Starting phenix.real_space_refine on Fri Mar 15 18:51:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhz_24472/03_2024/7rhz_24472_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhz_24472/03_2024/7rhz_24472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhz_24472/03_2024/7rhz_24472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhz_24472/03_2024/7rhz_24472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhz_24472/03_2024/7rhz_24472_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhz_24472/03_2024/7rhz_24472_neut.pdb" } resolution = 4.48 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= -0.003 sd= 0.083 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: 6 Type Number sf(0) Gaussians P 88 5.49 5 S 29 5.16 5 C 3888 2.51 5 N 1253 2.21 5 O 1417 1.98 5 H 5875 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12550 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 4987 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 7, 'TRANS': 307} Chain breaks: 1 Chain: "B" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4764 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 1 Chain: "C" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 1395 Classifications: {'DNA': 44} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 43} Chain: "D" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 1404 Classifications: {'DNA': 44} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 43} Time building chain proxies: 6.80, per 1000 atoms: 0.54 Number of scatterers: 12550 At special positions: 0 Unit cell: (73.718, 88.102, 163.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 88 15.00 O 1417 8.00 N 1253 7.00 C 3888 6.00 H 5875 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1146 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 66.7% alpha, 3.6% beta 44 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 7.36 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 38 through 59 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.609A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 126 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 154 through 171 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 214 through 229 Processing helix chain 'A' and resid 257 through 273 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.825A pdb=" N ALA A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.920A pdb=" N MET A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 38 through 59 Processing helix chain 'B' and resid 67 through 81 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 109 through 126 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 171 Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.552A pdb=" N ILE B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 189 through 191 No H-bonds generated for 'chain 'B' and resid 189 through 191' Processing helix chain 'B' and resid 214 through 229 Processing helix chain 'B' and resid 257 through 273 Processing helix chain 'B' and resid 287 through 303 removed outlier: 4.113A pdb=" N ALA B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 314 Processing helix chain 'B' and resid 318 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 187 removed outlier: 4.282A pdb=" N MET B 193 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 242 through 243 300 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 107 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 12.