Starting phenix.real_space_refine on Sun May 11 23:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etv_28600/05_2025/8etv_28600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etv_28600/05_2025/8etv_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/cci-nas-00/data/ceres_data/8etv_28600/05_2025/8etv_28600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etv_28600/05_2025/8etv_28600.map" model { file = "/net/cci-nas-00/data/ceres_data/8etv_28600/05_2025/8etv_28600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etv_28600/05_2025/8etv_28600_neut.cif" } 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. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 6.72, per 1000 atoms: 0.77 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 - 3.00 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: 2.21 Conformation dependent library (CDL) restraints added in 547.5 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: 4.19 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: 3.19 Time building geometry restraints manager: 2.61 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: 0.00 - 2.90: 13333 2.90 - 5.80: 118 5.80 - 8.70: 21 8.70 - 11.60: 3 11.60 - 14.50: 2 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 3.040 nonbonded pdb=" OG1 THR B 30 " pdb=" OP1 DC I -12 " model vdw 2.324 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.346 3.040 nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.366 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 7.560 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.850 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.770 ------------------------------------------------------------------------------- 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= 0.275 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 Details of bonding type rmsd hydrogen bonds : bond 0.11601 ( 559) hydrogen bonds : angle 3.96683 ( 1378) covalent geometry : bond 0.00601 ( 9282) covalent geometry : angle 0.87399 (13477) *********************** 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 to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.605 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: 0.3269 time to fit residues: 88.4708 Evaluate side-chains 220 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.131540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107718 restraints weight = 16509.559| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.98 r_work: 0.3494 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1542 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= 0.245 Angle : 0.636 11.708 13477 Z= 0.376 Chirality : 0.036 0.189 1536 Planarity : 0.005 0.064 944 Dihedral : 30.906 176.698 2968 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.97 % Allowed : 16.70 % Favored : 80.32 % 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: 1.08 (0.36), residues: 512 helix: 1.30 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.016 0.002 PHE D 67 TYR 0.026 0.002 TYR B 88 ARG 0.006 0.001 ARG C 77 Details of bonding type rmsd hydrogen bonds : bond 0.05432 ( 559) hydrogen bonds : angle 3.10660 ( 1378) covalent geometry : bond 0.00529 ( 9282) covalent geometry : angle 0.63628 (13477) *********************** 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 247 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 234 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8689 (tp) cc_final: 0.8361 (tt) REVERT: A 109 LEU cc_start: 0.8753 (mm) cc_final: 0.8339 (mm) REVERT: B 27 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8245 (mm-40) REVERT: B 55 ARG cc_start: 0.8780 (mtt180) cc_final: 0.8548 (mtt180) REVERT: B 82 THR cc_start: 0.8686 (t) cc_final: 0.8219 (p) REVERT: B 88 TYR cc_start: 0.7908 (m-80) cc_final: 0.7522 (m-80) REVERT: B 90 LEU cc_start: 0.9214 (mm) cc_final: 0.8952 (mp) REVERT: C 17 ARG cc_start: 0.7949 (ptm160) cc_final: 0.7394 (ptm160) REVERT: C 56 GLU cc_start: 0.7996 (tt0) cc_final: 0.7758 (tp30) REVERT: C 64 GLU cc_start: 0.8244 (tp30) cc_final: 0.7940 (tp30) REVERT: C 68 ASN cc_start: 0.8195 (m-40) cc_final: 0.6769 (m-40) REVERT: C 72 ASP cc_start: 0.8288 (m-30) cc_final: 0.7874 (m-30) REVERT: C 99 ARG cc_start: 0.8177 (mpt180) cc_final: 0.7863 (mpt180) REVERT: D 43 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8639 (mmmm) REVERT: D 44 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8393 (tm-30) REVERT: D 54 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8696 (mmmm) REVERT: D 60 ASN cc_start: 0.8646 (t0) cc_final: 0.8426 (t0) REVERT: D 69 ARG cc_start: 0.8862 (ttm170) cc_final: 0.8561 (mtp180) REVERT: D 117 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8215 (tmmt) REVERT: E 69 ARG cc_start: 0.8491 (mtm-85) cc_final: 