Starting phenix.real_space_refine on Wed Jul 30 14:18:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rhz_24472/07_2025/7rhz_24472_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rhz_24472/07_2025/7rhz_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/cci-nas-00/data/ceres_data/7rhz_24472/07_2025/7rhz_24472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rhz_24472/07_2025/7rhz_24472.map" model { file = "/net/cci-nas-00/data/ceres_data/7rhz_24472/07_2025/7rhz_24472_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rhz_24472/07_2025/7rhz_24472_neut.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.98, per 1000 atoms: 0.56 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 - 3.00 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: 3.19 Conformation dependent library (CDL) restraints added in 805.8 milliseconds 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: 5.65 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: 4.57 Time building geometry restraints manager: 3.81 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: 0.00 - 2.37: 21070 2.37 - 4.74: 1302 4.74 - 7.11: 598 7.11 - 9.47: 122 9.47 - 11.84: 69 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 2.450 nonbonded pdb="HH21 ARG B 106 " pdb=" OP1 DA C 20 " model vdw 1.467 2.450 nonbonded pdb=" H ARG B 181 " pdb=" OD2 ASP B 184 " model vdw 1.492 2.450 nonbonded pdb=" O LEU B 215 " pdb=" HG1 THR B 218 " model vdw 1.494 2.450 nonbonded pdb=" H TYR A 283 " pdb=" OP1 DC D 26 " model vdw 1.498 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 0.370 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.980 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- 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= 1.063 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 Details of bonding type rmsd hydrogen bonds : bond 0.12436 ( 407) hydrogen bonds : angle 5.70280 ( 1102) covalent geometry : bond 0.01962 ( 6973) covalent geometry : angle 1.62057 ( 9788) *********************** 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 to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.826 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: 0.6742 time to fit residues: 143.9820 Evaluate side-chains 135 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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: 0.9980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 94 GLN A 124 ASN B 89 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047666 restraints weight = 126638.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.050191 restraints weight = 65888.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.052023 restraints weight = 41758.772| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6973 Z= 0.197 Angle : 0.669 5.413 9788 Z= 0.405 Chirality : 0.041 0.140 1080 Planarity : 0.005 0.041 959 Dihedral : 24.540 86.126 1664 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.30 (0.33), residues: 607 helix: 0.75 (0.26), residues: 383 sheet: 0.01 (0.86), residues: 33 loop : -0.73 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 52 HIS 0.004 0.002 HIS B 196 PHE 0.009 0.001 PHE B 163 TYR 0.008 0.002 TYR B 324 ARG 0.005 0.001 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.05930 ( 407) hydrogen bonds : angle 4.69228 ( 1102) covalent geometry : bond 0.00400 ( 6973) covalent geometry : angle 0.66901 ( 9788) *********************** 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 148 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.809 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: A 43 LYS cc_start: 0.8823 (tttt) cc_final: 0.8500 (tmmt) REVERT: A 108 SER cc_start: 0.9209 (m) cc_final: 0.9001 (m) REVERT: A 109 ASP cc_start: 0.9104 (m-30) cc_final: 0.8830 (p0) REVERT: A 130 ARG cc_start: 0.9013 (mtt180) cc_final: 0.8652 (pmt-80) REVERT: A 265 PHE cc_start: 0.9676 (m-80) cc_final: 0.9308 (m-80) REVERT: A 289 HIS cc_start: 0.9051 (m90) cc_final: 0.8789 (m-70) REVERT: A 298 ASP cc_start: 0.9518 (t0) cc_final: 0.9040 (t0) REVERT: B 77 TYR cc_start: 0.9107 (t80) cc_final: 0.8739 (t80) REVERT: B 89 GLN cc_start: 0.9792 (mt0) cc_final: 0.9559 (mt0) REVERT: B 213 LEU cc_start: 0.8095 (tp) cc_final: 0.7709 (tp) REVERT: B 273 TYR cc_start: 0.8965 (m-80) cc_final: 0.8398 (m-80) REVERT: B 277 ASP cc_start: 0.9566 (m-30) cc_final: 0.9054 (p0) REVERT: B 319 ASN cc_start: 0.9548 (m-40) cc_final: 0.9263 (t0) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.6707 time to fit residues: 118.4484 Evaluate side-chains 126 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 245 ASN ** A 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.059821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.044632 restraints weight = 137729.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.046901 restraints weight = 73523.