767 (m-40) REVERT: F 63 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8164 (tm-30) REVERT: G 64 GLU cc_start: 0.8780 (tp30) cc_final: 0.8209 (tp30) REVERT: G 95 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8753 (mmmt) REVERT: H 113 GLU cc_start: 0.9047 (tp30) cc_final: 0.8815 (tp30) outliers start: 23 outliers final: 14 residues processed: 131 average time/residue: 0.3004 time to fit residues: 57.9399 Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 0.0010 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14386 Z= 0.224 Angle : 0.740 27.461 20853 Z= 0.413 Chirality : 0.055 1.936 2376 Planarity : 0.004 0.049 1478 Dihedral : 32.847 173.046 4581 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 22.08 % Favored : 76.48 % 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: 0.73 (0.28), residues: 825 helix: 1.03 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.79 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 49 PHE 0.032 0.002 PHE E 104 TYR 0.025 0.002 TYR H 83 ARG 0.004 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8889 (m-80) cc_final: 0.8562 (m-80) REVERT: A 93 GLN cc_start: 0.8891 (tt0) cc_final: 0.8507 (tm-30) REVERT: A 94 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8903 (mt-10) REVERT: A 105 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8531 (mt-10) REVERT: B 44 LYS cc_start: 0.8032 (pttt) cc_final: 0.7666 (pttp) REVERT: B 79 LYS cc_start: 0.9296 (tptt) cc_final: 0.9024 (tppt) REVERT: C 25 PHE cc_start: 0.8429 (m-80) cc_final: 0.8107 (m-80) REVERT: D 46 LYS cc_start: 0.8616 (mmtt) cc_final: 0.7743 (mmmt) REVERT: E 74 ILE cc_start: 0.9089 (mm) cc_final: 0.8814 (mm) REVERT: E 77 ASP cc_start: 0.9278 (m-30) cc_final: 0.8938 (p0) REVERT: E 79 LYS cc_start: 0.8401 (tmtt) cc_final: 0.7791 (tmtt) REVERT: E 97 GLU cc_start: 0.8065 (pt0) cc_final: 0.7634 (mt-10) REVERT: E 104 PHE cc_start: 0.9095 (m-80) cc_final: 0.8648 (m-80) REVERT: F 63 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8118 (tm-30) REVERT: G 36 LYS cc_start: 0.8912 (mppt) cc_final: 0.8701 (mmtm) REVERT: G 64 GLU cc_start: 0.8694 (tp30) cc_final: 0.7855 (tp30) REVERT: G 68 ASN cc_start: 0.9173 (m-40) cc_final: 0.8743 (m-40) REVERT: G 95 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8746 (mmmt) REVERT: H 113 GLU cc_start: 0.8986 (tp30) cc_final: 0.8738 (tp30) outliers start: 10 outliers final: 8 residues processed: 140 average time/residue: 0.2937 time to fit residues: 58.9782 Evaluate side-chains 126 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14386 Z= 0.233 Angle : 0.732 27.574 20853 Z= 0.407 Chirality : 0.055 1.937 2376 Planarity : 0.004 0.051 1478 Dihedral : 32.657 170.976 4581 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.88 % Allowed : 23.38 % Favored : 74.75 % 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: 0.85 (0.28), residues: 825 helix: 1.10 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.70 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 49 PHE 0.032 0.002 PHE E 104 TYR 0.046 0.003 TYR H 83 ARG 0.009 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8730 (m-80) cc_final: 0.8480 (m-80) REVERT: A 93 GLN cc_start: 0.8917 (tt0) cc_final: 0.8446 (tm-30) REVERT: A 105 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8541 (mt-10) REVERT: B 44 LYS cc_start: 0.7977 (pttt) cc_final: 0.7602 (pttp) REVERT: C 25 PHE cc_start: 0.8393 (m-80) cc_final: 0.7971 (m-80) REVERT: C 61 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8696 (tm-30) REVERT: D 46 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8371 (mmtt) REVERT: E 79 LYS cc_start: 0.8362 (tmtt) cc_final: 0.8013 (tmmt) REVERT: E 97 GLU cc_start: 0.8048 (pt0) cc_final: 0.7646 (mt-10) REVERT: E 104 PHE cc_start: 0.8966 (m-80) cc_final: 0.8531 (m-80) REVERT: F 63 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8092 (tm-30) REVERT: G 95 LYS cc_start: 0.9042 (mmmt) cc_final: 0.8742 (mmmt) REVERT: H 71 GLU cc_start: 0.8136 (tt0) cc_final: 0.7688 (tm-30) REVERT: H 113 GLU cc_start: 0.8989 (tp30) cc_final: 0.8741 (tp30) outliers start: 13 outliers final: 11 residues processed: 137 average time/residue: 0.3073 time to fit residues: 60.7413 Evaluate side-chains 130 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 40 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14386 Z= 0.361 Angle : 0.802 28.588 20853 Z= 0.446 Chirality : 0.057 1.925 2376 Planarity : 0.005 0.060 1478 Dihedral : 32.925 171.266 4581 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 23.52 % Favored : 73.59 % 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: 0.44 (0.28), residues: 825 helix: 0.83 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.85 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 49 PHE 0.027 0.002 PHE E 104 TYR 0.048 0.003 TYR F 88 ARG 0.005 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9006 (m-80) cc_final: 0.8674 (m-80) REVERT: A 93 GLN cc_start: 0.8964 (tt0) cc_final: 0.8472 (tm-30) REVERT: A 94 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8752 (pt0) REVERT: A 105 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8567 (mt-10) REVERT: C 61 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8722 (tm-30) REVERT: D 37 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7962 (m-80) REVERT: E 54 TYR cc_start: 0.7979 (m-80) cc_final: 0.7721 (m-80) REVERT: E 79 