0.8227 (ttm110) REVERT: E 116 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7290 (mtm110) REVERT: E 129 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8232 (tmm-80) REVERT: F 88 TYR cc_start: 0.8470 (m-80) cc_final: 0.8152 (m-80) outliers start: 13 outliers final: 9 residues processed: 234 average time/residue: 0.3368 time to fit residues: 95.5017 Evaluate side-chains 239 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.129631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.105967 restraints weight = 16758.410| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.98 r_work: 0.3458 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9282 Z= 0.282 Angle : 0.644 11.716 13477 Z= 0.383 Chirality : 0.038 0.186 1536 Planarity : 0.005 0.059 944 Dihedral : 30.907 175.410 2968 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.58 % Allowed : 21.97 % Favored : 73.46 % 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: 1.52 (0.36), residues: 512 helix: 1.64 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 136 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 0.027 0.003 TYR F 51 ARG 0.006 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05657 ( 559) hydrogen bonds : angle 3.18356 ( 1378) covalent geometry : bond 0.00609 ( 9282) covalent geometry : angle 0.64378 (13477) *********************** 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 248 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8225 (tpp80) cc_final: 0.8018 (tpp80) REVERT: B 59 LYS cc_start: 0.8819 (tttm) cc_final: 0.8597 (tttm) REVERT: B 67 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8048 (ttm-80) REVERT: B 88 TYR cc_start: 0.7972 (m-80) cc_final: 0.7617 (m-80) REVERT: C 17 ARG cc_start: 0.8000 (ptm160) cc_final: 0.7434 (ptm160) REVERT: C 56 GLU cc_start: 0.7988 (tt0) cc_final: 0.7768 (tt0) REVERT: C 68 ASN cc_start: 0.8141 (m-40) cc_final: 0.7083 (m-40) REVERT: C 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.7920 (m-30) REVERT: C 99 ARG cc_start: 0.8114 (mpt180) cc_final: 0.7793 (mpt180) REVERT: D 39 TYR cc_start: 0.8319 (t80) cc_final: 0.8100 (t80) REVERT: D 43 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8665 (mmmm) REVERT: D 60 ASN cc_start: 0.8686 (t0) cc_final: 0.8461 (t0) REVERT: D 65 ASP cc_start: 0.8048 (t0) cc_final: 0.7827 (t0) REVERT: D 69 ARG cc_start: 0.8827 (ttm170) cc_final: 0.8607 (mtp180) REVERT: E 99 TYR cc_start: 0.8432 (t80) cc_final: 0.8161 (t80) REVERT: E 129 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8225 (tmm-80) REVERT: F 88 TYR cc_start: 0.8465 (m-80) cc_final: 0.8261 (m-80) outliers start: 20 outliers final: 16 residues processed: 228 average time/residue: 0.3258 time to fit residues: 90.5666 Evaluate side-chains 242 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL 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 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 71 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.130196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106360 restraints weight = 16670.385| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.97 r_work: 0.3465 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 9282 Z= 0.257 Angle : 0.638 11.932 13477 Z= 0.375 Chirality : 0.037 0.179 1536 Planarity : 0.005 0.058 944 Dihedral : 30.849 175.218 2968 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.03 % Allowed : 25.40 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.36), residues: 512 helix: 1.85 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.58 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.011 0.002 PHE F 61 TYR 0.022 0.002 TYR C 57 ARG 0.007 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05362 ( 559) hydrogen bonds : angle 3.09977 ( 1378) covalent geometry : bond 0.00556 ( 9282) covalent geometry : angle 0.63817 (13477) *********************** 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 252 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: B 45 ARG cc_start: 0.8243 (tpp80) cc_final: 0.7977 (tpp80) REVERT: B 88 TYR cc_start: 0.7978 (m-80) cc_final: 0.7546 (m-80) REVERT: C 17 ARG cc_start: 0.7988 (ptm160) cc_final: 0.7416 (ptm160) REVERT: C 56 GLU cc_start: 0.8019 (tt0) cc_final: 0.7791 (tt0) REVERT: C 68 ASN cc_start: 0.8133 (m-40) cc_final: 0.7644 (m110) REVERT: C 72 ASP cc_start: 0.8354 (m-30) cc_final: 0.7942 (m-30) REVERT: C 99 ARG cc_start: 0.8141 (mpt180) cc_final: 0.7836 (mpt180) REVERT: D 43 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8638 (mmmm) REVERT: D 60 ASN cc_start: 0.8701 (t0) cc_final: 0.8473 (t0) REVERT: D 65 ASP cc_start: 0.8087 (t0) cc_final: 0.7825 (t0) REVERT: D 69 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8584 (mtp180) REVERT: D 80 TYR cc_start: 0.7414 (m-10) cc_final: 0.7174 (m-10) REVERT: E 69 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8356 (mtm-85) REVERT: E 120 MET cc_start: 0.7466 (mtp) cc_final: 0.7189 (mtp) REVERT: E 129 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8311 (mtp85) REVERT: E 131 ARG cc_start: 0.8513 (mtt180) cc_final: 0.8309 (mtt180) REVERT: F 87 VAL cc_start: 0.9160 (t) cc_final: 0.8729 (t) REVERT: F 88 TYR cc_start: 0.8497 (m-80) cc_final: 0.7903 (m-80) REVERT: F 91 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7977 (mtmt) outliers start: 22 outliers final: 14 residues processed: 231 average time/residue: 0.3272 time to fit residues: 91.9095 Evaluate side-chains 242 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 16 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 107 VAL 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 109 LEU Chi-restraints excluded: chain F residue 26 ILE 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 47 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 82 HIS ** 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 = 0.4045 r_free = 0.4045 target = 0.131493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107728 restraints weight = 16679.558| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.97 r_work: 0.3489 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9282 Z= 0.208 Angle : 0.612 12.169 13477 Z= 0.360 Chirality : 0.035 0.156 1536 Planarity : 0.004 0.050 944 Dihedral : 30.799 175.302 2968 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.26 % Allowed : 25.40 % Favored : 69.34 % 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: 2.17 (0.37), residues: 512 helix: 2.12 (0.27), residues: 375 sheet: None (None), residues: 0 loop : -0.48 (0.50), 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 0.024 0.002 TYR C 57 ARG 0.009 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 559) hydrogen bonds : angle 3.00151 ( 1378) covalent geometry : bond 0.00453 ( 9282) covalent geometry : angle 0.61170 (13477) *********************** 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 252 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: B 88 TYR cc_start: 0.7956 (m-80) cc_final: 0.7355 (m-80) REVERT: C 56 GLU cc_start: 0.7970 (tt0) cc_final: 0.7732 (tt0) REVERT: C 68 ASN cc_start: 0.8086 (m-40) cc_final: 0.7479 (m110) REVERT: C 72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7906 (m-30) REVERT: C 99 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7829 (mpt180) REVERT: D 43 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8610 (mmmm) REVERT: D 60 ASN cc_start: 0.8638 (t0) cc_final: 0.8408 (t0) REVERT: D 65 ASP cc_start: 0.8044 (t0) cc_final: 0.7789 (t0) REVERT: D 69 ARG cc_start: 0.8811 (ttm170) cc_final: 0.8558 (mtp180) REVERT: D 80 TYR cc_start: 0.7393 (m-10) cc_final: 0.7076 (m-10) REVERT: E 69 ARG cc_start: 0.8544 (ttm110) cc_final: 0.8275 (mtm-85) REVERT: E 83 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7091 (mtm110) REVERT: E 129 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8260 (tmm-80) outliers start: 23 outliers final: 17 residues processed: 230 average time/residue: 0.3237 time to fit residues: 90.7144 Evaluate side-chains 246 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 C residue 16 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL 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 83 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 60 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 31 optimal weight: 0.4980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.133322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109442 restraints weight = 16516.284| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.96 r_work: 0.3512 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9282 Z= 0.180 Angle : 0.593 12.554 13477 Z= 0.351 Chirality : 0.034 0.149 1536 Planarity : 0.004 0.048 944 Dihedral : 30.734 175.110 2968 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.26 % Allowed : 25.86 % Favored : 68.88 % 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: 2.25 (0.37), residues: 512 helix: 2.16 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.55 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.008 0.001 PHE A 67 TYR 0.035 0.002 TYR F 88 ARG 0.008 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 559) hydrogen bonds : angle 2.91877 ( 1378) covalent geometry : bond 0.00392 ( 9282) covalent geometry : angle 0.59313 (13477) *********************** 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 253 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7206 (mp10) REVERT: A 128 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8209 (mmm-85) REVERT: B 67 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8097 (ttm-80) REVERT: B 88 TYR cc_start: 0.7976 (m-80) cc_final: 0.7137 (m-80) REVERT: C 17 ARG cc_start: 0.8528 (mtm180) cc_final: 0.8178 (mtm180) REVERT: C 56 GLU cc_start: 0.7970 (tt0) cc_final: 0.7726 (tt0) REVERT: C 68 ASN cc_start: 0.8021 (m-40) cc_final: 0.7454 (m110) REVERT: C 72 ASP cc_start: 0.8310 (m-30) cc_final: 0.7889 (m-30) REVERT: C 99 ARG cc_start: 0.8132 (mpt180) cc_final: 0.7825 (mpt180) REVERT: D 43 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8589 (mmmm) REVERT: D 54 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8711 (mtpp) REVERT: D 60 ASN cc_start: 0.8596 (t0) cc_final: 0.8367 (t0) REVERT: D 65 ASP cc_start: 0.8059 (t0) cc_final: 0.7788 (t0) REVERT: D 69 ARG cc_start: 0.8809 (ttm170) cc_final: 0.8537 (mtp180) REVERT: D 80 TYR cc_start: 0.7395 (m-10) cc_final: 0.6937 (m-10) REVERT: D 118 TYR cc_start: 0.8185 (t80) cc_final: 0.7621 (t80) REVERT: E 69 ARG cc_start: 0.8522 (ttm110) cc_final: 0.8238 (mtm-85) REVERT: E 83 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.7112 (mtm110) REVERT: E 107 THR cc_start: 0.8694 (m) cc_final: 0.8404 (p) REVERT: E 108 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8172 (t0) REVERT: E 120 MET cc_start: 0.7368 (mtp) cc_final: 0.7085 (mtm) REVERT: E 129 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8295 (mmm-85) REVERT: F 88 TYR cc_start: 0.8457 (m-80) cc_final: 0.7920 (m-80) outliers start: 23 outliers final: 16 residues processed: 234 average time/residue: 0.3262 time to fit residues: 93.1663 Evaluate side-chains 246 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 227 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 36 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL 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 83 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 108 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.130557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106598 restraints weight = 16771.327| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.96 r_work: 0.3471 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9282 Z= 0.256 Angle : 0.634 11.845 13477 Z= 0.373 Chirality : 0.037 0.151 1536 Planarity : 0.005 0.062 944 Dihedral : 30.760 175.327 2968 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.95 % Allowed : 26.77 % Favored : 67.28 % 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: 2.03 (0.37), residues: 512 helix: 2.03 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.69 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.002 PHE A 67 TYR 0.033 0.002 TYR C 57 ARG 0.010 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.05367 ( 559) hydrogen bonds : angle 3.16081 ( 1378) covalent geometry : bond 0.00558 ( 9282) covalent geometry : angle 0.63373 (13477) *********************** 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 260 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: A 128 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8219 (mmm-85) REVERT: B 67 ARG cc_start: 0.8303 (ttm170) cc_final: 0.8092 (ttm-80) REVERT: B 72 TYR cc_start: 0.9061 (m-10) cc_final: 0.8852 (m-10) REVERT: B 88 TYR cc_start: 0.8058 (m-10) cc_final: 0.7209 (m-80) REVERT: B 91 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8388 (mttm) REVERT: C 17 ARG cc_start: 0.8479 (mtm180) cc_final: 0.8271 (mtm180) REVERT: C 56 GLU cc_start: 0.8019 (tt0) cc_final: 0.7786 (tt0) REVERT: C 61 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: C 68 ASN cc_start: 0.8101 (m-40) cc_final: 0.7553 (m110) REVERT: C 72 ASP cc_start: 0.8358 (m-30) cc_final: 0.7938 (m-30) REVERT: C 99 ARG cc_start: 0.8167 (mpt180) cc_final: 0.7875 (mpt180) REVERT: D 43 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8596 (mmmm) REVERT: D 60 ASN cc_start: 0.8650 (t0) cc_final: 0.8421 (t0) REVERT: D 65 ASP cc_start: 0.8061 (t0) cc_final: 0.7786 (t0) REVERT: D 69 ARG cc_start: 0.8846 (ttm170) cc_final: 0.8557 (mtp180) REVERT: D 80 TYR cc_start: 0.7415 (m-10) cc_final: 0.6866 (m-10) REVERT: E 83 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7092 (mtm110) REVERT: E 107 THR cc_start: 0.8715 (m) cc_final: 0.8437 (p) REVERT: E 129 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8265 (tmm-80) REVERT: F 71 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8570 (p) REVERT: F 88 TYR cc_start: 0.8572 (m-80) cc_final: 0.7673 (m-80) REVERT: F 91 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7956 (mtmt) outliers start: 26 outliers final: 18 residues processed: 236 average time/residue: 0.3169 time to fit residues: 91.6151 Evaluate side-chains 253 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL 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 83 ARG 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 71 