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.048524 restraints weight = 47771.227| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6973 Z= 0.285 Angle : 0.703 6.410 9788 Z= 0.430 Chirality : 0.044 0.145 1080 Planarity : 0.005 0.044 959 Dihedral : 24.629 83.490 1664 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -0.26 (0.32), residues: 607 helix: 0.35 (0.26), residues: 385 sheet: -0.51 (0.79), residues: 29 loop : -1.00 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 42 HIS 0.004 0.001 HIS A 289 PHE 0.016 0.002 PHE B 163 TYR 0.013 0.002 TYR A 283 ARG 0.007 0.001 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.07560 ( 407) hydrogen bonds : angle 5.02823 ( 1102) covalent geometry : bond 0.00573 ( 6973) covalent geometry : angle 0.70320 ( 9788) *********************** 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 136 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.955 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 43 LYS cc_start: 0.9128 (tttt) cc_final: 0.8713 (tmmt) REVERT: A 91 HIS cc_start: 0.9776 (m90) cc_final: 0.9455 (m90) REVERT: A 94 GLN cc_start: 0.9613 (tm-30) cc_final: 0.9399 (tm-30) REVERT: A 129 GLU cc_start: 0.6660 (mp0) cc_final: 0.6327 (mp0) REVERT: A 130 ARG cc_start: 0.8854 (mtt180) cc_final: 0.8345 (ptt90) REVERT: A 173 ARG cc_start: 0.8894 (ttt180) cc_final: 0.8613 (ttt180) REVERT: A 265 PHE cc_start: 0.9679 (m-80) cc_final: 0.9333 (m-80) REVERT: A 289 HIS cc_start: 0.9090 (m90) cc_final: 0.8827 (m-70) REVERT: B 97 MET cc_start: 0.8696 (mtt) cc_final: 0.8260 (mmp) REVERT: B 273 TYR cc_start: 0.9017 (m-80) cc_final: 0.8527 (m-80) REVERT: B 277 ASP cc_start: 0.9484 (m-30) cc_final: 0.8844 (p0) REVERT: B 319 ASN cc_start: 0.9594 (m-40) cc_final: 0.9323 (t0) REVERT: B 327 ASN cc_start: 0.8762 (t0) cc_final: 0.8537 (t0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.7941 time to fit residues: 131.7024 Evaluate side-chains 113 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.046609 restraints weight = 138972.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049028 restraints weight = 72533.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.050760 restraints weight = 46323.397| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6973 Z= 0.187 Angle : 0.624 5.533 9788 Z= 0.384 Chirality : 0.039 0.132 1080 Planarity : 0.004 0.048 959 Dihedral : 24.511 86.271 1664 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: 0.37 (0.33), residues: 607 helix: 0.91 (0.26), residues: 384 sheet: -0.33 (0.83), residues: 29 loop : -0.88 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 224 HIS 0.004 0.001 HIS A 91 PHE 0.017 0.002 PHE B 163 TYR 0.010 0.001 TYR A 283 ARG 0.005 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.05306 ( 407) hydrogen bonds : angle 4.64388 ( 1102) covalent geometry : bond 0.00379 ( 6973) covalent geometry : angle 0.62351 ( 9788) *********************** 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 136 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.812 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 37 PHE cc_start: 0.8291 (m-80) cc_final: 0.7955 (m-80) REVERT: A 43 LYS cc_start: 0.9056 (tttt) cc_final: 0.8853 (tttt) REVERT: A 108 SER cc_start: 0.8704 (m) cc_final: 0.8292 (p) REVERT: A 130 ARG cc_start: 0.8910 (mtt180) cc_final: 0.8533 (pmt-80) REVERT: A 256 LEU cc_start: 0.8958 (mt) cc_final: 0.8699 (mt) REVERT: A 265 PHE cc_start: 0.9747 (m-80) cc_final: 0.9450 (m-80) REVERT: A 289 HIS cc_start: 0.9059 (m90) cc_final: 0.8805 (m-70) REVERT: B 74 TYR cc_start: 0.9324 (t80) cc_final: 0.9079 (t80) REVERT: B 97 MET cc_start: 0.8888 (mtt) cc_final: 0.8520 (mmt) REVERT: B 273 TYR cc_start: 0.8993 (m-80) cc_final: 0.8534 (m-80) REVERT: B 277 ASP cc_start: 0.9385 (m-30) cc_final: 0.8736 (p0) REVERT: B 319 ASN cc_start: 0.9550 (m-40) cc_final: 0.9214 (t0) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.6404 time to fit residues: 104.8715 Evaluate side-chains 112 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.063053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.047775 restraints weight = 135023.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050289 restraints weight = 69439.