Starting phenix.real_space_refine on Sat Nov 16 02:24:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubb_42081/11_2024/8ubb_42081.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubb_42081/11_2024/8ubb_42081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubb_42081/11_2024/8ubb_42081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubb_42081/11_2024/8ubb_42081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubb_42081/11_2024/8ubb_42081.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ubb_42081/11_2024/8ubb_42081.cif" } resolution = 3.23 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= 0.030 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 148 5.49 5 S 36 5.16 5 C 6052 2.51 5 N 1862 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10349 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 269 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 6.64, per 1000 atoms: 0.64 Number of scatterers: 10349 At special positions: 0 Unit cell: (80, 99, 129, 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 36 16.00 P 148 15.00 O 2251 8.00 N 1862 7.00 C 6052 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: 2.77 Conformation dependent library (CDL) restraints added in 927.7 milliseconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 1 sheets defined 77.1% alpha, 1.9% beta 38 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.867A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 93 through 99 removed outlier: 3.783A pdb=" N ILE A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 4.043A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 207 removed outlier: 4.397A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.530A pdb=" N GLY A 262 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.893A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TRP A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.555A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 39 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.634A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 64 through 88 Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 62 removed outlier: 3.756A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 32 removed outlier: 3.637A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 38 through 62 removed outlier: 4.083A pdb=" N GLY E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.547A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 34 removed outlier: 4.376A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.534A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.211A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 213 removed outlier: 3.844A pdb=" N HIS A 133 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 3.88 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1685 1.33 - 1.45: 3592 1.45 - 1.57: 5249 1.57 - 1.69: 294 1.69 - 1.81: 61 Bond restraints: 10881 Sorted by residual: bond pdb=" CB ARG B 122 " pdb=" CG ARG B 122 " ideal model delta sigma weight residual 1.520 1.412 0.108 3.00e-02 1.11e+03 1.29e+01 bond pdb=" CG1 ILE C 24 " pdb=" CD1 ILE C 24 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.26e+01 bond pdb=" CG1 ILE F 24 " pdb=" CD1 ILE F 24 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.21e+01 bond pdb=" CG1 ILE D 88 " pdb=" CD1 ILE D 88 " ideal model delta sigma weight residual 1.513 1.379 0.134 3.90e-02 6.57e+02 1.18e+01 bond pdb=" CB PRO C 91 " pdb=" CG PRO C 91 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.18e+01 ... (remaining 10876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 14711 2.60 - 5.20: 592 5.20 - 7.80: 99 7.80 - 10.39: 18 10.39 - 12.99: 4 Bond angle restraints: 15424 Sorted by residual: angle pdb=" C3' C I 104 " pdb=" O3' C I 104 " pdb=" P G I 105 " ideal model delta sigma weight residual 120.20 110.38 9.82 1.50e+00 4.44e-01 4.28e+01 angle pdb=" N GLN E 32 " pdb=" CA GLN E 32 " pdb=" C GLN E 32 " ideal model delta sigma weight residual 113.38 105.47 7.91 1.23e+00 6.61e-01 4.14e+01 angle pdb=" C ALA A 153 " pdb=" N MET A 154 " pdb=" CA MET A 154 " ideal model delta sigma weight residual 120.58 131.13 -10.55 1.71e+00 3.42e-01 3.81e+01 angle pdb=" C3' U I 3 " pdb=" O3' U I 3 " pdb=" P G I 4 " ideal model delta sigma weight residual 120.20 111.15 9.05 1.50e+00 4.44e-01 3.64e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 120.20 111.28 8.92 1.50e+00 4.44e-01 3.54e+01 ... (remaining 15419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 5887 35.55 - 71.10: 771 71.10 - 106.65: 78 106.65 - 142.20: 4 142.20 - 177.75: 5 Dihedral angle restraints: 6745 sinusoidal: 4152 harmonic: 2593 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual -128.00 46.57 -174.57 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 76.28 155.72 1 1.70e+01 3.46e-03 6.35e+01 dihedral pdb=" C5' C I 20 " pdb=" C4' C I 20 " pdb=" C3' C I 20 " pdb=" O3' C I 20 " ideal model delta sinusoidal sigma weight residual 147.00 108.63 38.37 1 8.00e+00 1.56e-02 3.24e+01 ... (remaining 