THR 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 34 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.128602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104799 restraints weight = 16837.282| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.96 r_work: 0.3443 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9282 Z= 0.303 Angle : 0.670 13.528 13477 Z= 0.394 Chirality : 0.039 0.175 1536 Planarity : 0.005 0.045 944 Dihedral : 30.818 175.215 2968 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.41 % Allowed : 27.00 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.36), residues: 512 helix: 1.82 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.77 (0.50), residues: 130 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 0.039 0.002 TYR C 57 ARG 0.009 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05828 ( 559) hydrogen bonds : angle 3.30121 ( 1378) covalent geometry : bond 0.00659 ( 9282) covalent geometry : angle 0.66964 (13477) *********************** 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 263 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: A 128 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8208 (mmm-85) REVERT: B 44 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8350 (mptm) REVERT: B 72 TYR cc_start: 0.9014 (m-10) cc_final: 0.8779 (m-10) REVERT: B 88 TYR cc_start: 0.8065 (m-10) cc_final: 0.7364 (m-80) REVERT: C 17 ARG cc_start: 0.8442 (mtm180) cc_final: 0.8222 (mtm180) REVERT: C 56 GLU cc_start: 0.8015 (tt0) cc_final: 0.7795 (tt0) REVERT: C 61 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: C 68 ASN cc_start: 0.8099 (m-40) cc_final: 0.7546 (m110) REVERT: C 72 ASP cc_start: 0.8387 (m-30) cc_final: 0.7971 (m-30) REVERT: C 99 ARG cc_start: 0.8198 (mpt180) cc_final: 0.7963 (mpt180) REVERT: D 39 TYR cc_start: 0.8336 (t80) cc_final: 0.8103 (t80) REVERT: D 43 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8636 (mmmm) REVERT: D 60 ASN cc_start: 0.8692 (t0) cc_final: 0.8469 (t0) REVERT: D 65 ASP cc_start: 0.8042 (t0) cc_final: 0.7774 (t0) REVERT: D 69 ARG cc_start: 0.8840 (ttm170) cc_final: 0.8551 (mtp180) REVERT: D 80 TYR cc_start: 0.7419 (m-10) cc_final: 0.7034 (m-10) REVERT: F 87 VAL cc_start: 0.9198 (t) cc_final: 0.8724 (t) REVERT: F 88 TYR cc_start: 0.8477 (m-80) cc_final: 0.7742 (m-80) REVERT: F 91 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7986 (mtmt) outliers start: 28 outliers final: 20 residues processed: 237 average time/residue: 0.3279 time to fit residues: 94.8233 Evaluate side-chains 257 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 C residue 36 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL 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 83 ARG 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 71 THR 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 30 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 17 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.131293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107598 restraints weight = 16704.133| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.94 r_work: 0.3485 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9282 Z= 0.215 Angle : 0.630 13.170 13477 Z= 0.369 Chirality : 0.036 0.165 1536 Planarity : 0.004 0.047 944 Dihedral : 30.778 175.488 2968 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.03 % Allowed : 28.60 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.37), residues: 512 helix: 2.07 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.60 (0.51), residues: 129 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 0.042 0.002 TYR C 57 ARG 0.008 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 559) hydrogen bonds : angle 3.13183 ( 1378) covalent geometry : bond 0.00472 ( 9282) covalent geometry : angle 0.63022 (13477) *********************** 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 to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: A 128 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8225 (mmm-85) REVERT: B 72 TYR cc_start: 0.9048 (m-10) cc_final: 0.8786 (m-10) REVERT: B 88 TYR cc_start: 0.8033 (m-10) cc_final: 0.7418 (m-80) REVERT: C 17 ARG cc_start: 0.8434 (mtm180) cc_final: 0.8229 (mtm180) REVERT: C 56 GLU cc_start: 0.7975 (tt0) cc_final: 0.7759 (tt0) REVERT: C 68 ASN cc_start: 0.8022 (m-40) cc_final: 0.7413 (m110) REVERT: C 72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7942 (m-30) REVERT: C 99 ARG cc_start: 0.8189 (mpt180) cc_final: 0.7982 (mpt180) REVERT: D 39 TYR cc_start: 0.8267 (t80) cc_final: 0.8024 (t80) REVERT: D 43 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8607 (mmmm) REVERT: D 60 ASN cc_start: 0.8639 (t0) cc_final: 0.8435 (t0) REVERT: D 65 ASP cc_start: 0.8079 (t0) cc_final: 