Starting phenix.real_space_refine on Mon Mar 11 17:30:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/03_2024/8etv_28600_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/03_2024/8etv_28600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/03_2024/8etv_28600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/03_2024/8etv_28600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/03_2024/8etv_28600_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etv_28600/03_2024/8etv_28600_neut.pdb" } resolution = 3.16 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= 0.011 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 218 5.49 5 S 8 5.16 5 C 4769 2.51 5 N 1634 2.21 5 O 2053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8682 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2240 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2264 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Time building chain proxies: 5.15, per 1000 atoms: 0.59 Number of scatterers: 8682 At special positions: 0 Unit cell: (117.735, 103.54, 105.21, 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 8 16.00 P 218 15.00 O 2053 8.00 N 1634 7.00 C 4769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 991.6 milliseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 986 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 75.8% alpha, 2.7% beta 108 base pairs and 192 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.541A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.546A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.844A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.034A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.666A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.139A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.382A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.532A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.772A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.560A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.860A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.625A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.541A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (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 77 removed outlier: 4.299A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.619A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.311A 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 'C' and resid 42 through 43 removed outlier: 7.380A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.406A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.762A 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 119 278 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 192 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 4.99 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: 1737 1.33 - 1.45: 3088 1.45 - 1.57: 4005 1.57 - 1.69: 436 1.69 - 1.81: 16 Bond restraints: 9282 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.486 -0.064 3.00e-02 1.11e+03 4.56e+00 bond pdb=" CG GLU C 61 " pdb=" CD GLU C 61 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.52e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.41e+00 bond pdb=" C ALA C 60 " pdb=" N GLU C 61 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.31e-02 5.83e+03 2.41e+00 bond pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta sigma weight residual 1.459 1.478 -0.019 1.21e-02 6.83e+03 2.40e+00 ... (remaining 9277 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.22: 988 105.22 - 112.22: 5012 112.22 - 119.22: 2780 119.22 - 126.22: 4012 126.22 - 133.22: 685 Bond angle restraints: 13477 Sorted by residual: angle pdb=" N GLU C 61 " pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " ideal model delta sigma weight residual 110.12 118.88 -8.76 1.47e+00 4.63e-01 3.55e+01 angle pdb=" CB MET D 56 " pdb=" CG MET D 56 " pdb=" SD MET D 56 " ideal model delta sigma weight residual 112.70 127.20 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " pdb=" CG GLU C 61 " ideal model delta sigma weight