6742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1718 0.113 - 0.225: 95 0.225 - 0.338: 13 0.338 - 0.450: 4 0.450 - 0.563: 2 Chirality restraints: 1832 Sorted by residual: chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" P A I 81 " pdb=" OP1 A I 81 " pdb=" OP2 A I 81 " pdb=" O5' A I 81 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" P U I 120 " pdb=" OP1 U I 120 " pdb=" OP2 U I 120 " pdb=" O5' U I 120 " both_signs ideal model delta sigma weight residual True 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 1829 not shown) Planarity restraints: 1399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 90 " -0.087 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO C 91 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " -0.064 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO A 71 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 231 " -0.038 2.00e-02 2.50e+03 2.59e-02 1.18e+01 pdb=" CG PHE A 231 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 231 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 231 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 231 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 231 " -0.010 2.00e-02 2.50e+03 ... (remaining 1396 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1413 2.74 - 3.28: 11235 3.28 - 3.82: 23299 3.82 - 4.36: 28718 4.36 - 4.90: 40236 Nonbonded interactions: 104901 Sorted by model distance: nonbonded pdb=" OH TYR F 26 " pdb=" OG1 THR F 101 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" O LEU A 242 " model vdw 2.210 3.040 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.251 3.120 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.252 3.040 nonbonded pdb=" NE2 HIS A 202 " pdb=" O2' G I 129 " model vdw 2.260 3.120 ... (remaining 104896 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 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = chain 'D' selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 2.400 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.680 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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 : 0.010 0.172 10881 Z= 0.692 Angle : 1.206 12.992 15424 Z= 0.653 Chirality : 0.064 0.563 1832 Planarity : 0.010 0.133 1399 Dihedral : 25.815 177.753 5073 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 41.97 Ramachandran Plot: Outliers : 3.64 % Allowed : 10.69 % Favored : 85.67 % Rotamer: Outliers : 20.00 % Allowed : 14.23 % Favored : 65.77 % Cbeta Deviations : 0.12 % 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: -4.10 (0.24), residues: 879 helix: -2.03 (0.17), residues: 643 sheet: -3.81 (1.05), residues: 26 loop : -4.23 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP D 81 HIS 0.015 0.003 HIS E 38 PHE 0.054 0.006 PHE A 231 TYR 0.026 0.004 TYR A 41 ARG 0.014 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 265 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6612 (ppp) REVERT: A 3 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6719 (mttm) REVERT: A 33 TRP cc_start: 0.7820 (t-100) cc_final: 0.7283 (t60) REVERT: A 37 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: A 52 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: A 59 GLU cc_start: 0.8373 (mp0) cc_final: 0.8119 (pt0) REVERT: A 74 ARG cc_start: 0.5299 (OUTLIER) cc_final: 0.5073 (ptt180) REVERT: A 109 CYS cc_start: 0.8194 (m) cc_final: 0.7899 (t) REVERT: A 123 GLN cc_start: 0.7862 (tt0) cc_final: 0.7647 (tt0) REVERT: A 130 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7616 (mmm160) REVERT: A 154 MET cc_start: 0.8389 (mtt) cc_final: 0.8017 (mtt) REVERT: A 158 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8367 (mmmm) REVERT: A 172 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7987 (tt) REVERT: A 200 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7762 (tt) REVERT: A 203 ASP cc_start: 0.8292 (m-30) cc_final: 0.8089 (m-30) REVERT: A 214 MET cc_start: 0.8472 (tpp) cc_final: 0.8245 (mmm) REVERT: A 226 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: A 256 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7570 (mmm-85) REVERT: A 270 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8152 (ttpp) REVERT: A 272 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7202 (mp) REVERT: B 14 MET cc_start: 0.8383 (mtt) cc_final: 0.7992 (mtp) REVERT: B 77 MET cc_start: 0.8611 (tpt) cc_final: 0.7987 (tpp) REVERT: C 14 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6973 (ttp) REVERT: C 18 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8289 (tt0) REVERT: C 20 TYR cc_start: 0.8729 (t80) cc_final: 0.8527 (t80) REVERT: C 48 CYS cc_start: 0.8823 (t) cc_final: 0.8613 (t) REVERT: C 57 ILE cc_start: 0.8462 (mm) cc_final: 0.8200 (mp) REVERT: D 18 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7520 (tp30) REVERT: D 19 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7943 (mmt-90) REVERT: D 38 HIS cc_start: 0.8698 (m-70) cc_final: 0.7821 (m-70) REVERT: D 52 