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5236 1.03 - 1.22: 685 1.22 - 1.42: 3191 1.42 - 1.62: 3686 1.62 - 1.81: 50 Bond restraints: 12848 Sorted by residual: bond pdb=" ND1 HIS A 40 " pdb=" CE1 HIS A 40 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.72e+01 bond pdb=" ND1 HIS A 289 " pdb=" CE1 HIS A 289 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.51e+01 bond pdb=" ND1 HIS A 91 " pdb=" CE1 HIS A 91 " ideal model delta sigma weight residual 1.321 1.235 0.086 1.00e-02 1.00e+04 7.46e+01 bond pdb=" CZ ARG A 292 " pdb=" NH2 ARG A 292 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.83e+01 bond pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.82e+01 ... (remaining 12843 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.44: 826 105.44 - 113.23: 13804 113.23 - 121.02: 5411 121.02 - 128.81: 2970 128.81 - 136.60: 150 Bond angle restraints: 23161 Sorted by residual: angle pdb=" CA HIS A 40 " pdb=" CB HIS A 40 " pdb=" CG HIS A 40 " ideal model delta sigma weight residual 113.80 120.58 -6.78 1.00e+00 1.00e+00 4.59e+01 angle pdb=" CA HIS A 91 " pdb=" CB HIS A 91 " pdb=" CG HIS A 91 " ideal model delta sigma weight residual 113.80 120.42 -6.62 1.00e+00 1.00e+00 4.38e+01 angle pdb=" H61 DA D 14 " pdb=" N6 DA D 14 " pdb=" H62 DA D 14 " ideal model delta sigma weight residual 120.00 110.12 9.88 1.50e+00 4.44e-01 4.34e+01 angle pdb=" H61 DA D 25 " pdb=" N6 DA D 25 " pdb=" H62 DA D 25 " ideal model delta sigma weight residual 120.00 110.17 9.83 1.50e+00 4.44e-01 4.30e+01 angle pdb=" H41 DC D 21 " pdb=" N4 DC D 21 " pdb=" H42 DC D 21 " ideal model delta sigma weight residual 120.00 110.19 9.81 1.50e+00 4.44e-01 4.28e+01 ... (remaining 23156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4677 17.96 - 35.92: 502 35.92 - 53.88: 319 53.88 - 71.84: 157 71.84 - 89.80: 11 Dihedral angle restraints: 5666 sinusoidal: 3639 harmonic: 2027 Sorted by residual: dihedral pdb=" CA TRP B 315 " pdb=" C TRP B 315 " pdb=" N THR B 316 " pdb=" CA THR B 316 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO B 107 " pdb=" C PRO B 107 " pdb=" N SER B 108 " pdb=" CA SER B 108 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA LEU B 172 " pdb=" C LEU B 172 " pdb=" N ARG B 173 " pdb=" CA ARG B 173 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 5663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 936 0.146 - 0.292: 19 0.292 - 0.437: 30 0.437 - 0.583: 79 0.583 - 0.729: 16 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CB ILE A 320 " pdb=" CA ILE A 320 " pdb=" CG1 ILE A 320 " pdb=" CG2 ILE A 320 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB VAL B 113 " pdb=" CA VAL B 113 " pdb=" CG1 VAL B 113 " pdb=" CG2 VAL B 113 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.71 2.00e-01 2.50e+01 1.28e+01 ... (remaining 1077 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA C 16 " -0.243 2.00e-02 2.50e+03 9.63e-02 3.01e+02 pdb=" N9 DA C 16 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DA C 16 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DA C 16 " 0.083 2.00e-02 2.50e+03 pdb=" C5 DA C 16 " 0.051 2.00e-02 2.50e+03 pdb=" C6 DA C 16 " -0.025 2.00e-02 2.50e+03 pdb=" N6 DA C 16 " -0.183 2.00e-02 2.50e+03 pdb=" N1 DA C 16 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DA C 16 " 0.039 2.00e-02 2.50e+03 pdb=" N3 DA C 16 " 0.037 2.00e-02 2.50e+03 pdb=" C4 DA C 16 " 0.049 2.00e-02 2.50e+03 pdb=" H8 DA C 16 " 0.061 2.00e-02 2.50e+03 pdb=" H2 DA C 16 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 17 " -0.199 2.00e-02 2.50e+03 7.92e-02 1.88e+02 pdb=" N1 DT C 17 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DT C 17 " 0.059 2.00e-02 2.50e+03 pdb=" O2 DT C 17 " 0.049 2.00e-02 2.50e+03 pdb=" N3 DT C 17 " 0.080 2.00e-02 2.50e+03 pdb=" C4 DT C 17 " -0.014 2.00e-02 2.50e+03 pdb=" O4 DT C 17 " -0.115 2.00e-02 2.50e+03 pdb=" C5 DT C 17 " 0.020 2.00e-02 2.50e+03 pdb=" C7 DT C 17 " -0.013 2.00e-02 2.50e+03 pdb=" C6 DT C 17 " 0.058 2.00e-02 2.50e+03 pdb=" H3 DT C 17 " -0.019 2.00e-02 2.50e+03 pdb=" H6 DT C 17 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 