0.7795 (t0) REVERT: D 69 ARG cc_start: 0.8844 (ttm170) cc_final: 0.8540 (mtp180) REVERT: D 80 TYR cc_start: 0.7415 (m-10) cc_final: 0.7007 (m-10) REVERT: E 120 MET cc_start: 0.7443 (mtp) cc_final: 0.7113 (mtm) REVERT: F 87 VAL cc_start: 0.9158 (t) cc_final: 0.8635 (t) REVERT: F 88 TYR cc_start: 0.8447 (m-80) cc_final: 0.7688 (m-80) REVERT: F 91 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7963 (mtmt) outliers start: 22 outliers final: 17 residues processed: 233 average time/residue: 0.3234 time to fit residues: 91.9719 Evaluate side-chains 248 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL 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 83 ARG 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 70 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** 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 = 0.4014 r_free = 0.4014 target = 0.129187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105297 restraints weight = 16758.167| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.96 r_work: 0.3451 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9282 Z= 0.284 Angle : 0.664 13.059 13477 Z= 0.390 Chirality : 0.039 0.198 1536 Planarity : 0.005 0.044 944 Dihedral : 30.758 175.578 2968 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.49 % Allowed : 28.83 % Favored : 65.68 % 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: 1.88 (0.36), residues: 512 helix: 1.91 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.71 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.011 0.002 PHE F 61 TYR 0.073 0.003 TYR C 57 ARG 0.008 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05624 ( 559) hydrogen bonds : angle 3.33108 ( 1378) covalent geometry : bond 0.00620 ( 9282) covalent geometry : angle 0.66382 (13477) ********************** 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 257 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7593 (mmp-170) cc_final: 0.7126 (mmp-170) REVERT: A 125 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: A 128 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8254 (mmm-85) REVERT: B 72 TYR cc_start: 0.9064 (m-10) cc_final: 0.8794 (m-10) REVERT: B 88 TYR cc_start: 0.8061 (m-10) cc_final: 0.7338 (m-80) REVERT: C 17 ARG cc_start: 0.8435 (mtm180) cc_final: 0.8218 (mtm180) REVERT: C 56 GLU cc_start: 0.8025 (tt0) cc_final: 0.7761 (tp30) REVERT: C 61 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: C 68 ASN cc_start: 0.8058 (m-40) cc_final: 0.7508 (m110) REVERT: C 72 ASP cc_start: 0.8364 (m-30) cc_final: 0.7954 (m-30) REVERT: C 99 ARG cc_start: 0.8171 (mpt180) cc_final: 0.7947 (mpt180) REVERT: D 43 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8627 (mmmm) REVERT: D 44 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8379 (tm-30) REVERT: D 60 ASN cc_start: 0.8666 (t0) cc_final: 0.8464 (t0) REVERT: D 65 ASP cc_start: 0.8069 (t0) cc_final: 0.7788 (t0) REVERT: D 69 ARG cc_start: 0.8853 (ttm170) cc_final: 0.8600 (mtp180) REVERT: D 80 TYR cc_start: 0.7449 (m-10) cc_final: 0.6956 (m-10) REVERT: F 87 VAL cc_start: 0.9199 (t) cc_final: 0.8722 (t) REVERT: F 88 TYR cc_start: 0.8464 (m-80) cc_final: 0.7739 (m-80) REVERT: F 91 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7985 (mtmt) outliers start: 24 outliers final: 19 residues processed: 236 average time/residue: 0.3202 time to fit residues: 91.7574 Evaluate side-chains 252 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 36 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL 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 83 ARG 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 67 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.129417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105582 restraints weight = 16740.111| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.94 r_work: 0.3456 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2811 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= 0.269 Angle : 0.660 12.938 13477 Z= 0.387 Chirality : 0.038 0.212 1536 Planarity : 0.005 0.045 944 Dihedral : 30.741 175.822 2968 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.95 % Allowed : 28.60 % Favored : 65.45 % 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: 1.85 (0.36), residues: 512 helix: 1.88 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.68 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE F 61 TYR 0.072 0.003 TYR C 57 ARG 0.008 0.001 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 559) hydrogen bonds : angle 3.29244 ( 1378) covalent geometry : bond 0.00588 ( 9282) covalent geometry : angle 0.65979 (13477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4488.36 seconds wall clock time: 78 minutes 50.30 seconds (4730.30 seconds total)