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8125 (tp40) REVERT: D 62 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.6069 (p) REVERT: D 67 LYS cc_start: 0.8107 (mptt) cc_final: 0.7895 (mmmt) REVERT: D 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7930 (t0) REVERT: D 75 LEU cc_start: 0.8342 (mt) cc_final: 0.7994 (mt) REVERT: D 95 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7374 (p) REVERT: D 103 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8288 (mm-40) REVERT: D 108 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: E 18 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (tp30) REVERT: E 43 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: E 52 GLN cc_start: 0.8192 (tm-30) cc_final: 0.6689 (tm-30) REVERT: E 69 TYR cc_start: 0.8132 (m-10) cc_final: 0.7925 (m-80) REVERT: E 111 ARG cc_start: 0.8426 (mtm110) cc_final: 0.8102 (ttp-110) REVERT: F 14 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6752 (tmm) REVERT: F 19 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7857 (mmm160) REVERT: F 20 TYR cc_start: 0.8393 (t80) cc_final: 0.7979 (t80) REVERT: F 25 SER cc_start: 0.9279 (t) cc_final: 0.8998 (p) REVERT: F 54 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: F 55 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7198 (mp) REVERT: F 92 HIS cc_start: 0.6308 (m-70) cc_final: 0.5962 (m90) outliers start: 149 outliers final: 33 residues processed: 356 average time/residue: 0.3396 time to fit residues: 152.8898 Evaluate side-chains 271 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 18 GLU Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 87 GLN A 290 HIS A 306 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN C 92 HIS C 121 ASN D 13 GLN E 32 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 GLN F 97 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 10881 Z= 0.353 Angle : 0.820 9.577 15424 Z= 0.420 Chirality : 0.043 0.233 1832 Planarity : 0.008 0.123 1399 Dihedral : 24.948 173.757 3470 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.74 % Favored : 91.24 % Rotamer: Outliers : 8.86 % Allowed : 18.93 % Favored : 72.21 % 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: -2.06 (0.27), residues: 879 helix: -0.61 (0.19), residues: 658 sheet: -3.02 (1.07), residues: 26 loop : -3.37 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.010 0.002 HIS C 92 PHE 0.040 0.003 PHE A 231 TYR 0.020 0.002 TYR C 28 ARG 0.007 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 238 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7080 (mmt) cc_final: 0.6867 (tmm) REVERT: A 3 LYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6413 (mmtp) REVERT: A 7 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: A 74 ARG cc_start: 0.5592 (OUTLIER) cc_final: 0.5368 (ptt180) REVERT: A 115 THR cc_start: 0.9009 (m) cc_final: 0.8585 (p) REVERT: A 116 HIS cc_start: 0.8483 (m-70) cc_final: 0.8205 (m-70) REVERT: A 130 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7296 (mmm160) REVERT: A 139 PHE cc_start: 0.7621 (m-80) cc_final: 0.7416 (m-10) REVERT: A 165 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7607 (mtt180) REVERT: A 172 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 214 MET cc_start: 0.8511 (tpp) cc_final: 0.8261 (mmm) REVERT: A 222 ASP cc_start: 0.8084 (p0) cc_final: 0.7428 (m-30) REVERT: A 226 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: A 256 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7158 (mmm-85) REVERT: A 272 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7489 (pp) REVERT: B 2 GLU cc_start: 0.8496 (tp30) cc_final: 0.8229 (tp30) REVERT: B 67 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8129 (mtmm) REVERT: B 69 TYR cc_start: 0.8469 (m-80) cc_final: 0.7963 (m-80) REVERT: B 89 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7541 (mm110) REVERT: B 103 GLN cc_start: 0.8353 (tp40) cc_final: 0.8027 (mm-40) REVERT: C 18 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8063 (mm-30) REVERT: C 69 TYR cc_start: 0.8102 (m-10) cc_final: 0.7763 (m-10) REVERT: C 89 GLN cc_start: 0.6939 (tp-100) cc_final: 0.6737 (pp30) REVERT: C 92 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6805 (m-70) REVERT: D 18 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: D 19 ARG cc_start: 0.7711 (mmt-90) cc_final: 0.7428 (mmt-90) REVERT: D 26 TYR cc_start: 0.8460 (t80) cc_final: 0.7776 (t80) REVERT: D 52 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8331 (tp40) REVERT: D 54 GLU cc_start: 0.8008 (tp30) cc_final: 0.7657 (tp30) REVERT: D 62 SER cc_start: 0.6334 (OUTLIER) cc_final: 0.6002 (p) REVERT: D 67 LYS cc_start: 0.8216 (mptt) cc_final: 0.7958 (mmmt) REVERT: D 108 GLU cc_start: 0.6983 (tt0) cc_final: 0.6624 (tm-30) REVERT: E 42 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8129 (ttp-170) REVERT: E 52 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: E 54 GLU cc_start: 0.8285 (tt0) cc_final: 0.7852 (tm-30) REVERT: E 111 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7744 (ttp-110) REVERT: F 14 MET cc_start: 0.6840 (mmp) cc_final: 0.6022 (tmm) REVERT: F 20 TYR cc_start: 0.8440 (t80) cc_final: 0.7956 (t80) REVERT: F 54 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7804 (tt0) outliers start: 66 outliers final: 23 residues processed: 276 average time/residue: 0.3070 time to fit residues: 109.7403 Evaluate side-chains 241 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 74 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 62 optimal weight: 0.0870 chunk 25 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 73 optimal weight: 0.0570 chunk 90 optimal weight: 2.