14 " -0.165 2.00e-02 2.50e+03 6.69e-02 1.57e+02 pdb=" N9 DG C 14 " 0.003 2.00e-02 2.50e+03 pdb=" C8 DG C 14 " 0.060 2.00e-02 2.50e+03 pdb=" N7 DG C 14 " 0.031 2.00e-02 2.50e+03 pdb=" C5 DG C 14 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DG C 14 " -0.059 2.00e-02 2.50e+03 pdb=" O6 DG C 14 " -0.058 2.00e-02 2.50e+03 pdb=" N1 DG C 14 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DG C 14 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 14 " 0.107 2.00e-02 2.50e+03 pdb=" N3 DG C 14 " 0.020 2.00e-02 2.50e+03 pdb=" C4 DG C 14 " 0.007 2.00e-02 2.50e+03 pdb=" H8 DG C 14 " 0.097 2.00e-02 2.50e+03 pdb=" H1 DG C 14 " 0.015 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 293 2.08 - 2.71: 19222 2.71 - 3.34: 35324 3.34 - 3.97: 43437 3.97 - 4.60: 66634 Nonbonded interactions: 164910 Sorted by model distance: nonbonded pdb="HH21 ARG A 106 " pdb=" OP1 DG D 20 " model vdw 1.453 1.850 nonbonded pdb="HH21 ARG B 106 " pdb=" OP1 DA C 20 " model vdw 1.467 1.850 nonbonded pdb=" H ARG B 181 " pdb=" OD2 ASP B 184 " model vdw 1.492 1.850 nonbonded pdb=" O LEU B 215 " pdb=" HG1 THR B 218 " model vdw 1.494 1.850 nonbonded pdb=" H TYR A 283 " pdb=" OP1 DC D 26 " model vdw 1.498 1.850 ... (remaining 164905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 32 or resid 34 through 35 or resid 37 through 7 \ 1 or resid 73 through 114 or resid 116 through 118 or resid 120 through 191 or r \ esid 193 through 327)) selection = (chain 'B' and (resid 20 through 32 or resid 34 through 35 or resid 37 through 7 \ 1 or resid 73 through 114 or resid 116 through 118 or resid 120 through 191 or r \ esid 193 through 198 or resid 208 through 327)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.190 Extract box with map and model: 1.320 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 51.180 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 0.020 0.134 6973 Z= 1.194 Angle : 1.621 11.844 9788 Z= 1.046 Chirality : 0.180 0.729 1080 Planarity : 0.012 0.102 959 Dihedral : 21.166 89.798 2838 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.59 % Allowed : 1.76 % Favored : 97.65 % Cbeta Deviations : 5.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.29), residues: 607 helix: -1.03 (0.23), residues: 378 sheet: 0.59 (1.02), residues: 28 loop : -1.03 (0.38), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP B 52 HIS 0.008 0.002 HIS B 99 PHE 0.007 0.001 PHE A 163 TYR 0.049 0.006 TYR A 283 ARG 0.023 0.002 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 0.953 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8914 (tttt) cc_final: 0.8674 (tmmt) REVERT: A 109 ASP cc_start: 0.8909 (m-30) cc_final: 0.8335 (p0) REVERT: A 129 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6431 (mm-30) REVERT: A 130 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8167 (ptm-80) REVERT: A 172 LEU cc_start: 0.8169 (mt) cc_final: 0.7058 (mt) REVERT: A 265 PHE cc_start: 0.9737 (m-80) cc_final: 0.9365 (m-80) REVERT: A 289 HIS cc_start: 0.9049 (m90) cc_final: 0.8714 (m-70) REVERT: A 298 ASP cc_start: 0.9312 (t0) cc_final: 0.9019 (m-30) REVERT: A 315 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.7654 (t60) REVERT: B 273 TYR cc_start: 0.8783 (m-80) cc_final: 0.8195 (m-80) REVERT: B 277 ASP cc_start: 0.9384 (m-30) cc_final: 0.9018 (p0) REVERT: B 319 ASN cc_start: 0.9517 (m-40) cc_final: 0.9234 (t0) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.6814 time to fit residues: 145.7223 Evaluate side-chains 135 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN B 89 GLN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6973 Z= 0.201 Angle : 0.647 5.413 9788 Z= 0.393 Chirality : 0.039 0.145 1080 Planarity : 0.004 0.038 959 Dihedral : 24.389 85.824 1664 