Starting phenix.real_space_refine on Wed Sep 25 12:12:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/09_2024/7d69_30591.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/09_2024/7d69_30591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/09_2024/7d69_30591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/09_2024/7d69_30591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/09_2024/7d69_30591.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d69_30591/09_2024/7d69_30591.cif" } resolution = 3.57 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= 1.000 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: 5 Type Number sf(0) Gaussians P 250 5.49 5 S 13 5.16 5 C 6015 2.51 5 N 2012 2.21 5 O 2567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10857 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 716 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 779 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 621 Classifications: {'peptide': 78} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "G" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "I" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2561 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "J" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2564 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Time building chain proxies: 6.37, per 1000 atoms: 0.59 Number of scatterers: 10857 At special positions: 0 Unit cell: (84, 121.8, 114.45, 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 13 16.00 P 250 15.00 O 2567 8.00 N 2012 7.00 C 6015 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: 2.90 Conformation dependent library (CDL) restraints added in 732.1 milliseconds 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 74.0% alpha, 1.9% beta 121 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 51 through 58 removed outlier: 3.897A pdb=" N TYR A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 45 through 72 removed outlier: 3.698A pdb=" N GLY B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.607A pdb=" N ILE D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 84 Processing helix chain 'D' and resid 89 through 101 Processing helix chain 'D' and resid 103 through 122 Processing helix chain 'E' and resid 45 through 58 removed outlier: 4.096A pdb=" N VAL E 49 " --> pdb=" O GLY E 45 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS E 50 " --> pdb=" O MET E 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 58 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 79 Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 133 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 26 through 38 Processing helix chain 'F' and resid 44 through 72 removed outlier: 4.273A pdb=" N GLN F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 54 through 84 Processing helix chain 'H' and resid 89 through 101 Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 42 through 68 removed outlier: 4.162A pdb=" N VAL C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.604A pdb=" N ASP C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 23 through 34 Processing helix chain 'G' and resid 43 through 68 removed outlier: 3.618A pdb=" N TYR G 47 " --> pdb=" O ASP G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 4.103A pdb=" N ASP G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 7.028A pdb=" N ARG A 86 " --> pdb=" O VAL B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94 removed outlier: 3.681A pdb=" N TYR B 94 " --> pdb=" O THR G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87 removed outlier: 7.127A pdb=" N ARG E 86 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 121 through 122 Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.189A pdb=" N THR F 92 " --> pdb=" O THR C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 392 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 121 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 3.37 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: 1840 1.33 - 1.45: 3827 1.45 - 1.57: 5355 1.57 - 1.68: 498 1.68 - 1.80: 22 Bond restraints: 11542 Sorted by residual: bond pdb=" CG1 ILE G 24 " pdb=" CD1 ILE G 24 " ideal model delta sigma weight residual 1.513 1.430 0.083 3.90e-02 6.57e+02 4.50e+00 bond pdb=" CG GLN B 89 " pdb=" CD GLN B 89 " ideal model delta sigma weight residual 1.516 1.473 0.043 2.50e-02 1.60e+03 2.89e+00 bond pdb=" CB VAL A 76 " pdb=" CG1 VAL A 76 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.86e+00 bond pdb=" CG LEU F 86 " pdb=" CD1 LEU F 86 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CB VAL D 37 " pdb=" CG1 VAL D 37 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 ... (remaining 