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 10881 Z= 0.282 Angle : 0.717 13.795 15424 Z= 0.365 Chirality : 0.041 0.260 1832 Planarity : 0.008 0.160 1399 Dihedral : 24.481 174.059 3394 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.53 % Favored : 90.56 % Rotamer: Outliers : 6.04 % Allowed : 22.01 % Favored : 71.95 % 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: -1.24 (0.28), residues: 879 helix: -0.06 (0.19), residues: 665 sheet: -2.38 (1.07), residues: 26 loop : -3.03 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 116 HIS 0.005 0.001 HIS A 121 PHE 0.029 0.003 PHE A 231 TYR 0.024 0.002 TYR C 28 ARG 0.010 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 TYR cc_start: 0.7844 (m-80) cc_final: 0.6861 (m-80) REVERT: A 115 THR cc_start: 0.9060 (m) cc_final: 0.8751 (p) REVERT: A 116 HIS cc_start: 0.8412 (m-70) cc_final: 0.8114 (m-70) REVERT: A 130 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7180 (mmm160) REVERT: A 165 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7647 (mtt180) REVERT: A 172 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8372 (tt) REVERT: A 205 LEU cc_start: 0.8321 (mt) cc_final: 0.7641 (mp) REVERT: A 222 ASP cc_start: 0.8051 (p0) cc_final: 0.7375 (m-30) REVERT: A 226 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 256 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6841 (mmm-85) REVERT: A 272 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7743 (pp) REVERT: B 9 LYS cc_start: 0.8114 (ptpt) cc_final: 0.7886 (ttpt) REVERT: B 67 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7907 (mtmm) REVERT: B 69 TYR cc_start: 0.8299 (m-80) cc_final: 0.7746 (m-80) REVERT: B 82 LEU cc_start: 0.8914 (mt) cc_final: 0.8625 (mp) REVERT: B 103 GLN cc_start: 0.8441 (tp40) cc_final: 0.8170 (mm-40) REVERT: C 77 MET cc_start: 0.8664 (tpt) cc_final: 0.7898 (tpt) REVERT: C 92 HIS cc_start: 0.7077 (m-70) cc_final: 0.6694 (m-70) REVERT: C 111 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7531 (ttp80) REVERT: D 18 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: D 19 ARG cc_start: 0.7714 (mmt-90) cc_final: 0.7027 (mmp80) REVERT: D 26 TYR cc_start: 0.8413 (t80) cc_final: 0.7834 (t80) REVERT: D 52 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8278 (tp40) REVERT: D 54 GLU cc_start: 0.7899 (tp30) cc_final: 0.7599 (tp30) REVERT: D 62 SER cc_start: 0.6274 (OUTLIER) cc_final: 0.5868 (p) REVERT: D 67 LYS cc_start: 0.8178 (mptt) cc_final: 0.7940 (mmmt) REVERT: D 108 GLU cc_start: 0.6838 (tt0) cc_final: 0.6614 (tm-30) REVERT: E 52 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: E 77 MET cc_start: 0.8752 (tpt) cc_final: 0.7900 (tpt) REVERT: E 92 HIS cc_start: 0.8702 (m170) cc_final: 0.8435 (m170) REVERT: E 94 MET cc_start: 0.8855 (ttm) cc_final: 0.8621 (mtp) REVERT: E 111 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7698 (ttp-110) REVERT: F 14 MET cc_start: 0.6408 (mmp) cc_final: 0.5949 (tmm) outliers start: 45 outliers final: 21 residues processed: 264 average time/residue: 0.3149 time to fit residues: 107.8279 Evaluate side-chains 248 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 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 57 ASN B 32 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10881 Z= 0.315 Angle : 0.699 8.858 15424 Z= 0.355 Chirality : 0.040 0.201 1832 Planarity : 0.007 0.136 1399 Dihedral : 24.098 172.678 3377 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.19 % Favored : 91.01 % Rotamer: Outliers : 5.37 % Allowed : 22.28 % Favored : 72.35 % 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 (0.28), residues: 879 helix: 0.06 (0.19), residues: 669 sheet: -1.89 (1.13), residues: 26 loop : -2.85 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 116 HIS 0.005 0.001 HIS C 92 PHE 0.030 0.003 PHE A 231 TYR 0.026 0.002 TYR C 28 ARG 0.009 0.001 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7939 (m-40) cc_final: 0.7316 (m-40) REVERT: A 115 THR cc_start: 0.9056 (m) cc_final: 0.8766 (p) REVERT: A 165 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7609 (mtt180) REVERT: A 172 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8333 (tt) REVERT: A 222 ASP cc_start: 0.8167 (p0) cc_final: 0.7502 (m-30) REVERT: A 224 PRO cc_start: 0.7157 (Cg_exo) cc_final: 0.6935 (Cg_endo) REVERT: A 226 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: A 256 