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.32), residues: 607 helix: 0.94 (0.26), residues: 382 sheet: 0.47 (0.87), residues: 28 loop : -0.62 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 315 HIS 0.004 0.001 HIS B 91 PHE 0.010 0.001 PHE B 163 TYR 0.009 0.001 TYR B 324 ARG 0.006 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.965 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: 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: 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: 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: 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: 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: 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: symmetry clash REVERT: A 43 LYS cc_start: 0.8718 (tttt) cc_final: 0.8450 (tmmt) REVERT: A 108 SER cc_start: 0.9026 (m) cc_final: 0.8735 (m) REVERT: A 109 ASP cc_start: 0.9124 (m-30) cc_final: 0.8870 (p0) REVERT: A 129 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6599 (mm-30) REVERT: A 265 PHE cc_start: 0.9756 (m-80) cc_final: 0.9417 (m-80) REVERT: A 289 HIS cc_start: 0.9099 (m90) cc_final: 0.8887 (m-70) REVERT: A 298 ASP cc_start: 0.9445 (t0) cc_final: 0.8961 (t0) REVERT: B 77 TYR cc_start: 0.9013 (t80) cc_final: 0.8698 (t80) REVERT: B 213 LEU cc_start: 0.8075 (tp) cc_final: 0.7708 (tp) REVERT: B 256 LEU cc_start: 0.9234 (tt) cc_final: 0.8860 (mm) REVERT: B 258 THR cc_start: 0.8183 (p) cc_final: 0.7973 (p) REVERT: B 273 TYR cc_start: 0.8863 (m-80) cc_final: 0.8319 (m-80) REVERT: B 277 ASP cc_start: 0.9505 (m-30) cc_final: 0.9066 (p0) REVERT: B 319 ASN cc_start: 0.9476 (m-40) cc_final: 0.9107 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.6420 time to fit residues: 117.4123 Evaluate side-chains 128 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 6973 Z= 0.265 Angle : 0.653 5.514 9788 Z= 0.400 Chirality : 0.041 0.134 1080 Planarity : 0.004 0.041 959 Dihedral : 24.374 83.944 1664 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.57 (0.33), residues: 607 helix: 0.99 (0.27), residues: 385 sheet: -0.24 (0.80), residues: 29 loop : -0.64 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 42 HIS 0.004 0.001 HIS B 91 PHE 0.009 0.001 PHE A 163 TYR 0.009 0.002 TYR A 283 ARG 0.006 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.786 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.6199 (tpt) cc_final: 0.5749 (tpp) REVERT: A 43 LYS cc_start: 0.9075 (tttt) cc_final: 0.8843 (tmmt) REVERT: A 108 SER cc_start: 0.8750 (m) cc_final: 0.8098 (p) REVERT: A 129 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6241 (mm-30) REVERT: A 130 ARG cc_start: 0.8989 (mtt180) cc_final: 0.8574 (pmt-80) REVERT: A 176 GLU cc_start: 0.9756 (tp30) cc_final: 0.9390 (tp30) REVERT: A 265 PHE cc_start: 0.9803 (m-80) cc_final: 0.9496 (m-80) REVERT: A 289 HIS cc_start: 0.9105 (m90) cc_final: 0.8876 (m-70) REVERT: B 42 TRP cc_start: 0.9546 (t60) cc_final: 0.9308 (t-100) REVERT: B 273 TYR cc_start: 0.8940 (m-80) cc_final: 0.8439 (m-80) REVERT: B 277 ASP cc_start: 0.9525 (m-30) cc_final: 0.8958 (p0) REVERT: B 319 ASN cc_start: 0.9497 (m-40) cc_final: 0.9145 (t0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.6217 time to fit residues: 101.3479 Evaluate side-chains 116 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS B 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6973 Z= 0.216 Angle : 0.615 6.314 9788 Z= 0.378 Chirality : 0.039 0.141 1080 Planarity : 0.004 0.028 959 Dihedral : 24.285 86.154 1664 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.33), residues: 607 helix: 1.15 (0.26), residues: 383 sheet: -0.20 (0.84), residues: 29 loop : -0.66 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 224 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE B 163 TYR 0.008 0.001 TYR A 283 ARG 0.009 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.846 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.7977 (m-80) cc_final: 0.7682 (m-80) REVERT: A 43 LYS cc_start: 0.8956 (tttt) cc_final: 0.8496 (tmmt) REVERT: A 108 SER cc_start: 0.8307 (m) cc_final: 0.7820 (p) REVERT: A 130 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8463 (ptt90) REVERT: A 172 LEU cc_start: 0.8112 (mt) cc_final: 0.7836 (mt) REVERT: A 176 GLU cc_start: 0.9751 (tp30) cc_final: 0.9384 (tp30) REVERT: A 197 ILE cc_start: 0.9498 (tp) cc_final: 0.9275 (tp) REVERT: A 265 PHE cc_start: 0.9782 (m-80) cc_final: 0.9503 (m-80) REVERT: A 289 HIS cc_start: 0.9073 (m90) cc_final: 0.8857 (m-70) REVERT: B 42 TRP cc_start: 0.9670 (t60) cc_final: 0.9407 (t-100) REVERT: B 77 TYR cc_start: 0.9236 (t80) cc_final: 0.8954 (t80) REVERT: B 273 TYR cc_start: 0.8942 (m-80) cc_final: 0.8451 (m-80) REVERT: B 277 ASP cc_start: 0.9534 (m-30) cc_final: 0.8981 (p0) REVERT: B 283 TYR cc_start: 0.8573 (m-10) cc_final: 0.8145 (m-10) REVERT: B 289 HIS cc_start: 0.9171 (m90) cc_final: 0.8948 (m-70) REVERT: B 319 ASN cc_start: 0.9557 (m-40) cc_final: 0.9228 (t0) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.5513 time to fit residues: 86.1571 Evaluate side-chains 111 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6973 Z= 0.290 Angle : 0.654 5.866 9788 Z= 0.402 Chirality : 0.042 0.134 1080 Planarity : 0.006 0.088 959 Dihedral : 24.492 88.891 1664 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -0.04 (0.32), residues: 607 helix: 0.51 (0.25), residues: 383 sheet: -0.63 (0.82), residues: 29 loop : -0.84 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 224 HIS 0.004 0.001 HIS B 196 PHE 0.011 0.002 PHE B 163 TYR 0.010 0.002 TYR B 77 ARG 0.008 0.001 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.941 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5687 (mm-30) REVERT: A 130 ARG cc_start: 0.9111 (mtt180) cc_final: 0.8490 (ptt90) REVERT: A 172 LEU cc_start: 0.8294 (mt) cc_final: 0.7987 (mt) REVERT: A 176 GLU cc_start: 0.9775 (tp30) cc_final: 0.9368 (tp30) REVERT: A 289 HIS cc_start: 0.9186 (m90) cc_final: 0.8876 (m-70) REVERT: B 42 TRP cc_start: 0.9591 (t60) cc_final: 0.9143 (t-100) REVERT: B 74 TYR cc_start: 0.9212 (t80) cc_final: 0.8815 (t80) REVERT: B 77 TYR cc_start: 0.9174 (t80) cc_final: 0.8859 (t80) REVERT: B 273 TYR cc_start: 0.8918 (m-80) cc_final: 0.8491 (m-80) REVERT: B 277 ASP cc_start: 0.9348 (m-30) cc_final: 0.8698 (p0) REVERT: B 319 ASN cc_start: 0.9578 (m-40) cc_final: 0.9251 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5397 time to fit residues: 83.5214 Evaluate side-chains 106 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6973 Z= 0.272 Angle : 0.640 5.094 9788 Z= 0.392 Chirality : 0.040 0.130 1080 Planarity : 0.005 0.050 959 Dihedral : 24.715 87.234 1664 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.32), residues: 607 helix: 0.54 (0.25), residues: 383 sheet: -0.86 (0.80), residues: 29 loop : -0.85 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 224 HIS 0.007 0.002 HIS B 91 PHE 0.011 0.002 PHE A 137 TYR 0.010 0.002 TYR A 74 ARG 0.019 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.996 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.9557 (tm-30) cc_final: 0.9320 (tm-30) REVERT: A 120 ILE cc_start: 0.9059 (mm) cc_final: 0.8746 (tp) REVERT: A 129 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6124 (mm-30) REVERT: A 130 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8564 (pmt-80) REVERT: A 172 LEU cc_start: 0.8559 (mt) cc_final: 0.8268 (mt) REVERT: A 176 GLU cc_start: 0.9787 (tp30) cc_final: 0.9362 (tp30) REVERT: A 265 PHE cc_start: 0.9813 (m-80) cc_final: 0.9551 (m-80) REVERT: A 289 HIS cc_start: 