residual 114.10 123.44 -9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" CA LEU C 115 " pdb=" CB LEU C 115 " pdb=" CG LEU C 115 " ideal model delta sigma weight residual 116.30 129.46 -13.16 3.50e+00 8.16e-02 1.41e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 127.63 -5.17 1.41e+00 5.03e-01 1.34e+01 ... (remaining 13472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 3935 35.02 - 70.04: 1052 70.04 - 105.07: 14 105.07 - 140.09: 0 140.09 - 175.11: 2 Dihedral angle restraints: 5003 sinusoidal: 3480 harmonic: 1523 Sorted by residual: dihedral pdb=" CA LYS F 77 " pdb=" C LYS F 77 " pdb=" N ARG F 78 " pdb=" CA ARG F 78 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ILE F 50 " pdb=" C ILE F 50 " pdb=" N TYR F 51 " pdb=" CA TYR F 51 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.11 -175.11 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1336 0.071 - 0.142: 184 0.142 - 0.213: 12 0.213 - 0.284: 3 0.284 - 0.354: 1 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CG LEU E 61 " pdb=" CB LEU E 61 " pdb=" CD1 LEU E 61 " pdb=" CD2 LEU E 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1533 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO C 80 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " -0.032 2.00e-02 2.50e+03 1.46e-02 5.84e+00 pdb=" N9 DA I -54 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " -0.023 2.00e-02 2.50e+03 1.69e-02 5.74e+00 pdb=" CG TYR D 80 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " 0.001 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2066 2.82 - 3.34: 7286 3.34 - 3.86: 17089 3.86 - 4.38: 19200 4.38 - 4.90: 26702 Nonbonded interactions: 72343 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 48 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR B 30 " pdb=" OP1 DC I -12 " model vdw 2.324 2.440 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.329 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.346 2.440 nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.366 2.520 ... (remaining 72338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 24 through 94) selection = (chain 'F' and resid 24 through 94) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.420 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: 21.750 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.130 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 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 0.066 9282 Z= 0.335 Angle : 0.874 14.501 13477 Z= 0.496 Chirality : 0.050 0.354 1536 Planarity : 0.008 0.083 944 Dihedral : 28.214 175.111 4017 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.99 (0.33), residues: 512 helix: -0.35 (0.24), residues: 373 sheet: None (None), residues: 0 loop : -1.14 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.016 0.003 PHE E 84 TYR 0.039 0.004 TYR D 80 ARG 0.015 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8711 (mm) cc_final: 0.8504 (mm) REVERT: A 125 GLN cc_start: 0.7609 (mp10) cc_final: 0.7356 (mp10) REVERT: B 36 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: B 66 ILE cc_start: 0.8802 (mm) cc_final: 0.8581 (tp) REVERT: B 73 THR cc_start: 0.8696 (m) cc_final: 0.8432 (m) REVERT: B 81 VAL cc_start: 0.8703 (t) cc_final: 0.8437 (t) REVERT: B 82 THR cc_start: 0.8609 (t) cc_final: 0.8055 (p) REVERT: B 88 TYR cc_start: 0.7286 (m-80) cc_final: 0.6780 (m-80) REVERT: B 91 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7925 (mtmm) REVERT: C 17 ARG cc_start: 0.7434 (ptm160) cc_final: 0.6956 (ptm160) REVERT: C 64 GLU cc_start: 0.7762 (tp30) cc_final: 0.7316 (tp30) REVERT: C 68 ASN cc_start: 0.8035 (m-40) cc_final: 0.6704 (m-40) REVERT: C 72 ASP cc_start: 0.7911 (m-30) cc_final: 0.7525 (m-30) REVERT: C 73 ASN cc_start: 0.8115 (t160) cc_final: 0.7804 (t0) REVERT: C 81 ARG cc_start: 0.7909 (tpt170) cc_final: 0.7549 (tpt170) REVERT: C 99 ARG cc_start: 0.6990 (mpt180) cc_final: 0.6750 (mpt180) REVERT: D 43 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8387 (mmmm) REVERT: D 54 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8510 (mmmm) REVERT: D 60 ASN cc_start: 