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6605 (mmm-85) REVERT: B 67 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7899 (mtmm) REVERT: B 69 TYR cc_start: 0.8336 (m-10) cc_final: 0.7702 (m-80) REVERT: B 82 LEU cc_start: 0.8939 (mt) cc_final: 0.8648 (mp) REVERT: C 22 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7844 (mtt180) REVERT: C 77 MET cc_start: 0.8659 (tpt) cc_final: 0.8176 (tpt) REVERT: C 111 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7573 (ttp80) REVERT: D 18 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: D 19 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7458 (mmt-90) REVERT: D 26 TYR cc_start: 0.8505 (t80) cc_final: 0.7922 (t80) REVERT: D 37 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7445 (mmmt) REVERT: D 52 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8192 (tp-100) REVERT: D 108 GLU cc_start: 0.6878 (tt0) cc_final: 0.6653 (tm-30) REVERT: E 52 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: E 92 HIS cc_start: 0.8731 (m170) cc_final: 0.8038 (m170) REVERT: E 111 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7651 (ttp-110) REVERT: F 14 MET cc_start: 0.6377 (mmp) cc_final: 0.5873 (tmm) outliers start: 40 outliers final: 27 residues processed: 254 average time/residue: 0.3101 time to fit residues: 102.2034 Evaluate side-chains 253 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.7980 chunk 1 optimal weight: 0.0070 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10881 Z= 0.263 Angle : 0.677 10.515 15424 Z= 0.343 Chirality : 0.038 0.194 1832 Planarity : 0.007 0.123 1399 Dihedral : 23.749 171.673 3364 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.30 % Favored : 91.13 % Rotamer: Outliers : 5.10 % Allowed : 23.49 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.74 (0.28), residues: 879 helix: 0.20 (0.19), residues: 666 sheet: -1.45 (1.20), residues: 26 loop : -2.59 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 116 HIS 0.008 0.001 HIS A 121 PHE 0.028 0.002 PHE A 231 TYR 0.023 0.002 TYR C 28 ARG 0.012 0.001 ARG C 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7808 (mt) cc_final: 0.7592 (mm) REVERT: A 105 TYR cc_start: 0.8393 (m-10) cc_final: 0.8168 (m-10) REVERT: A 107 TYR cc_start: 0.8133 (m-80) cc_final: 0.7226 (m-80) REVERT: A 165 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7654 (mtt180) REVERT: A 212 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8292 (ttp80) REVERT: A 224 PRO cc_start: 0.7049 (Cg_exo) cc_final: 0.6836 (Cg_endo) REVERT: A 256 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.6054 (mmm-85) REVERT: B 11 TYR cc_start: 0.7516 (t80) cc_final: 0.7232 (t80) REVERT: B 67 LYS cc_start: 0.8196 (mtpt) cc_final: 0.7837 (mtmm) REVERT: B 69 TYR cc_start: 0.8151 (m-10) cc_final: 0.7909 (m-80) REVERT: B 82 LEU cc_start: 0.8896 (mt) cc_final: 0.8584 (mp) REVERT: B 89 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7337 (mm110) REVERT: C 12 ASP cc_start: 0.5693 (m-30) cc_final: 0.5327 (m-30) REVERT: C 19 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7253 (mmm-85) REVERT: C 77 MET cc_start: 0.8599 (tpt) cc_final: 0.7858 (tpt) REVERT: C 111 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7558 (ttp80) REVERT: D 18 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: D 19 ARG cc_start: 0.7687 (mmt-90) cc_final: 0.7384 (mmt-90) REVERT: D 26 TYR cc_start: 0.8423 (t80) cc_final: 0.7878 (t80) REVERT: D 37 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7363 (mmmt) REVERT: D 52 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8068 (tp-100) REVERT: E 52 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: E 92 HIS cc_start: 0.8681 (m170) cc_final: 0.7945 (m170) REVERT: E 111 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7586 (ttp-110) REVERT: F 14 MET cc_start: 0.6175 (mmp) cc_final: 0.5881 (tmm) REVERT: F 54 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: F 69 TYR cc_start: 0.7491 (m-10) cc_final: 0.7175 (m-10) REVERT: F 88 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7287 (tt) REVERT: F 108 GLU cc_start: 0.8062 (tp30) cc_final: 0.7598 (mt-10) outliers start: 38 outliers final: 19 residues processed: 260 average time/residue: 0.3280 time to fit residues: 109.3178 Evaluate side-chains 248 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0670 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.0570 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10881 Z= 0.251 Angle : 0.664 8.487 15424 Z= 0.337 Chirality : 0.038 0.193 1832 Planarity : 0.007 0.122 1399 Dihedral : 23.587 176.822 3353 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.51 % Favored : 91.92 % Rotamer: Outliers : 5.10 % Allowed : 23.22 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.28), residues: 879 helix: 0.29 (0.19), residues: 663 sheet: -1.51 (1.20), residues: 26 loop : -2.48 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 116 HIS 0.006 0.001 HIS A 121 PHE 0.027 0.002 PHE A 231 TYR 0.020 0.002 TYR C 28 ARG 0.009 0.001 ARG E 