0.9188 (m90) cc_final: 0.8898 (m-70) REVERT: B 74 TYR cc_start: 0.9225 (t80) cc_final: 0.8721 (t80) REVERT: B 77 TYR cc_start: 0.9250 (t80) cc_final: 0.8954 (t80) REVERT: B 256 LEU cc_start: 0.9522 (tp) cc_final: 0.9196 (mm) REVERT: B 273 TYR cc_start: 0.8803 (m-80) cc_final: 0.8385 (m-80) REVERT: B 277 ASP cc_start: 0.9395 (m-30) cc_final: 0.8753 (p0) REVERT: B 289 HIS cc_start: 0.9355 (m-70) cc_final: 0.9090 (m-70) REVERT: B 319 ASN cc_start: 0.9574 (m-40) cc_final: 0.9240 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5265 time to fit residues: 81.8140 Evaluate side-chains 108 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6973 Z= 0.202 Angle : 0.591 4.836 9788 Z= 0.360 Chirality : 0.038 0.129 1080 Planarity : 0.004 0.045 959 Dihedral : 24.545 87.605 1664 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.33), residues: 607 helix: 1.02 (0.26), residues: 383 sheet: -0.78 (0.79), residues: 29 loop : -0.71 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 224 HIS 0.003 0.001 HIS A 196 PHE 0.009 0.001 PHE B 37 TYR 0.012 0.001 TYR A 168 ARG 0.005 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.007 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ILE cc_start: 0.9058 (mm) cc_final: 0.8743 (tp) REVERT: A 129 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5898 (mm-30) REVERT: A 130 ARG cc_start: 0.9075 (mtt180) cc_final: 0.8447 (ppt170) REVERT: A 265 PHE cc_start: 0.9815 (m-80) cc_final: 0.9559 (m-80) REVERT: B 74 TYR cc_start: 0.9247 (t80) cc_final: 0.8763 (t80) REVERT: B 77 TYR cc_start: 0.9230 (t80) cc_final: 0.8931 (t80) REVERT: B 256 LEU cc_start: 0.9490 (tp) cc_final: 0.9148 (mm) REVERT: B 273 TYR cc_start: 0.8964 (m-80) cc_final: 0.8593 (m-80) REVERT: B 277 ASP cc_start: 0.9561 (m-30) cc_final: 0.9065 (p0) REVERT: B 283 TYR cc_start: 0.8639 (m-10) cc_final: 0.8186 (m-10) REVERT: B 289 HIS cc_start: 0.9367 (m-70) cc_final: 0.9151 (m-70) REVERT: B 319 ASN cc_start: 0.9524 (m-40) cc_final: 0.9151 (t0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.5259 time to fit residues: 79.6017 Evaluate side-chains 108 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6973 Z= 0.280 Angle : 0.636 4.509 9788 Z= 0.389 Chirality : 0.041 0.138 1080 Planarity : 0.005 0.049 959 Dihedral : 24.750 89.024 1664 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.33), residues: 607 helix: 0.59 (0.26), residues: 382 sheet: -1.21 (0.78), residues: 29 loop : -0.78 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 52 HIS 0.005 0.001 HIS B 91 PHE 0.012 0.002 PHE A 163 TYR 0.014 0.002 TYR A 168 ARG 0.004 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.928 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.9602 (tm-30) cc_final: 0.9362 (tm-30) REVERT: A 120 ILE cc_start: 0.9136 (mm) cc_final: 0.8668 (tp) REVERT: A 129 GLU cc_start: 0.6525 (mm-30) cc_final: 0.5972 (mm-30) REVERT: A 130 ARG cc_start: 0.9119 (mtt180) cc_final: 0.8443 (ppt170) REVERT: B 74 TYR cc_start: 0.9357 (t80) cc_final: 0.9024 (t80) REVERT: B 77 TYR cc_start: 0.9330 (t80) cc_final: 0.9034 (t80) REVERT: B 256 LEU cc_start: 0.9547 (tp) cc_final: 0.9227 (mm) REVERT: B 273 TYR cc_start: 0.8855 (m-80) cc_final: 0.8477 (m-80) REVERT: B 277 ASP cc_start: 0.9572 (m-30) cc_final: 0.9083 (p0) REVERT: B 283 TYR cc_start: 0.8689 (m-10) cc_final: 0.8273 (m-10) REVERT: B 289 HIS cc_start: 0.9309 (m-70) cc_final: 0.9049 (m-70) REVERT: B 319 ASN cc_start: 0.9556 (m-40) cc_final: 0.9241 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.5140 time to fit residues: 76.2206 Evaluate side-chains 102 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6973 Z= 0.312 Angle : 0.677 6.646 9788 Z= 0.410 Chirality : 0.043 0.139 1080 Planarity : 0.006 0.052 959 Dihedral : 24.941 89.162 1664 