11537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 15163 1.54 - 3.07: 1325 3.07 - 4.61: 121 4.61 - 6.14: 19 6.14 - 7.68: 9 Bond angle restraints: 16637 Sorted by residual: angle pdb=" C3' DT J 114 " pdb=" O3' DT J 114 " pdb=" P DC J 115 " ideal model delta sigma weight residual 120.20 125.46 -5.26 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C3' DT I 120 " pdb=" O3' DT I 120 " pdb=" P DC I 121 " ideal model delta sigma weight residual 120.20 124.81 -4.61 1.50e+00 4.44e-01 9.45e+00 angle pdb=" O4' DA I 113 " pdb=" C1' DA I 113 " pdb=" N9 DA I 113 " ideal model delta sigma weight residual 108.40 104.02 4.38 1.50e+00 4.44e-01 8.51e+00 angle pdb=" C4' DA I 72 " pdb=" C3' DA I 72 " pdb=" O3' DA I 72 " ideal model delta sigma weight residual 110.00 105.80 4.20 1.50e+00 4.44e-01 7.83e+00 angle pdb=" O4' DG J 11 " pdb=" C1' DG J 11 " pdb=" C2' DG J 11 " ideal model delta sigma weight residual 106.40 102.23 4.17 1.50e+00 4.44e-01 7.72e+00 ... (remaining 16632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.69: 4776 30.69 - 61.37: 1489 61.37 - 92.05: 46 92.05 - 122.74: 8 122.74 - 153.42: 4 Dihedral angle restraints: 6323 sinusoidal: 4214 harmonic: 2109 Sorted by residual: dihedral pdb=" C4' DT I 120 " pdb=" C3' DT I 120 " pdb=" O3' DT I 120 " pdb=" P DC I 121 " ideal model delta sinusoidal sigma weight residual 220.00 66.58 153.42 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DT J 114 " pdb=" C3' DT J 114 " pdb=" O3' DT J 114 " pdb=" P DC J 115 " ideal model delta sinusoidal sigma weight residual 220.00 76.89 143.11 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DC I 100 " pdb=" C3' DC I 100 " pdb=" O3' DC I 100 " pdb=" P DT I 101 " ideal model delta sinusoidal sigma weight residual 220.00 94.95 125.05 1 3.50e+01 8.16e-04 1.23e+01 ... (remaining 6320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1230 0.048 - 0.095: 510 0.095 - 0.143: 142 0.143 - 0.190: 19 0.190 - 0.237: 1 Chirality restraints: 1902 Sorted by residual: chirality pdb=" C3' DT J 114 " pdb=" C4' DT J 114 " pdb=" O3' DT J 114 " pdb=" C2' DT J 114 " both_signs ideal model delta sigma weight residual False -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB THR G 98 " pdb=" CA THR G 98 " pdb=" OG1 THR G 98 " pdb=" CG2 THR G 98 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" C4' DA I 83 " pdb=" C5' DA I 83 " pdb=" O4' DA I 83 " pdb=" C3' DA I 83 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1899 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 9 " -0.036 2.00e-02 2.50e+03 1.88e-02 7.92e+00 pdb=" N1 DC I 9 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 9 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC I 9 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I 9 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 9 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 9 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 9 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 9 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 9 " -0.024 2.00e-02 2.50e+03 1.78e-02 7.11e+00 pdb=" N1 DC J 9 " 0.044 2.00e-02 2.50e+03 pdb=" C2 DC J 9 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC J 9 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC J 9 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 9 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J 9 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 9 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 31 " -0.038 2.00e-02 2.50e+03 1.60e-02 7.00e+00 pdb=" N9 DA I 31 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 31 " 0.014 2.00e-02 2.50e+03 pdb=" N7 DA I 31 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 31 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 31 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 31 " -0.013 2.00e-02 2.50e+03 pdb=" N1 DA I 31 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 31 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA I 31 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 31 " 0.004 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 186 2.63 - 3.20: 9662 3.20 - 3.76: 21647 3.76 - 4.33: 27367 4.33 - 4.90: 38963 Nonbonded interactions: 97825 Sorted by model distance: nonbonded pdb=" OG SER E 69 " pdb=" NH1 ARG E 73 " model vdw 2.062 3.120 nonbonded pdb=" N ASN D 55 " pdb=" OP1 DA I 12 " model vdw 2.134 3.120 nonbonded pdb=" OG SER C 41 " pdb=" OP1 DG J 98 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR F 68 " pdb=" OE2 GLU H 75 " model vdw 2.203 3.040 nonbonded pdb=" N2 DG I 114 " pdb=" O2 DT J 13 " model vdw 2.210 3.120 ... (remaining 97820 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' and resid 51 through 140) } ncs_group { reference = (chain 'B' and (resid 