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7857 (mt) cc_final: 0.7461 (mm) REVERT: A 57 ASN cc_start: 0.8281 (m-40) cc_final: 0.7992 (t0) REVERT: A 105 TYR cc_start: 0.8519 (m-10) cc_final: 0.8224 (m-10) REVERT: A 130 ARG cc_start: 0.6637 (mmm160) cc_final: 0.6166 (mmp80) REVERT: A 158 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7596 (mtpp) REVERT: A 165 ARG cc_start: 0.8121 (mtp85) cc_final: 0.7731 (mtt180) REVERT: A 189 PHE cc_start: 0.8473 (m-10) cc_final: 0.7855 (m-10) REVERT: A 208 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6057 (mpt180) REVERT: A 212 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8545 (ttp80) REVERT: A 240 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: A 256 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.5564 (mmm-85) REVERT: B 11 TYR cc_start: 0.7414 (t80) cc_final: 0.6992 (t80) REVERT: B 67 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7831 (mtmm) REVERT: B 69 TYR cc_start: 0.8087 (m-10) cc_final: 0.7851 (m-80) REVERT: B 82 LEU cc_start: 0.8720 (mt) cc_final: 0.8384 (mp) REVERT: C 19 ARG cc_start: 0.7600 (mmm-85) cc_final: 0.7324 (mmm160) REVERT: C 77 MET cc_start: 0.8620 (tpt) cc_final: 0.7858 (tpt) REVERT: C 90 LYS cc_start: 0.7152 (tptt) cc_final: 0.6862 (mttm) REVERT: C 111 ARG cc_start: 0.8158 (mtm110) cc_final: 0.7637 (ttp80) REVERT: D 18 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: D 19 ARG cc_start: 0.7620 (mmt-90) cc_final: 0.7181 (mmp80) REVERT: D 26 TYR cc_start: 0.8473 (t80) cc_final: 0.7925 (t80) REVERT: D 37 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7332 (mmmt) REVERT: D 52 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (tp-100) REVERT: E 52 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: E 77 MET cc_start: 0.8758 (tpt) cc_final: 0.8053 (tpt) REVERT: E 92 HIS cc_start: 0.8563 (m170) cc_final: 0.7905 (m170) REVERT: E 111 ARG cc_start: 0.7884 (mtm110) cc_final: 0.7532 (ttp-110) REVERT: F 54 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: F 69 TYR cc_start: 0.7529 (m-10) cc_final: 0.7232 (m-10) REVERT: F 88 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7210 (tt) REVERT: F 108 GLU cc_start: 0.8031 (tp30) cc_final: 0.7579 (mt-10) outliers start: 38 outliers final: 16 residues processed: 254 average time/residue: 0.3268 time to fit residues: 108.0872 Evaluate side-chains 241 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10881 Z= 0.279 Angle : 0.667 9.226 15424 Z= 0.338 Chirality : 0.038 0.225 1832 Planarity : 0.007 0.121 1399 Dihedral : 23.487 179.912 3350 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.83 % Favored : 92.49 % Rotamer: Outliers : 5.50 % Allowed : 23.89 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.60 (0.28), residues: 879 helix: 0.30 (0.19), residues: 660 sheet: -1.54 (1.18), residues: 26 loop : -2.44 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.008 0.001 HIS A 121 PHE 0.023 0.002 PHE A 231 TYR 0.027 0.002 TYR F 20 ARG 0.008 0.001 ARG E 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.7751 (m-40) cc_final: 0.7192 (m-40) REVERT: A 57 ASN cc_start: 0.8323 (m-40) cc_final: 0.8102 (t0) REVERT: A 158 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7598 (mtpp) REVERT: A 165 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7650 (mtt180) REVERT: A 208 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6281 (mpt180) REVERT: A 212 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8200 (ttp80) REVERT: A 240 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8196 (mm-30) REVERT: A 256 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5366 (mtm-85) REVERT: B 67 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7814 (mtmm) REVERT: B 69 TYR cc_start: 0.8046 (m-10) cc_final: 0.7834 (m-80) REVERT: B 82 LEU cc_start: 0.8652 (mt) cc_final: 0.8318 (mp) REVERT: B 89 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7609 (mm110) REVERT: B 98 GLN cc_start: 0.7546 (tt0) cc_final: 0.7313 (tt0) REVERT: C 111 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7567 (ttp80) REVERT: D 18 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: D 19 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.7096 (mmp80) REVERT: D 26 TYR cc_start: 0.8516 (t80) cc_final: 0.7965 (t80) REVERT: D 37 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7458 (mmmt) REVERT: D 52 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8300 (tp-100) REVERT: E 47 LYS cc_start: 0.8076 (mttm) cc_final: 0.7819 (mttp) REVERT: E 52 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: E 92 HIS cc_start: 0.8615 (m170) cc_final: 0.8008 (m170) REVERT: E 111 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7627 (ttp-110) REVERT: F 20 TYR cc_start: 0.8195 (t80) cc_final: 0.7979 (t80) REVERT: F 26 TYR cc_start: 0.8021 (t80) cc_final: 0.7753 (t80) REVERT: F 54 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: F 69 TYR cc_start: 0.7576 (m-10) cc_final: 0.7285 (m-10) REVERT: F 92 HIS cc_start: 0.7475 (m170) cc_final: 0.7003 (m-70) REVERT: F 108 