Starting phenix.real_space_refine on Thu Mar 13 02:25:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8etv_28600/03_2025/8etv_28600_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8etv_28600/03_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_28600/03_2025/8etv_28600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8etv_28600/03_2025/8etv_28600.map" model { file = "/net/cci-nas-00/data/ceres_data/8etv_28600/03_2025/8etv_28600_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8etv_28600/03_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-5624/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: 6.84, per 1000 atoms: 0.79 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: 2.75 Conformation dependent library (CDL) restraints added in 494.8 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: 4.34 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: 3.45 Time building geometry restraints manager: 2.73 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: 6.350 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.000 Find NCS groups from input model: 0.130 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.586 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: 0.3320 time to fit residues: 89.9127 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 : 0.583 ------------------------------------------------------------------------------- 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: 0.7819 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= 0.287 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 *********************** 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 : 0.569 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: 0.8362 (tt) REVERT: A 109 LEU cc_start: 0.8754 (mm) cc_final: 0.8342 (mm) REVERT: B 27 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8244 (mm-40) REVERT: B 55 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8547 (mtt180) REVERT: B 82 THR cc_start: 0.8687 (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: 0.9216 (mm) cc_final: 0.8953 (mp) REVERT: C 17 ARG cc_start: 0.7949 (ptm160) cc_final: 0.7393 (ptm160) REVERT: C 56 GLU cc_start: 0.7999 (tt0) cc_final: 0.7761 (tp30) REVERT: C 64 GLU cc_start: 0.8244 (tp30) cc_final: 0.7941 (tp30) REVERT: C 68 ASN cc_start: 0.8197 (m-40) cc_final: 0.6771 (m-40) REVERT: C 72 ASP cc_start: 0.8291 (m-30) cc_final: 0.7877 (m-30) REVERT: C 99 ARG cc_start: 0.8183 (mpt180) cc_final: 0.7869 (mpt180) REVERT: D 43 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8639 (mmmm) REVERT: D 44 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8394 (tm-30) REVERT: D 54 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8697 (mmmm) REVERT: D 60 ASN cc_start: 0.8645 (t0) cc_final: 0.8424 (t0) REVERT: D 69 ARG cc_start: 0.8863 (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: 0.8492 (mtm-85) cc_final: 0.8227 (ttm110) REVERT: E 116 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7293 (mtm110) REVERT: E 129 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8235 (tmm-80) REVERT: F 88 TYR cc_start: 0.8473 (m-80) cc_final: 0.8153 (m-80) outliers start: 13 outliers final: 9 residues processed: 234 average time/residue: 0.3614 time to fit residues: 102.3522 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 : 0.601 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.129951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106146 restraints weight = 16781.869| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.99 r_work: 0.3461 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9282 Z= 0.322 Angle : 0.638 11.654 13477 Z= 0.380 Chirality : 0.037 0.186 1536 Planarity : 0.005 0.059 944 Dihedral : 30.902 175.302 2968 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.58 % Allowed : 21.74 % Favored : 73.68 % 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: 1.53 (0.36), residues: 512 helix: 1.66 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 137 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 0.024 0.003 TYR F 51 ARG 0.007 0.001 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 249 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 0.592 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: 0.8228 (tpp80) cc_final: 0.8018 (tpp80) REVERT: B 59 LYS cc_start: 0.8814 (tttm) cc_final: 0.8591 (tttm) REVERT: B 67 ARG cc_start: 0.8307 (ttm170) cc_final: 0.8045 (ttm-80) REVERT: B 88 TYR cc_start: 0.7970 (m-80) cc_final: 0.7637 (m-80) REVERT: C 17 ARG cc_start: 0.8009 (ptm160) cc_final: 0.7438 (ptm160) REVERT: C 56 GLU cc_start: 0.8008 (tt0) cc_final: 0.7788 (tt0) REVERT: C 68 ASN cc_start: 0.8135 (m-40) cc_final: 0.7060 (m-40) REVERT: C 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.7908 (m-30) REVERT: C 99 ARG cc_start: 0.8140 (mpt180) cc_final: 0.7816 (mpt180) REVERT: D 39 TYR