0.8471 (t0) cc_final: 0.8212 (t0) REVERT: D 69 ARG cc_start: 0.8833 (ttm170) cc_final: 0.8524 (mtp180) REVERT: E 59 GLU cc_start: 0.7117 (tm-30) cc_final: 0.6670 (tm-30) REVERT: E 60 LEU cc_start: 0.7951 (mt) cc_final: 0.7077 (mt) REVERT: E 68 GLN cc_start: 0.7923 (tt0) cc_final: 0.7698 (tt0) REVERT: E 69 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7795 (ttm110) REVERT: E 92 LEU cc_start: 0.8634 (mt) cc_final: 0.8412 (mt) REVERT: E 96 SER cc_start: 0.8309 (m) cc_final: 0.8067 (m) REVERT: F 26 ILE cc_start: 0.8937 (tp) cc_final: 0.8690 (tt) REVERT: F 36 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7214 (mtm-85) REVERT: F 88 TYR cc_start: 0.8081 (m-80) cc_final: 0.7820 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3402 time to fit residues: 91.7673 Evaluate side-chains 220 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9282 Z= 0.291 Angle : 0.641 11.939 13477 Z= 0.379 Chirality : 0.036 0.189 1536 Planarity : 0.005 0.065 944 Dihedral : 30.887 176.553 2968 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.20 % Allowed : 17.62 % Favored : 79.18 % 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: 1.05 (0.36), residues: 512 helix: 1.29 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.84 (0.48), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.015 0.002 PHE D 67 TYR 0.030 0.002 TYR B 88 ARG 0.007 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 232 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.8651 (mm) cc_final: 0.8125 (mm) REVERT: B 81 VAL cc_start: 0.8692 (t) cc_final: 0.8451 (t) REVERT: B 82 THR cc_start: 0.8662 (t) cc_final: 0.8285 (p) REVERT: B 88 TYR cc_start: 0.7472 (m-80) cc_final: 0.7098 (m-80) REVERT: B 90 LEU cc_start: 0.9171 (mm) cc_final: 0.8902 (mp) REVERT: C 17 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7032 (ptm160) REVERT: C 56 GLU cc_start: 0.7618 (tt0) cc_final: 0.7376 (tp30) REVERT: C 57 TYR cc_start: 0.7741 (t80) cc_final: 0.7528 (t80) REVERT: C 64 GLU cc_start: 0.7785 (tp30) cc_final: 0.7559 (tp30) REVERT: C 68 ASN cc_start: 0.8124 (m-40) cc_final: 0.6432 (m-40) REVERT: C 72 ASP cc_start: 0.7956 (m-30) cc_final: 0.7529 (m-30) REVERT: C 99 ARG cc_start: 0.7015 (mpt180) cc_final: 0.6797 (mpt180) REVERT: D 43 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8433 (mmmm) REVERT: D 44 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8072 (tm-30) REVERT: D 60 ASN cc_start: 0.8467 (t0) cc_final: 0.8228 (t0) REVERT: D 69 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8518 (mtp180) REVERT: D 117 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8070 (tmmt) REVERT: E 68 GLN cc_start: 0.8082 (tt0) cc_final: 0.7870 (tt0) REVERT: E 129 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.7827 (tmm-80) REVERT: F 88 TYR cc_start: 0.8222 (m-80) cc_final: 0.7926 (m-80) outliers start: 14 outliers final: 10 residues processed: 233 average time/residue: 0.3444 time to fit residues: 97.4552 Evaluate side-chains 239 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 229 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 17 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9282 Z= 0.274 Angle : 0.616 11.490 13477 Z= 0.366 Chirality : 0.036 0.183 1536 Planarity : 0.005 0.059 944 Dihedral : 30.831 175.215 2968 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.35 % Allowed : 21.05 % 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: 1.69 (0.37), residues: 512 helix: 1.79 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.72 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE F 61 TYR 0.022 0.002 TYR F 51 ARG 0.007 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8483 (tp) cc_final: 0.8262 (tt) REVERT: A 109 LEU cc_start: 0.8671 (mm) cc_final: 0.8166 (mm) REVERT: B 45 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7692 (tpp80) REVERT: B 67 ARG cc_start: 0.7948 (ttm170) cc_final: 0.7659 (ttm-80) REVERT: B 88 TYR cc_start: 0.7521 (m-80) cc_final: 0.7208 (m-80) REVERT: C 17 ARG cc_start: 0.7614 (ptm160) cc_final: 0.7052 (ptm160) REVERT: C 56 GLU cc_start: 0.7607 (tt0) cc_final: 0.7346 (tp30) REVERT: C 68 ASN cc_start: 0.7966 (m-40) cc_final: 0.6521 (m-40) REVERT: C 72 ASP cc_start: 0.7954 (m-30) cc_final: 0.7531 (m-30) REVERT: C 99 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6743 (mpt180) REVERT: D 39 TYR cc_start: 0.7743 (t80) cc_final: 0.7524 (t80) REVERT: D 43 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8429 (mmmm) REVERT: D 44 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8068 (tm-30) REVERT: D 60 ASN cc_start: 0.8503 (t0) cc_final: 0.8262 (t0) REVERT: D 69 ARG cc_start: 0.8700 (ttm170) cc_final: 0.8465 (mtp180) REVERT: E 69 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8046 (mtm-85) REVERT: E 129 ARG cc_start: 0.8139 (mmm-85) cc_final: 0.7828 (tmm-80) outliers start: 19 outliers final: 16 residues processed: 232 average time/residue: 0.3365 time to fit residues: 94.7574 Evaluate side-chains 246 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9282 Z= 0.257 Angle : 0.616 11.650 13477 Z= 0.363 Chirality : 0.035 0.174 1536 Planarity : 0.004 0.056 944 Dihedral : 30.780 175.336 2968 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.49 % Allowed : 24.71 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.37), residues: 512 helix: 2.01 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.57 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE E 78 TYR 0.036 0.003 TYR F 88 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 230 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8487 (tp) cc_final: 0.8260 (tt) REVERT: A 125 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: B 88 TYR cc_start: 0.7523 (m-80) cc_final: 0.7089 (m-80) REVERT: B 91 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8262 (mtmm) REVERT: C 17 ARG cc_start: 0.7606 (ptm160) cc_final: 0.7045 (ptm160) REVERT: C 56 GLU cc_start: 0.7617 (tt0) cc_final: 0.7347 (tt0) REVERT: C 68 ASN cc_start: 0.7814 (m-40) cc_final: 0.7002 (m-40) REVERT: C 72 ASP cc_start: 0.7967 (m-30) cc_final: 0.7552 (m-30) REVERT: C 99 ARG cc_start: 0.6983 (mpt180) cc_final: 0.6738 (mpt180) REVERT: D 43 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8405 (mmmm) REVERT: D 44 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8187 (tm-30) REVERT: D 54 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8607 (mmmm) REVERT: D 60 ASN cc_start: 0.8487 (t0) cc_final: 0.8248 (t0) REVERT: D 69 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8432 (mtp180) REVERT: D 80 TYR cc_start: 0.7051 (m-10) cc_final: 0.6833 (m-10) REVERT: E 69 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8055 (mtm-85) REVERT: E 99 TYR cc_start: 0.7674 (t80) cc_final: 0.7418 (t80) REVERT: E 129 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7894 (mmm-85) REVERT: F 88 TYR cc_start: 0.8270 (m-80) cc_final: 0.7446 (m-80) REVERT: F 91 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7789 (mtmt) outliers start: 24 outliers final: 19 residues processed: 231 average time/residue: 0.3349 time to fit residues: 94.0092 Evaluate side-chains 249 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9282 Z= 0.268 Angle : 0.614 12.113 13477 Z= 0.363 Chirality : 0.035 0.173 1536 Planarity : 0.004 0.057 944 Dihedral : 30.759 175.105 2968 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.64 % Allowed : 24.26 % Favored : 69.11 % 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: 2.18 (0.37), residues: 512 helix: 2.12 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.44 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE F 61 TYR 0.025 0.002 TYR C 57 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8510 (tp) cc_final: 0.8268 (tt) REVERT: A 125 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6679 (mp10) REVERT: B 44 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8181 (mptm) REVERT: B 72 TYR cc_start: 0.8874 (m-10) cc_final: 0.8576 (m-10) REVERT: B 88 TYR cc_start: 0.7589 (m-80) cc_final: 0.6897 (m-80) REVERT: C 56 GLU cc_start: 0.7619 (tt0) cc_final: 0.7364 (tt0) REVERT: C 68 ASN cc_start: 0.7801 (m-40) cc_final: 0.7019 (m-40) REVERT: C 72 ASP cc_start: 0.8000 (m-30) cc_final: 0.7563 (m-30) REVERT: D 43 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8415 (mmmm) REVERT: D 44 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8153 (tm-30) REVERT: D 54 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8613 (mmmm) REVERT: D 60 ASN cc_start: 0.8477 (t0) cc_final: 0.8239 (t0) REVERT: D 80 TYR cc_start: 0.7077 (m-10) cc_final: 0.6720 (m-10) REVERT: E 99 TYR cc_start: 0.7688 (t80) cc_final: 0.7430 (t80) REVERT: E 129 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: F 71 THR cc_start: 0.8733 (m) cc_final: 0.8455 (p) REVERT: F 87 VAL cc_start: 0.8996 (t) cc_final: 0.8502 (t) REVERT: F 88 TYR cc_start: 0.8359 (m-80) cc_final: 0.7373 (m-80) REVERT: F 91 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7791 (mtmt) outliers start: 29 outliers final: 22 residues processed: 231 average time/residue: 0.3361 time to fit residues: 94.6143 Evaluate side-chains 250 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9282 Z= 0.307 Angle : 0.635 12.552 13477 Z= 0.376 Chirality : 0.037 0.176 1536 Planarity : 0.004 0.055 944 Dihedral : 30.764 175.170 2968 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.18 % Allowed : 25.63 % Favored : 68.19 % 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: 1.94 (0.37), residues: 512 helix: 1.93 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.63 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.002 PHE F 61 TYR 0.029 0.002 TYR C 57 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 233 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8570 (tp) cc_final: 0.8321 (tt) REVERT: A 125 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: B 44 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (mptm) REVERT: B 67 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7706 (ttm-80) REVERT: B 72 TYR cc_start: 0.8751 (m-10) cc_final: 0.8507 (m-10) REVERT: B 88 TYR cc_start: 0.7668 (m-80) cc_final: 0.6970 (m-80) REVERT: B 91 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8300 (mttm) REVERT: C 17 ARG cc_start: 0.8065 (mtm180) cc_final: 0.7820 (mtm180) REVERT: C 56 GLU cc_start: 0.7659 (tt0) cc_final: 0.7388 (tt0) REVERT: C 68 ASN cc_start: 0.7796 (m-40) cc_final: 0.7037 (m-40) REVERT: C 72 ASP cc_start: 0.8006 (m-30) cc_final: 0.7568 (m-30) REVERT: D 43 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8401 (mmmm) REVERT: D 44 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 60 ASN cc_start: 0.8509 (t0) cc_final: 0.8268 (t0) REVERT: D 69 ARG cc_start: 0.8717 (mtp180) cc_final: 0.8504 (mtm-85) REVERT: D 80 TYR cc_start: 0.7139 (m-10) cc_final: 0.6632 (m-10) REVERT: E 99 TYR cc_start: 0.7700 (t80) cc_final: 0.7437 (t80) REVERT: E 129 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7864 (tmm-80) REVERT: F 87 VAL cc_start: 0.9046 (t) cc_final: 0.8573 (t) REVERT: F 88 TYR cc_start: 0.8355 (m-80) cc_final: 0.7486 (m-80) REVERT: F 91 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7798 (mtmt) outliers start: 27 outliers final: 21 residues processed: 235 average time/residue: 0.3315 time to fit residues: 94.0869 Evaluate side-chains 253 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 82 HIS C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9282 Z= 0.250 Angle : 0.625 11.940 13477 Z= 0.367 Chirality : 0.035 0.175 1536 Planarity : 0.004 0.047 944 Dihedral : 30.751 175.011 2968 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.26 % Allowed : 28.83 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.37), residues: 512 helix: 2.06 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.49 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.010 0.001 PHE F 61 TYR 0.034 0.002 TYR C 57 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8559 (tp) cc_final: 0.8316 (tt) REVERT: A 125 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6619 (mp10) REVERT: A 128 ARG cc_start: 0.7991 (mmm-85) cc_final: 0.7764 (mmm-85) REVERT: B 67 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7684 (ttm-80) REVERT: B 72 TYR cc_start: 0.8787 (m-10) cc_final: 0.8513 (m-10) REVERT: B 88 TYR cc_start: 0.7657 (m-80) cc_final: 0.6963 (m-80) REVERT: B 91 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8345 (mttm) REVERT: C 17 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7802 (mtm180) REVERT: C 56 GLU cc_start: 0.7617 (tt0) cc_final: 0.7346 (tt0) REVERT: C 68 ASN cc_start: 0.7747 (m-40) cc_final: 0.6937 (m-40) REVERT: C 72 ASP cc_start: 0.7970 (m-30) cc_final: 0.7533 (m-30) REVERT: D 43 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8371 (mmmm) REVERT: D 44 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8130 (tm-30) REVERT: D 60 ASN cc_start: 0.8463 (t0) cc_final: 0.8235 (t0) REVERT: D 69 ARG cc_start: 0.8707 (mtp180) cc_final: 0.8487 (mtm-85) REVERT: D 80 TYR cc_start: 0.7136 (m-10) cc_final: 0.6620 (m-10) REVERT: E 99 TYR cc_start: 0.7681 (t80) cc_final: 0.7421 (t80) REVERT: E 120 MET cc_start: 0.6727 (mtp) cc_final: 0.6515 (mtm) REVERT: E 129 ARG cc_start: 0.8151 (mmm-85) cc_final: 0.7845 (tmm-80) REVERT: F 71 THR cc_start: 0.8758 (m) cc_final: 0.8486 (p) REVERT: F 88 TYR cc_start: 0.8316 (m-80) cc_final: 0.7838 (m-80) outliers start: 23 outliers final: 19 residues processed: 231 average time/residue: 0.3394 time to fit residues: 94.8241 Evaluate side-chains 249 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 229 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 27 optimal weight: 0.0870 chunk 50 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9282 Z= 0.271 Angle : 0.635 13.357 13477 Z= 0.371 Chirality : 0.036 0.163 1536 Planarity : 0.004 0.043 944 Dihedral : 30.738 175.057 2968 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.49 % Allowed : 29.98 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.37), residues: 512 helix: 2.03 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.58 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE F 61 TYR 0.040 0.002 TYR C 57 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 227 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8573 (tp) cc_final: 0.8324 (tt) REVERT: A 125 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6638 (mp10) REVERT: A 128 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7781 (mmm-85) REVERT: B 72 TYR cc_start: 0.8797 (m-10) cc_final: 0.8511 (m-10) REVERT: B 88 TYR cc_start: 0.7675 (m-10) cc_final: 0.7048 (m-80) REVERT: B 91 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8362 (mttm) REVERT: C 17 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7814 (mtm180) REVERT: C 56 GLU cc_start: 0.7628 (tt0) cc_final: 0.7345 (tt0) REVERT: C 61 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: C 68 ASN cc_start: 0.7752 (m-40) cc_final: 0.6994 (m-40) REVERT: C 72 ASP cc_start: 0.7981 (m-30) cc_final: 0.7562 (m-30) REVERT: D 43 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8407 (mmmm) REVERT: D 44 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8132 (tm-30) REVERT: D 60 ASN cc_start: 0.8458 (t0) cc_final: 0.8235 (t0) REVERT: D 80 TYR cc_start: 0.7154 (m-10) cc_final: 0.6696 (m-10) REVERT: E 99 TYR cc_start: 0.7682 (t80) cc_final: 0.7423 (t80) REVERT: E 129 ARG cc_start: 0.8152 (mmm-85) cc_final: 0.7845 (tmm-80) REVERT: F 71 THR cc_start: 0.8766 (m) cc_final: 0.8486 (p) REVERT: F 88 TYR cc_start: 0.8295 (m-80) cc_final: 0.7850 (m-80) outliers start: 24 outliers final: 19 residues processed: 228 average time/residue: 0.3413 time to fit residues: 94.5750 Evaluate side-chains 248 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 73 ASN C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9282 Z= 0.309 Angle : 0.654 12.817 13477 Z= 0.383 Chirality : 0.037 0.178 1536 Planarity : 0.004 0.043 944 Dihedral : 30.765 175.160 2968 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.26 % Allowed : 29.75 % Favored : 64.99 % 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: 1.93 (0.37), residues: 512 helix: 1.93 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.61 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.011 0.002 PHE F 61 TYR 0.048 0.003 TYR C 57 ARG 0.008 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8571 (tp) cc_final: 0.8317 (tt) REVERT: A 125 