20 through 96 or (resid 97 and (name N or name CA or name \ C )))) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 7 through 65 or resid 67 through 125)) selection = (chain 'J' and (resid 1 through 59 or resid 61 through 119)) } 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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.009 0.083 11542 Z= 0.528 Angle : 0.883 7.680 16637 Z= 0.522 Chirality : 0.054 0.237 1902 Planarity : 0.005 0.042 1240 Dihedral : 28.860 153.423 4955 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: -1.18 (0.29), residues: 711 helix: -0.22 (0.21), residues: 513 sheet: None (None), residues: 0 loop : -2.04 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.002 HIS G 79 PHE 0.025 0.004 PHE C 94 TYR 0.020 0.003 TYR C 47 ARG 0.013 0.001 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7769 (mp0) REVERT: B 35 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7724 (mtt90) REVERT: D 78 ASN cc_start: 0.8833 (t0) cc_final: 0.8304 (t0) REVERT: D 82 ILE cc_start: 0.9136 (mt) cc_final: 0.8678 (mt) REVERT: F 31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: F 87 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8581 (ttmt) REVERT: H 51 LEU cc_start: 0.7360 (pp) cc_final: 0.7109 (pp) REVERT: C 96 ASN cc_start: 0.8080 (p0) cc_final: 0.7802 (p0) REVERT: C 101 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7940 (mt-10) REVERT: G 85 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7337 (mtt180) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.3447 time to fit residues: 54.7283 Evaluate side-chains 100 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN E 44 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11542 Z= 0.219 Angle : 0.636 6.431 16637 Z= 0.373 Chirality : 0.038 0.170 1902 Planarity : 0.005 0.059 1240 Dihedral : 31.892 177.650 3513 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % 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: 0.42 (0.29), residues: 711 helix: 0.90 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.32 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS G 79 PHE 0.021 0.002 PHE G 60 TYR 0.013 0.001 TYR E 55 ARG 0.004 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7618 (mtt90) REVERT: F 31 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8022 (mmm160) REVERT: F 51 ARG cc_start: 0.8121 (mtt180) cc_final: 0.7865 (mtt-85) REVERT: F 87 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8515 (ttmt) REVERT: H 41 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8089 (tm-30) REVERT: H 84 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7754 (mmtt) REVERT: H 98 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8396 (ttmm) REVERT: C 101 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7843 (mt-10) REVERT: G 62 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7353 (mm-30) outliers start: 10 outliers final: 3 residues processed: 120 average time/residue: 0.2865 time to fit residues: 45.5476 Evaluate side-chains 98 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN C 30 HIS C 78 ASN C 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11542 Z= 0.375 Angle : 0.669 8.118 16637 Z= 0.384 Chirality : 0.040 0.177 1902 Planarity : 0.005 0.048 1240 Dihedral : 31.914 176.623 3513 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.56 % Allowed : 17.96 % Favored : 78.48 % 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: 0.48 (0.29), residues: 711 helix: 0.96 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 79 PHE 0.018 0.002 PHE G 60 TYR 0.015 0.002 TYR E 102 ARG 0.008 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 78 ASN cc_start: 0.8849 (t0) cc_final: 0.8292 (t0) REVERT: D 82 ILE cc_start: 0.9095 (mt) cc_final: 0.8667 (mt) REVERT: D 119 LYS cc_start: 0.8722 (ttmt) cc_final: 0.8168 (tmmt) REVERT: E 62 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7901 (mm) REVERT: F 36 ARG cc_start: 0.8778 (ttm170) cc_final: 0.8559 (ttm170) REVERT: F 87 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8505 (ttmt) REVERT: H 84 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7755 (mmtt) REVERT: H 104 GLU cc_start: 0.7577 (tp30) cc_final: 0.7358 (tp30) REVERT: C 62 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7383 (mm-30) REVERT: C 89 GLU cc_start: 0.7048 (mp0) cc_final: 0.6810 (pm20) REVERT: C 101 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7869 (mt-10) REVERT: G 81 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8378 (tp) outliers start: 22 outliers final: 14 residues processed: 118 average time/residue: 0.2881 time to fit residues: 45.5154 Evaluate side-chains 110 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11542 Z= 0.283 Angle : 0.624 13.179 16637 Z= 