cc_start: 0.8315 (t80) cc_final: 0.8094 (t80) REVERT: D 43 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8671 (mmmm) REVERT: D 60 ASN cc_start: 0.8689 (t0) cc_final: 0.8464 (t0) REVERT: D 65 ASP cc_start: 0.8072 (t0) cc_final: 0.7836 (t0) REVERT: D 69 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8619 (mtp180) REVERT: E 99 TYR cc_start: 0.8417 (t80) cc_final: 0.8151 (t80) REVERT: E 129 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8231 (tmm-80) REVERT: F 87 VAL cc_start: 0.9210 (t) cc_final: 0.8774 (t) REVERT: F 88 TYR cc_start: 0.8471 (m-80) cc_final: 0.7911 (m-80) REVERT: F 91 LYS cc_start: 0.8225 (mtmt) cc_final: 0.8006 (mtmt) outliers start: 20 outliers final: 16 residues processed: 229 average time/residue: 0.3327 time to fit residues: 92.6858 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 : 0.629 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.129816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.105977 restraints weight = 16697.497| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.98 r_work: 0.3465 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2201 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= 0.307 Angle : 0.640 11.895 13477 Z= 0.377 Chirality : 0.037 0.179 1536 Planarity : 0.005 0.058 944 Dihedral : 30.846 175.212 2968 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.03 % Allowed : 24.94 % Favored : 70.02 % 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: 1.82 (0.36), residues: 512 helix: 1.84 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -0.56 (0.50), 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 0.020 0.002 TYR C 57 ARG 0.007 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 250 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: B 45 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7977 (tpp80) REVERT: B 88 TYR cc_start: 0.7958 (m-80) cc_final: 0.7535 (m-80) REVERT: C 17 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7427 (ptm160) REVERT: C 56 GLU cc_start: 0.7992 (tt0) cc_final: 0.7776 (tt0) REVERT: C 68 ASN cc_start: 0.8133 (m-40) cc_final: 0.7631 (m110) REVERT: C 72 ASP cc_start: 0.8360 (m-30) cc_final: 0.7957 (m-30) REVERT: C 99 ARG cc_start: 0.8108 (mpt180) cc_final: 0.7797 (mpt180) REVERT: D 43 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8635 (mmmm) REVERT: D 60 ASN cc_start: 0.8676 (t0) cc_final: 0.8449 (t0) REVERT: D 65 ASP cc_start: 0.8038 (t0) cc_final: 0.7794 (t0) REVERT: D 69 ARG cc_start: 0.8822 (ttm170) cc_final: 0.8569 (mtp180) REVERT: D 80 TYR cc_start: 0.7387 (m-10) cc_final: 0.7156 (m-10) REVERT: E 69 ARG cc_start: 0.8585 (ttm110) cc_final: 0.8361 (mtm-85) REVERT: E 120 MET cc_start: 0.7462 (mtp) cc_final: 0.7190 (mtp) REVERT: E 129 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8320 (mtp85) outliers start: 22 outliers final: 16 residues processed: 229 average time/residue: 0.3295 time to fit residues: 91.9495 Evaluate side-chains 243 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.130671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106951 restraints weight = 16724.665| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.95 r_work: 0.3473 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9282 Z= 0.279 Angle : 0.627 12.315 13477 Z= 0.369 Chirality : 0.036 0.154 1536 Planarity : 0.005 0.049 944 Dihedral : 30.793 175.337 2968 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.81 % Allowed : 26.09 % 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: 2.05 (0.37), residues: 512 helix: 2.02 (0.26), residues: 375 sheet: None (None), residues: 0 loop : -0.50 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 82 PHE 0.010 0.001 PHE F 61 TYR 0.029 0.003 TYR F 88 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 250 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 229 time to evaluate : 0.692 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: 0.8066 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: A 128 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: B 67 ARG cc_start: 0.8339 (ttm170) cc_final: 0.8121 (ttm-80) REVERT: B 88 TYR cc_start: 0.7996 (m-80) cc_final: 0.7353 (m-80) REVERT: C 56 GLU cc_start: 0.7999 (tt0) cc_final: 0.7763 (tt0) REVERT: C 68 ASN cc_start: 0.8099 (m-40) cc_final: 0.7521 (m110) REVERT: C 72 ASP cc_start: 0.8356 (m-30) cc_final: 0.7925 (m-30) REVERT: C 99 ARG cc_start: 0.8161 (mpt180) cc_final: 0.7861 (mpt180) REVERT: D 43 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8623 (mmmm) REVERT: D 54 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8623 (mmmm) REVERT: D 60 ASN cc_start: 0.8651 (t0) cc_final: 0.8428 (t0) REVERT: D 65 ASP cc_start: 0.8043 (t0) cc_final: 0.7791 (t0) REVERT: D 69 ARG cc_start: 0.8821 (ttm170) cc_final: 0.8553 (mtp180) REVERT: D 80 TYR cc_start: 0.7426 (m-10) cc_final: 0.7058 (m-10) REVERT: E 129 