GLU cc_start: 0.8017 (tp30) cc_final: 0.7592 (mt-10) outliers start: 41 outliers final: 21 residues processed: 249 average time/residue: 0.3139 time to fit residues: 101.3740 Evaluate side-chains 250 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 10881 Z= 0.278 Angle : 0.693 9.613 15424 Z= 0.349 Chirality : 0.039 0.254 1832 Planarity : 0.007 0.109 1399 Dihedral : 23.434 177.965 3350 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.39 % Favored : 91.92 % Rotamer: Outliers : 4.16 % Allowed : 24.83 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.59 (0.28), residues: 879 helix: 0.32 (0.19), residues: 664 sheet: 0.37 (1.46), residues: 14 loop : -2.67 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 266 HIS 0.012 0.001 HIS C 38 PHE 0.025 0.002 PHE A 231 TYR 0.023 0.002 TYR F 20 ARG 0.011 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8325 (m-40) cc_final: 0.8121 (t0) REVERT: A 130 ARG cc_start: 0.6419 (mmm160) cc_final: 0.5935 (mmp80) REVERT: A 158 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7610 (mtpp) REVERT: A 165 ARG cc_start: 0.8099 (mtp85) cc_final: 0.7659 (mtt180) REVERT: A 208 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6240 (mpt180) REVERT: A 212 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8367 (ttp80) REVERT: A 240 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8164 (mm-30) REVERT: B 43 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6871 (tm-30) REVERT: B 67 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7822 (mtmm) REVERT: B 69 TYR cc_start: 0.8067 (m-10) cc_final: 0.7850 (m-80) REVERT: B 82 LEU cc_start: 0.8637 (mt) cc_final: 0.8302 (mp) REVERT: B 89 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7628 (mm110) REVERT: B 92 HIS cc_start: 0.5377 (t70) cc_final: 0.5135 (t-90) REVERT: B 98 GLN cc_start: 0.7512 (tt0) cc_final: 0.7238 (tt0) REVERT: C 111 ARG cc_start: 0.8003 (mtm110) cc_final: 0.7473 (ttp80) REVERT: D 18 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: D 19 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7163 (mmp80) REVERT: D 26 TYR cc_start: 0.8507 (t80) cc_final: 0.7960 (t80) REVERT: D 37 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7329 (mmmt) REVERT: D 52 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8072 (tp-100) REVERT: E 47 LYS cc_start: 0.8067 (mttm) cc_final: 0.7803 (mttp) REVERT: E 52 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: E 77 MET cc_start: 0.8656 (tpt) cc_final: 0.7840 (tpt) REVERT: E 92 HIS cc_start: 0.8585 (m170) cc_final: 0.7999 (m170) REVERT: E 111 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7624 (ttp-110) REVERT: F 20 TYR cc_start: 0.8236 (t80) cc_final: 0.7980 (t80) REVERT: F 54 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: F 69 TYR cc_start: 0.7596 (m-10) cc_final: 0.7319 (m-10) REVERT: F 108 GLU cc_start: 0.7987 (tp30) cc_final: 0.7578 (mt-10) outliers start: 31 outliers final: 20 residues processed: 232 average time/residue: 0.3177 time to fit residues: 96.4043 Evaluate side-chains 235 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 58 optimal weight: 0.5980 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 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10881 Z= 0.291 Angle : 0.689 10.106 15424 Z= 0.347 Chirality : 0.039 0.250 1832 Planarity : 0.006 0.108 1399 Dihedral : 23.334 179.944 3346 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.05 % Favored : 92.26 % Rotamer: Outliers : 4.16 % Allowed : 24.16 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.50 (0.28), residues: 879 helix: 0.37 (0.19), residues: 666 sheet: 0.64 (1.50), residues: 14 loop : -2.64 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 266 HIS 0.013 0.001 HIS B 38 PHE 0.024 0.002 PHE A 231 TYR 0.025 0.002 TYR A 105 ARG 0.008 0.001 ARG E 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.6413 (mmm160) cc_final: 0.5922 (mmp80) REVERT: A 165 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7653 (mtt180) REVERT: A 212 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8355 (ttp80) REVERT: A 240 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8181 (mm-30) REVERT: B 43 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6915 (tm-30) REVERT: B 67 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7824 (mtmm) REVERT: B 69 TYR cc_start: 0.8081 (m-10) cc_final: 0.7854 (m-80) REVERT: B 82 LEU cc_start: 0.8616 (mt) cc_final: 0.8246 (mp) REVERT: B 89 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7440 (mm110) REVERT: B 92 HIS cc_start: 0.5249 (t70) cc_final: 0.4967 (t-90) REVERT: B 98 GLN cc_start: 0.7523 (tt0) cc_final: 0.7254 (tt0) REVERT: C 111 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7586 (ttp80) REVERT: D 18 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: D 19 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7160 (mmp80) REVERT: D 26 TYR cc_start: 0.8546 (t80) cc_final: 0.8016 (t80) REVERT: D 37 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7279 (mmmt) REVERT: D 52 