0.360 Chirality : 0.038 0.220 1902 Planarity : 0.004 0.046 1240 Dihedral : 31.602 177.216 3513 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.56 % Allowed : 18.28 % Favored : 78.16 % 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: 0.86 (0.29), residues: 711 helix: 1.24 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.26 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 79 PHE 0.022 0.002 PHE G 60 TYR 0.012 0.002 TYR E 102 ARG 0.008 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: D 119 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8149 (tmmt) REVERT: E 62 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7855 (mm) REVERT: F 31 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7998 (mmm160) REVERT: F 51 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7972 (mtt-85) REVERT: F 87 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8511 (ttmt) REVERT: H 84 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7728 (mmtt) REVERT: C 62 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 101 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7766 (mt-10) outliers start: 22 outliers final: 17 residues processed: 108 average time/residue: 0.3056 time to fit residues: 43.2294 Evaluate side-chains 108 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11542 Z= 0.216 Angle : 0.585 9.409 16637 Z= 0.343 Chirality : 0.035 0.135 1902 Planarity : 0.004 0.072 1240 Dihedral : 31.324 177.266 3513 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.56 % Allowed : 19.26 % Favored : 77.18 % 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: 1.38 (0.30), residues: 711 helix: 1.66 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.19 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS G 79 PHE 0.016 0.002 PHE G 60 TYR 0.011 0.001 TYR E 102 ARG 0.012 0.001 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.824 Fit side-chains REVERT: D 86 ASN cc_start: 0.7539 (m-40) cc_final: 0.7117 (m-40) REVERT: F 51 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7908 (mtt-85) REVERT: F 87 LYS cc_start: 0.8840 (ttpt) cc_final: 0.8493 (ttmt) REVERT: H 84 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7622 (mmtt) REVERT: H 104 GLU cc_start: 0.7626 (tp30) cc_final: 0.7410 (tp30) REVERT: C 62 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7387 (mm-30) REVERT: C 101 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7728 (mt-10) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.2942 time to fit residues: 44.0300 Evaluate side-chains 102 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11542 Z= 0.305 Angle : 0.619 11.672 16637 Z= 0.357 Chirality : 0.037 0.157 1902 Planarity : 0.004 0.045 1240 Dihedral : 31.416 177.613 3513 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.56 % Allowed : 21.04 % Favored : 75.40 % 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: 1.10 (0.29), residues: 711 helix: 1.47 (0.21), residues: 519 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 79 PHE 0.015 0.002 PHE G 60 TYR 0.017 0.002 TYR F 84 ARG 0.004 0.001 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.797 Fit side-chains REVERT: D 86 ASN cc_start: 0.7700 (m-40) cc_final: 0.7237 (m-40) REVERT: D 108 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8373 (mp) REVERT: D 119 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8353 (ttmt) REVERT: F 51 ARG cc_start: 0.8251 (mtt180) cc_final: 0.8045 (mtt-85) REVERT: F 87 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8543 (ttmt) REVERT: H 84 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7642 (mmtt) REVERT: H 104 GLU cc_start: 0.7828 (tp30) cc_final: 0.7258 (tp30) REVERT: H 107 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7545 (tmm-80) REVERT: C 101 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7795 (mt-10) outliers start: 22 outliers final: 18 residues processed: 111 average time/residue: 0.2874 time to fit residues: 43.1077 Evaluate side-chains 111 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 92 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11542 Z= 0.190 Angle : 0.573 9.934 16637 Z= 0.337 Chirality : 0.035 0.138 1902 Planarity : 0.004 0.043 1240 Dihedral : 31.096 179.099 3513 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.91 % Allowed : 22.65 % Favored : 74.43 % 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: 1.60 (0.30), residues: 711 helix: 1.84 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.17 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 79 PHE 0.014 0.002 PHE G 60 TYR 0.012 0.001 TYR F 84 ARG 0.006 0.000 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.783 Fit side-chains REVERT: D 86 ASN cc_start: 0.7655 (m-40) cc_final: 0.7243 (m-40) REVERT: D 108 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8355 (mp) outliers start: 18 outliers final: 15 residues processed: 104 average time/residue: 0.2492 time to fit residues: 35.4595 Evaluate side-chains 99 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN E 44 GLN C 96 ASN G 30 HIS G 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 11542 Z= 0.416 Angle : 0.662 9.877 16637 Z= 0.377 Chirality : 0.040 0.208 1902 Planarity : 0.005 0.051 1240 Dihedral : 31.473 176.649 3513 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.88 % Allowed : 20.87 % Favored : 75.24 % 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: 0.76 (0.29), residues: 711 helix: 1.17 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.31 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 71 PHE 0.014 0.002 PHE G 60 TYR 0.028 0.002 TYR F 84 ARG 0.006 0.001 ARG E 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.822 Fit side-chains REVERT: D 78 ASN cc_start: 0.8879 (t0) cc_final: 0.8311 (t0) REVERT: D 82 ILE cc_start: 0.8993 (mt) cc_final: 0.8584 (mp) REVERT: D 108 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8464 (mp) REVERT: H 104 GLU cc_start: 0.7737 (tp30) cc_final: 0.7266 (tp30) REVERT: H 107 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7594 (tmm-80) outliers start: 24 outliers final: 17 residues processed: 112 average time/residue: 0.2734 time to fit residues: 41.0476 Evaluate side-chains 106 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11542 Z= 0.227 Angle : 0.588 9.593 16637 Z= 0.343 Chirality : 0.036 0.161 1902 Planarity : 0.005 0.098 1240 Dihedral : 31.097 178.494 3513 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.91 % Allowed : 22.49 % Favored : 74.60 % 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: 1.22 (0.30), residues: 711 helix: 1.53 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.18 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 79 PHE 0.016 0.002 PHE G 60 TYR 0.018 0.002 TYR F 84 ARG 0.014 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: D 108 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 119 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8227 (tttp) outliers start: 18 outliers final: 15 residues processed: 102 average time/residue: 0.2626 time to fit residues: 36.6424 Evaluate side-chains 101 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN C 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11542 Z= 0.260 Angle : 0.596 8.994 16637 Z= 0.347 Chirality : 0.036 0.154 1902 Planarity : 0.005 0.080 1240 Dihedral : 31.104 177.922 3513 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.91 % Allowed : 22.98 % Favored : 74.11 % 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: 1.29 (0.30), residues: 711 helix: 1.59 (0.21), residues: 519 sheet: None (None), residues: 0 loop : -1.18 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 79 PHE 0.009 0.002 PHE E 68 TYR 0.019 0.002 TYR F 84 ARG 0.011 0.001 ARG B 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1422 Ramachandran restraints generated. 711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.816 Fit side-chains REVERT: D 86 ASN cc_start: 0.7725 (m-40) cc_final: 0.7270 (m-40) REVERT: D 108 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8532 (mp) REVERT: E 127 MET cc_start: 0.8721 (ttt) cc_final: 0.8372 (ttt) REVERT: H 104 GLU cc_start: 0.7612 (tp30) cc_final: 0.7300 (tp30) REVERT: H 107 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7581 (tmm-80) outliers start: 18 outliers final: 16 residues processed: 101 average time/residue: 0.2569 time to fit residues: 35.8263 Evaluate side-chains 102 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.1980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.180896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123293 restraints weight = 14945.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125093 restraints weight = 10404.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125052 restraints weight = 9464.819| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11542 Z= 0.180 Angle : 0.567 8.960 16637 Z= 0.334 Chirality : 0.035 0.147 1902 Planarity : 0.004 0.078 1240 Dihedral : 30.829 178.779 3513 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.27 % Allowed : 23.30 % Favored : 74.43 % 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: 1.81 (0.30), residues: 711 helix: 1.97 (0.22), residues: 519 sheet: None (None), residues: 0 loop : -0.98 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 79 PHE 0.013 0.001 PHE G 60 TYR 0.013 0.001 TYR F 84 ARG 0.008 0.001 ARG B 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1666.68 seconds wall clock time: 30 minutes 51.67 seconds (1851.67 seconds total)