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7682 (tmtt) REVERT: E 104 PHE cc_start: 0.9094 (m-80) cc_final: 0.8808 (m-80) REVERT: E 106 ASP cc_start: 0.8911 (m-30) cc_final: 0.8629 (m-30) REVERT: F 63 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8211 (tm-30) REVERT: G 95 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8769 (mmmt) REVERT: G 100 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8314 (p) REVERT: H 71 GLU cc_start: 0.8231 (tt0) cc_final: 0.7773 (tm-30) REVERT: H 85 LYS cc_start: 0.9481 (pttm) cc_final: 0.8801 (tptp) REVERT: H 113 GLU cc_start: 0.9011 (tp30) cc_final: 0.8766 (tp30) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.3238 time to fit residues: 62.3391 Evaluate side-chains 129 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14386 Z= 0.318 Angle : 0.785 28.132 20853 Z= 0.436 Chirality : 0.056 1.921 2376 Planarity : 0.005 0.058 1478 Dihedral : 32.938 172.339 4581 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.02 % Allowed : 24.68 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.28), residues: 825 helix: 0.70 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 49 PHE 0.029 0.002 PHE E 104 TYR 0.056 0.003 TYR F 88 ARG 0.005 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8971 (m-80) cc_final: 0.8681 (m-80) REVERT: A 93 GLN cc_start: 0.8957 (tt0) cc_final: 0.8463 (tm-30) REVERT: A 94 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8710 (pt0) REVERT: A 105 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8581 (mt-10) REVERT: B 44 LYS cc_start: 0.8364 (pttt) cc_final: 0.8103 (pttp) REVERT: C 25 PHE cc_start: 0.8417 (m-80) cc_final: 0.8138 (m-80) REVERT: C 61 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8726 (tm-30) REVERT: E 54 TYR cc_start: 0.8084 (m-80) cc_final: 0.7722 (m-80) REVERT: E 79 LYS cc_start: 0.8302 (tmtt) cc_final: 0.7650 (tmtt) REVERT: E 104 PHE cc_start: 0.9025 (m-80) cc_final: 0.8669 (m-80) REVERT: E 106 ASP cc_start: 0.8879 (m-30) cc_final: 0.8567 (m-30) REVERT: G 95 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8789 (mmmt) REVERT: G 100 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8228 (p) REVERT: H 71 GLU cc_start: 0.8217 (tt0) cc_final: 0.7731 (tm-30) REVERT: H 85 LYS cc_start: 0.9409 (pttm) cc_final: 0.8823 (tptp) outliers start: 14 outliers final: 10 residues processed: 130 average time/residue: 0.2913 time to fit residues: 54.5710 Evaluate side-chains 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.0270 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14386 Z= 0.242 Angle : 0.769 27.740 20853 Z= 0.424 Chirality : 0.055 1.918 2376 Planarity : 0.005 0.057 1478 Dihedral : 32.750 171.596 4581 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.30 % Allowed : 26.55 % Favored : 72.15 % 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: 0.31 (0.28), residues: 825 helix: 0.75 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 49 PHE 0.029 0.002 PHE E 104 TYR 0.037 0.003 TYR F 88 ARG 0.003 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8928 (m-80) cc_final: 0.8590 (m-80) REVERT: A 93 GLN cc_start: 0.8972 (tt0) cc_final: 0.8509 (tm-30) REVERT: A 94 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8711 (pt0) REVERT: A 105 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8528 (mt-10) REVERT: B 44 LYS cc_start: 0.8298 (pttt) cc_final: 0.7484 (pptt) REVERT: C 25 PHE cc_start: 0.8446 (m-80) cc_final: 0.8186 (m-80) REVERT: C 61 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8680 (tm-30) REVERT: E 54 TYR cc_start: 0.7886 (m-80) cc_final: 0.7482 (m-80) REVERT: E 97 GLU cc_start: 0.7942 (pt0) cc_final: 0.7437 (mt-10) REVERT: E 104 PHE cc_start: 0.8954 (m-80) cc_final: 0.8563 (m-80) REVERT: E 106 ASP cc_start: 0.8862 (m-30) cc_final: 0.8516 (m-30) REVERT: F 86 VAL cc_start: 0.8345 (t) cc_final: 0.8078 (t) REVERT: G 95 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8755 (mmmt) REVERT: H 71 GLU cc_start: 0.8098 (tt0) cc_final: 0.7683 (tm-30) REVERT: H 85 LYS cc_start: 0.9409 (pttm) cc_final: 0.8789 (tptp) REVERT: H 99 ARG cc_start: 0.9473 (mtp85) cc_final: 0.8973 (ttm110) REVERT: U 92 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6570 (tt) outliers start: 9 outliers final: 7 residues processed: 137 average time/residue: 0.2539 time to fit residues: 50.3711 Evaluate side-chains 129 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain U residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.051072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.042101 restraints weight = 126762.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.043191 restraints weight = 75064.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.043922 restraints weight = 52749.675| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14386 Z= 0.228 Angle : 0.761 27.373 20853 Z= 0.419 Chirality : 0.055 1.935 2376 Planarity : 0.005 0.050 1478 Dihedral : 32.550 170.046 4581 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.30 % Allowed : 26.98 % Favored : 71.72 % 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: 0.35 (0.28), residues: 825 helix: 0.78 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 39 PHE 0.028 0.002 PHE E 104 TYR 0.019 0.002 TYR F 88 ARG 0.004 0.000 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.68 seconds wall clock time: 43 minutes 53.61 seconds (2633.61 seconds total)