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7814 (tp-100) REVERT: E 52 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: E 92 HIS cc_start: 0.8623 (m170) cc_final: 0.7981 (m170) REVERT: E 111 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7632 (ttp-110) REVERT: F 20 TYR cc_start: 0.8257 (t80) cc_final: 0.7999 (t80) REVERT: F 26 TYR cc_start: 0.8043 (t80) cc_final: 0.7748 (t80) REVERT: F 54 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: F 69 TYR cc_start: 0.7668 (m-10) cc_final: 0.7409 (m-10) REVERT: F 108 GLU cc_start: 0.7979 (tp30) cc_final: 0.7571 (mt-10) outliers start: 31 outliers final: 23 residues processed: 227 average time/residue: 0.3056 time to fit residues: 90.1699 Evaluate side-chains 227 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 14 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10881 Z= 0.229 Angle : 0.699 20.796 15424 Z= 0.346 Chirality : 0.039 0.286 1832 Planarity : 0.007 0.178 1399 Dihedral : 23.203 178.505 3345 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.17 % Favored : 92.15 % Rotamer: Outliers : 3.36 % Allowed : 25.37 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.52 (0.28), residues: 879 helix: 0.37 (0.19), residues: 664 sheet: 1.08 (1.41), residues: 14 loop : -2.74 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 210 HIS 0.011 0.001 HIS B 38 PHE 0.021 0.002 PHE A 231 TYR 0.026 0.002 TYR A 105 ARG 0.008 0.001 ARG B 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.7714 (mt) cc_final: 0.7318 (mm) REVERT: A 22 TYR cc_start: 0.8953 (t80) cc_final: 0.8740 (t80) REVERT: A 80 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7386 (mp0) REVERT: A 130 ARG cc_start: 0.6362 (mmm160) cc_final: 0.5861 (mmp80) REVERT: A 165 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7762 (mtt180) REVERT: A 208 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.7037 (mmt-90) REVERT: A 240 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: B 11 TYR cc_start: 0.7263 (t80) cc_final: 0.6824 (t80) REVERT: B 66 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 67 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7679 (mtmm) REVERT: B 69 TYR cc_start: 0.8050 (m-10) cc_final: 0.7532 (m-80) REVERT: B 82 LEU cc_start: 0.8549 (mt) cc_final: 0.8234 (mp) REVERT: B 89 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7441 (mm110) REVERT: B 92 HIS cc_start: 0.5267 (t70) cc_final: 0.5030 (t-90) REVERT: B 98 GLN cc_start: 0.7544 (tt0) cc_final: 0.7271 (tt0) REVERT: C 77 MET cc_start: 0.8608 (tpt) cc_final: 0.7779 (tpt) REVERT: C 97 HIS cc_start: 0.8212 (t-90) cc_final: 0.7992 (t-90) REVERT: C 111 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7453 (ttp80) REVERT: D 18 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: D 19 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.7198 (mmp80) REVERT: D 26 TYR cc_start: 0.8417 (t80) cc_final: 0.7923 (t80) REVERT: D 37 LYS cc_start: 0.7773 (mtpp) cc_final: 0.7025 (mmmt) REVERT: D 52 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7751 (tp-100) REVERT: E 52 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7020 (tm-30) REVERT: E 92 HIS cc_start: 0.8550 (m170) cc_final: 0.7973 (m170) REVERT: F 20 TYR cc_start: 0.8225 (t80) cc_final: 0.7974 (t80) REVERT: F 26 TYR cc_start: 0.7963 (t80) cc_final: 0.7666 (t80) REVERT: F 69 TYR cc_start: 0.7558 (m-10) cc_final: 0.7310 (m-10) REVERT: F 90 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8039 (tptp) REVERT: F 92 HIS cc_start: 0.7538 (m170) cc_final: 0.7281 (m170) REVERT: F 108 GLU cc_start: 0.7983 (tp30) cc_final: 0.7570 (mt-10) outliers start: 25 outliers final: 17 residues processed: 219 average time/residue: 0.2988 time to fit residues: 85.8606 Evaluate side-chains 221 residues out of total 745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 52 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 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 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** E 32 GLN ** 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 = 0.4303 r_free = 0.4303 target = 0.180774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140831 restraints weight = 15648.012| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.61 r_work: 0.3607 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 10881 Z= 0.302 Angle : 0.714 16.656 15424 Z= 0.353 Chirality : 0.040 0.268 1832 Planarity : 0.007 0.166 1399 Dihedral : 23.129 177.286 3345 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.94 % Favored : 92.49 % Rotamer: Outliers : 3.09 % Allowed : 25.50 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.50 (0.28), residues: 879 helix: 0.38 (0.20), residues: 662 sheet: 1.42 (1.38), residues: 14 loop : -2.68 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 15 HIS 0.016 0.002 HIS B 38 PHE 0.023 0.002 PHE B 80 TYR 0.026 0.002 TYR A 105 ARG 0.012 0.001 ARG E 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.67 seconds wall clock time: 50 minutes 47.72 seconds (3047.72 seconds total)