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: B 72 TYR cc_start: 0.8790 (m-10) cc_final: 0.8513 (m-10) REVERT: B 88 TYR cc_start: 0.7702 (m-10) cc_final: 0.7111 (m-80) REVERT: B 91 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8334 (mttm) REVERT: C 17 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7791 (mtm180) REVERT: C 56 GLU cc_start: 0.7650 (tt0) cc_final: 0.7339 (tp30) REVERT: C 61 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: C 68 ASN cc_start: 0.7730 (m-40) cc_final: 0.7106 (m-40) REVERT: C 72 ASP cc_start: 0.8002 (m-30) cc_final: 0.7580 (m-30) REVERT: D 43 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8390 (mmmm) REVERT: D 44 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8152 (tm-30) REVERT: D 60 ASN cc_start: 0.8480 (t0) cc_final: 0.8256 (t0) REVERT: D 80 TYR cc_start: 0.7185 (m-10) cc_final: 0.6728 (m-10) REVERT: E 99 TYR cc_start: 0.7703 (t80) cc_final: 0.7431 (t80) REVERT: E 129 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7854 (tmm-80) REVERT: F 88 TYR cc_start: 0.8281 (m-80) cc_final: 0.7864 (m-80) outliers start: 23 outliers final: 18 residues processed: 231 average time/residue: 0.3423 time to fit residues: 95.8304 Evaluate side-chains 250 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 230 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9282 Z= 0.238 Angle : 0.629 12.747 13477 Z= 0.367 Chirality : 0.036 0.174 1536 Planarity : 0.004 0.042 944 Dihedral : 30.750 175.085 2968 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.72 % Allowed : 29.06 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.37), residues: 512 helix: 2.03 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.45 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE F 61 TYR 0.051 0.002 TYR C 57 ARG 0.009 0.001 ARG E 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8580 (tp) cc_final: 0.8335 (tt) REVERT: A 125 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6629 (mp10) REVERT: B 72 TYR cc_start: 0.8786 (m-10) cc_final: 0.8507 (m-10) REVERT: B 88 TYR cc_start: 0.7682 (m-10) cc_final: 0.6741 (m-80) REVERT: B 91 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8280 (mtmm) REVERT: C 56 GLU cc_start: 0.7599 (tt0) cc_final: 0.7308 (tp30) REVERT: C 68 ASN cc_start: 0.7753 (m-40) cc_final: 0.6950 (m-40) REVERT: C 72 ASP cc_start: 0.7964 (m-30) cc_final: 0.7569 (m-30) REVERT: D 43 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8380 (mmmm) REVERT: D 44 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 60 ASN cc_start: 0.8437 (t0) cc_final: 0.8224 (t0) REVERT: D 80 TYR cc_start: 0.7194 (m-10) cc_final: 0.6660 (m-10) REVERT: E 99 TYR cc_start: 0.7672 (t80) cc_final: 0.7413 (t80) REVERT: E 120 MET cc_start: 0.6745 (mtp) cc_final: 0.6533 (mtm) REVERT: E 129 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7829 (tmm-80) REVERT: F 71 THR cc_start: 0.8772 (m) cc_final: 0.8500 (p) REVERT: F 88 TYR cc_start: 0.8210 (m-80) cc_final: 0.7830 (m-80) outliers start: 25 outliers final: 17 residues processed: 229 average time/residue: 0.3423 time to fit residues: 94.8990 Evaluate side-chains 246 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 48 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 84 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.133335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109693 restraints weight = 16482.730| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.94 r_work: 0.3519 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9282 Z= 0.214 Angle : 0.619 12.515 13477 Z= 0.361 Chirality : 0.035 0.174 1536 Planarity : 0.004 0.039 944 Dihedral : 30.731 174.831 2968 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.58 % Allowed : 30.66 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.37), residues: 512 helix: 2.04 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.39 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.010 0.001 PHE D 67 TYR 0.069 0.003 TYR C 57 ARG 0.009 0.001 ARG E 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.94 seconds wall clock time: 46 minutes 55.43 seconds (2815.43 seconds total)