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.32), residues: 607 helix: 0.08 (0.25), residues: 385 sheet: -1.21 (0.78), residues: 28 loop : -0.82 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 52 HIS 0.007 0.002 HIS B 99 PHE 0.013 0.002 PHE A 163 TYR 0.015 0.002 TYR A 74 ARG 0.006 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.810 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ILE cc_start: 0.9140 (mm) cc_final: 0.8753 (tp) REVERT: A 129 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5710 (mm-30) REVERT: A 130 ARG cc_start: 0.9160 (mtt180) cc_final: 0.8458 (ppt170) REVERT: B 55 TRP cc_start: 0.8357 (t60) cc_final: 0.8059 (t60) REVERT: B 256 LEU cc_start: 0.9533 (tp) cc_final: 0.9204 (mm) REVERT: B 273 TYR cc_start: 0.8906 (m-80) cc_final: 0.8539 (m-80) REVERT: B 277 ASP cc_start: 0.9589 (m-30) cc_final: 0.9109 (p0) REVERT: B 289 HIS cc_start: 0.9288 (m-70) cc_final: 0.9081 (m90) REVERT: B 319 ASN cc_start: 0.9580 (m-40) cc_final: 0.9247 (t0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4697 time to fit residues: 67.7210 Evaluate side-chains 97 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6973 Z= 0.214 Angle : 0.616 5.760 9788 Z= 0.375 Chirality : 0.039 0.175 1080 Planarity : 0.005 0.046 959 Dihedral : 24.859 89.120 1664 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.00 (0.33), residues: 607 helix: 0.52 (0.26), residues: 383 sheet: -0.72 (0.80), residues: 28 loop : -0.76 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.003 TRP B 224 HIS 0.003 0.001 HIS A 196 PHE 0.010 0.001 PHE B 37 TYR 0.011 0.001 TYR A 168 ARG 0.004 0.001 ARG A 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1214 Ramachandran restraints generated. 607 Oldfield, 0 Emsley, 607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.986 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: 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: 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: 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: 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: symmetry clash REVERT: A 90 GLN cc_start: 0.9646 (tm-30) cc_final: 0.9411 (tm-30) REVERT: A 120 ILE cc_start: 0.9100 (mm) cc_final: 0.8685 (tp) REVERT: A 130 ARG cc_start: 0.9164 (mtt180) cc_final: 0.8487 (ppt170) REVERT: A 265 PHE cc_start: 0.9816 (m-80) cc_final: 0.9599 (m-80) REVERT: B 256 LEU cc_start: 0.9493 (tp) cc_final: 0.9147 (mm) REVERT: B 273 TYR cc_start: 0.8913 (m-80) cc_final: 0.8541 (m-80) REVERT: B 277 ASP cc_start: 0.9596 (m-30) cc_final: 0.9127 (p0) REVERT: B 283 TYR cc_start: 0.8750 (m-10) cc_final: 0.8411 (m-10) REVERT: B 289 HIS cc_start: 0.9244 (m-70) cc_final: 0.9040 (m-70) REVERT: B 319 ASN cc_start: 0.9542 (m-40) cc_final: 0.9135 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.4879 time to fit residues: 70.5998 Evaluate side-chains 103 residues out of total 511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052773 restraints weight = 190620.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.055131 restraints weight = 102278.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056742 restraints weight = 65881.655| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6973 Z= 0.195 Angle : 0.601 5.735 9788 Z= 0.363 Chirality : 0.038 0.145 1080 Planarity : 0.004 0.043 959 Dihedral : 24.766 89.812 1664 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: 0.35 (0.33), residues: 607 helix: 0.79 (0.26), residues: 385 sheet: -0.30 (0.85), residues: 28 loop : -0.67 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 224 HIS 0.005 0.001 HIS B 91 PHE 0.009 0.001 PHE B 37 TYR 0.009 0.001 TYR A 168 ARG 0.005 0.000 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.86 seconds wall clock time: 64 minutes 30.74 seconds (3870.74 seconds total)