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8265 (tmm-80) REVERT: F 88 TYR cc_start: 0.8520 (m-80) cc_final: 0.7659 (m-80) REVERT: F 91 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7967 (mtmt) outliers start: 21 outliers final: 18 residues processed: 230 average time/residue: 0.3670 time to fit residues: 102.8721 Evaluate side-chains 249 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 57 SER 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 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: 0.3980 chunk 44 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 31 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.132337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108603 restraints weight = 16532.002| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.95 r_work: 0.3502 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9282 Z= 0.224 Angle : 0.601 12.487 13477 Z= 0.355 Chirality : 0.034 0.148 1536 Planarity : 0.004 0.048 944 Dihedral : 30.741 175.309 2968 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 5.72 % Allowed : 26.09 % 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: 2.24 (0.37), residues: 512 helix: 2.15 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -0.53 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.027 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 256 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7225 (mp10) REVERT: A 128 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8208 (mmm-85) REVERT: B 67 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8118 (ttm-80) REVERT: B 72 TYR cc_start: 0.9087 (m-10) cc_final: 0.8879 (m-10) REVERT: B 88 TYR cc_start: 0.8002 (m-80) cc_final: 0.7310 (m-80) REVERT: C 56 GLU cc_start: 0.7983 (tt0) cc_final: 0.7740 (tt0) REVERT: C 68 ASN cc_start: 0.8036 (m-40) cc_final: 0.7397 (m110) REVERT: C 72 ASP cc_start: 0.8307 (m-30) cc_final: 0.7884 (m-30) REVERT: C 99 ARG cc_start: 0.8163 (mpt180) cc_final: 0.7848 (mpt180) REVERT: D 43 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8590 (mmmm) REVERT: D 54 LYS cc_start: 0.8874 (mtpp) cc_final: 0.8604 (mmmm) REVERT: D 60 ASN cc_start: 0.8627 (t0) cc_final: 0.8416 (t0) REVERT: D 65 ASP cc_start: 0.8046 (t0) cc_final: 0.7825 (t0) REVERT: D 69 ARG cc_start: 0.8813 (ttm170) cc_final: 0.8568 (mtp180) REVERT: D 80 TYR cc_start: 0.7399 (m-10) cc_final: 0.6945 (m-10) REVERT: D 118 TYR cc_start: 0.8193 (t80) cc_final: 0.7658 (t80) REVERT: E 107 THR cc_start: 0.8714 (m) cc_final: 0.8427 (p) REVERT: E 108 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8172 (t0) REVERT: E 120 MET cc_start: 0.7378 (mtp) cc_final: 0.7092 (mtm) REVERT: E 129 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8234 (tmm-80) REVERT: F 88 TYR cc_start: 0.8541 (m-80) cc_final: 0.7956 (m-80) outliers start: 25 outliers final: 19 residues processed: 235 average time/residue: 0.3310 time to fit residues: 95.2143 Evaluate side-chains 247 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 D residue 57 SER 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 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 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.128893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.104962 restraints weight = 16801.015| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.98 r_work: 0.3445 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2562 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= 0.362 Angle : 0.668 11.863 13477 Z= 0.393 Chirality : 0.039 0.152 1536 Planarity : 0.005 0.071 944 Dihedral : 30.797 175.453 2968 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 6.18 % Allowed : 27.00 % Favored : 66.82 % 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: 1.90 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.76 (0.51), 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 0.033 0.002 TYR C 57 ARG 0.010 0.001 ARG C 42 *********************** 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 261 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7925 (ttp-110) REVERT: A 125 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: A 128 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: B 44 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8302 (mptm) REVERT: B 67 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8120 (ttm-80) REVERT: B 87 VAL cc_start: 0.8994 (t) cc_final: 0.8705 (p) REVERT: B 88 TYR cc_start: 0.8054 (m-10) cc_final: 0.7298 (m-80) REVERT: B 91 LYS cc_start: 0.8613 (mttm) cc_final: 0.8284 (mtmm) REVERT: C 56 GLU cc_start: 0.8016 (tt0) cc_final: 0.7790 (tt0) REVERT: C 61 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: C 68 ASN cc_start: 0.8113 (m-40) cc_final: 0.7583 (m110) REVERT: C 72 ASP cc_start: 0.8383 (m-30) cc_final: 0.7970 (m-30) REVERT: C 99 ARG cc_start: 0.8186 (mpt180) cc_final: 0.7949 (mpt180) REVERT: D 43 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8611 (mmmm) REVERT: D 54 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8650 (mmmm) REVERT: D 65 ASP cc_start: 0.8048 (t0) cc_final: 0.7788 (t0) REVERT: D 69 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8547 (mtp180) REVERT: D 80 TYR cc_start: 0.7427 (m-10) cc_final: 0.6878 (m-10) REVERT: E 83 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7117 (mtm110) REVERT: F 71 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8588 (p) REVERT: F 87 VAL cc_start: 0.9159 (t) cc_final: 0.8693 (t) REVERT: F 88 TYR cc_start: 0.8537 (m-80) cc_final: 0.7801 (m-80) REVERT: F 91 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7990 (mtmt) outliers start: 27 outliers final: 18 residues processed: 236 average time/residue: 0.3368 time to fit residues: 97.5050 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 : 0.597 ------------------------------------------------------------------------------- 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 44 LYS 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 57 SER 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: 0.9990 chunk 29 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 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: 0.8980 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.129764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.106016 restraints weight = 16850.273| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.96 r_work: 0.3463 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2585 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= 0.308 Angle : 0.653 13.663 13477 Z= 0.382 Chirality : 0.037 0.147 1536 Planarity : 0.005 0.046 944 Dihedral : 30.794 175.531 2968 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 7.09 % Allowed : 27.69 % 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: 1.89 (0.36), residues: 512 helix: 1.92 (0.26), residues: 380 sheet: None (None), residues: 0 loop : -0.68 (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 F 61 TYR 0.039 0.003 TYR C 57 ARG 0.010 0.001 ARG C 42 *********************** 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 265 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: A 128 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8225 (mmm-85) REVERT: B 72 TYR cc_start: 0.9087 (m-10) cc_final: 0.8862 (m-10) REVERT: B 88 TYR cc_start: 0.8071 (m-10) cc_final: 0.7307 (m-80) REVERT: C 56 GLU cc_start: 0.7977 (tt0) cc_final: 0.7744 (tt0) REVERT: C 61 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: C 68 ASN cc_start: 0.8089 (m-40) cc_final: 0.7522 (m110) REVERT: C 72 ASP cc_start: 0.8342 (m-30) cc_final: 0.7908 (m-30) REVERT: C 99 ARG cc_start: 0.8178 (mpt180) cc_final: 0.7892 (mpt180) REVERT: D 43 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8603 (mmmm) REVERT: D 54 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8648 (mmmm) REVERT: D 65 ASP cc_start: 0.8062 (t0) cc_final: 0.7794 (t0) REVERT: D 69 ARG cc_start: 0.8837 (ttm170) cc_final: 0.8539 (mtp180) REVERT: D 80 TYR cc_start: 0.7458 (m-10) cc_final: 0.6890 (m-10) REVERT: F 71 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8585 (p) REVERT: F 88 TYR cc_start: 0.8519 (m-80) cc_final: 0.8119 (m-80) outliers start: 31 outliers final: 24 residues processed: 237 average time/residue: 0.3274 time to fit residues: 95.0902 Evaluate side-chains 260 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 B residue 66 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 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 79 ILE 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 57 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 30 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 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: 0.3980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 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 = 0.4040 r_free = 0.4040 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107266 restraints weight = 16729.158| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.97 r_work: 0.3480 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2647 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= 0.259 Angle : 0.636 13.016 13477 Z= 0.372 Chirality : 0.036 0.212 1536 Planarity : 0.004 0.047 944 Dihedral : 30.740 175.642 2968 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.41 % Allowed : 27.69 % 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: 2.05 (0.37), residues: 512 helix: 2.01 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.61 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE F 61 TYR 0.043 0.002 TYR C 57 ARG 0.008 0.001 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 259 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: A 128 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8218 (mmm-85) REVERT: B 44 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8315 (mptm) REVERT: B 72 TYR cc_start: 0.9071 (m-10) cc_final: 0.8803 (m-80) REVERT: B 88 TYR cc_start: 0.8083 (m-10) cc_final: 0.7054 (m-80) REVERT: C 56 GLU cc_start: 0.7969 (tt0) cc_final: 0.7751 (tt0) REVERT: C 61 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 68 ASN cc_start: 0.8018 (m-40) cc_final: 0.7486 (m110) REVERT: C 72 ASP cc_start: 0.8356 (m-30) cc_final: 0.7938 (m-30) REVERT: C 99 ARG cc_start: 0.8180 (mpt180) cc_final: 0.7925 (mpt180) REVERT: D 43 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8583 (mmmm) REVERT: D 65 ASP cc_start: 0.8080 (t0) cc_final: 0.7798 (t0) REVERT: D 69 ARG cc_start: 0.8841 (ttm170) cc_final: 0.8572 (mtp180) REVERT: D 80 TYR cc_start: 0.7435 (m-10) cc_final: 0.6669 (m-10) REVERT: E 120 MET cc_start: 0.7457 (mtp) cc_final: 0.7137 (mtm) REVERT: F 88 TYR cc_start: 0.8460 (m-80) cc_final: 0.8113 (m-80) outliers start: 28 outliers final: 23 residues processed: 233 average time/residue: 0.3415 time to fit residues: 96.5398 Evaluate side-chains 257 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 44 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 41 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 79 ILE 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 57 SER 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 70 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 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 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 = 0.4033 r_free = 0.4033 target = 0.130630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106646 restraints weight = 16753.939| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.98 r_work: 0.3472 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9282 Z= 0.277 Angle : 0.655 12.973 13477 Z= 0.378 Chirality : 0.037 0.221 1536 Planarity : 0.004 0.046 944 Dihedral : 30.692 175.815 2968 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.41 % Allowed : 28.83 % 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: 2.01 (0.36), residues: 512 helix: 1.99 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.64 (0.51), residues: 131 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 0.048 0.003 TYR C 57 ARG 0.008 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 259 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: B 72 TYR cc_start: 0.9072 (m-10) cc_final: 0.8802 (m-80) REVERT: B 88 TYR cc_start: 0.8105 (m-10) cc_final: 0.7400 (m-80) REVERT: C 56 GLU cc_start: 0.7993 (tt0) cc_final: 0.7717 (tp30) REVERT: C 57 TYR cc_start: 0.8129 (t80) cc_final: 0.7888 (t80) REVERT: C 68 ASN cc_start: 0.8038 (m-40) cc_final: 0.7480 (m110) REVERT: C 72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7938 (m-30) REVERT: C 99 ARG cc_start: 0.8161 (mpt180) cc_final: 0.7941 (mpt180) REVERT: D 43 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8604 (mmmm) REVERT: D 44 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8369 (tm-30) REVERT: D 65 ASP cc_start: 0.8078 (t0) cc_final: 0.7790 (t0) REVERT: D 69 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8600 (mtp180) REVERT: D 80 TYR cc_start: 0.7341 (m-10) cc_final: 0.6896 (m-10) REVERT: E 120 MET cc_start: 0.7468 (mtp) cc_final: 0.7143 (mtm) REVERT: F 88 TYR cc_start: 0.8455 (m-80) cc_final: 0.8120 (m-80) outliers start: 28 outliers final: 22 residues processed: 233 average time/residue: 0.3266 time to fit residues: 92.9588 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 : 0.631 ------------------------------------------------------------------------------- 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 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 79 ILE 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 57 SER 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: 0.0980 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: 0.1980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.131240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107377 restraints weight = 16698.076| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.96 r_work: 0.3483 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9282 Z= 0.260 Angle : 0.652 14.100 13477 Z= 0.375 Chirality : 0.036 0.192 1536 Planarity : 0.004 0.044 944 Dihedral : 30.677 175.879 2968 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.18 % Allowed : 28.83 % 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: 1.99 (0.36), residues: 512 helix: 1.99 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.66 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.011 0.002 PHE A 78 TYR 0.044 0.003 TYR C 57 ARG 0.008 0.001 ARG E 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.93 seconds wall clock time: 82 minutes 1.89 seconds (4921.89 seconds total)