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.052075 restraints weight = 43924.453| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5435 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= 0.167 Angle : 0.604 5.289 9788 Z= 0.369 Chirality : 0.038 0.146 1080 Planarity : 0.004 0.048 959 Dihedral : 24.447 89.988 1664 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: 0.62 (0.33), residues: 607 helix: 1.15 (0.26), residues: 383 sheet: -0.20 (0.86), residues: 28 loop : -0.90 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 224 HIS 0.002 0.001 HIS A 91 PHE 0.015 0.001 PHE B 163 TYR 0.010 0.001 TYR A 283 ARG 0.003 0.000 ARG A 154 Details of bonding type rmsd hydrogen bonds : bond 0.05002 ( 407) hydrogen bonds : angle 4.49642 ( 1102) covalent geometry : bond 0.00342 ( 6973) covalent geometry : angle 0.60439 ( 9788) *********************** 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 135 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.841 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: A 43 LYS cc_start: 0.8957 (tttt) cc_final: 0.8685 (ptmt) REVERT: A 108 SER cc_start: 0.8192 (m) cc_final: 0.7777 (p) REVERT: A 130 ARG cc_start: 0.8990 (mtt180) cc_final: 0.8368 (ptt90) REVERT: A 265 PHE cc_start: 0.9732 (m-80) cc_final: 0.9147 (m-80) REVERT: A 289 HIS cc_start: 0.9059 (m90) cc_final: 0.8635 (m-70) REVERT: B 273 TYR cc_start: 0.9020 (m-80) cc_final: 0.8580 (m-80) REVERT: B 277 ASP cc_start: 0.9630 (m-30) cc_final: 0.9127 (p0) REVERT: B 283 TYR cc_start: 0.8683 (m-10) cc_final: 0.8248 (m-10) REVERT: B 289 HIS cc_start: 0.9406 (m-70) cc_final: 0.9188 (m-70) REVERT: B 319 ASN cc_start: 0.9557 (m-40) cc_final: 0.9203 (t0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5851 time to fit residues: 96.3624 Evaluate side-chains 111 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 59 ASN B 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053796 restraints weight = 188650.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.056247 restraints weight = 104754.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057950 restraints weight = 68634.972| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6973 Z= 0.195 Angle : 0.609 5.253 9788 Z= 0.371 Chirality : 0.039 0.122 1080 Planarity : 0.004 0.048 959 Dihedral : 24.557 85.784 1664 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: 1.10 (0.26), residues: 386 sheet: -0.51 (0.84), residues: 29 loop : -0.86 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 55 HIS 0.003 0.001 HIS B 196 PHE 0.012 0.001 PHE B 163 TYR 0.016 0.002 TYR A 168 ARG 0.012 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.05465 ( 407) hydrogen bonds : angle 4.44897 ( 1102) covalent geometry : bond 0.00394 ( 6973) covalent geometry : angle 0.60879 ( 9788) *********************** 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 to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.817 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 106 ARG cc_start: 0.9227 (ttt180) cc_final: 0.9012 (tmt170) REVERT: A 108 SER cc_start: 0.8307 (m) cc_final: 0.7936 (p) REVERT: A 130 ARG cc_start: 0.8828 (mtt180) cc_final: 0.8412 (ptt90) REVERT: A 265 PHE cc_start: 0.9572 (m-80) cc_final: 0.9109 (m-80) REVERT: B 64 PHE cc_start: 0.8721 (t80) cc_final: 0.8423 (t80) REVERT: B 74 TYR cc_start: 0.9411 (t80) cc_final: 0.9191 (t80) REVERT: B 273 TYR cc_start: 0.9022 (m-80) cc_final: 0.8622 (m-80) REVERT: B 277 ASP cc_start: 0.9577 (m-30) cc_final: 0.9063 (p0) REVERT: B 289 HIS cc_start: 0.9318 (m-70) cc_final: 0.9073 (m-70) REVERT: B 319 ASN cc_start: 0.9522 (m-40) cc_final: 0.9133 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.6070 time to fit residues: 92.4985 Evaluate side-chains 106 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.063301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047549 restraints weight = 141621.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050111 restraints weight = 75179.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051908 restraints weight = 48050.182| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6973 Z= 0.168 Angle : 0.585 4.461 9788 Z= 0.357 Chirality : 0.038 0.150 1080 Planarity : 0.004 0.050 959 Dihedral : 24.524 86.105 1664 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 0.70 (0.33), residues: 607 helix: 1.23 (0.26), residues: 386 sheet: -0.82 (0.75), residues: 29 loop : -0.81 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 55 HIS 0.003 0.001 HIS B 196 PHE 0.009 0.001 PHE B 163 TYR 0.014 0.001 TYR A 168 ARG 0.005 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 407) hydrogen bonds : angle 4.34682 ( 1102) covalent geometry : bond 0.00340 ( 6973) covalent geometry : angle 0.58523 ( 9788) *********************** 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 126 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.830 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: A 106 ARG cc_start: 0.9209 (ttt180) cc_final: 0.9009 (tmt170) REVERT: A 108 SER cc_start: 0.8247 (m) cc_final: 0.7800 (p) REVERT: A 130 ARG cc_start: 0.8797 (mtt180) cc_final: 0.8393 (ptt90) REVERT: A 265 PHE cc_start: 0.9482 (m-80) cc_final: 0.8981 (m-80) REVERT: A 289 HIS cc_start: 0.8938 (m-70) cc_final: 0.8704 (m-70) REVERT: B 74 TYR cc_start: 0.9383 (t80) cc_final: 0.8815 (t80) REVERT: B 77 TYR cc_start: 0.9655 (t80) cc_final: 0.9210 (t80) REVERT: B 256 LEU cc_start: 0.9479 (tp) cc_final: 0.9034 (mm) REVERT: B 273 TYR cc_start: 0.9083 (m-80) cc_final: 0.8684 (m-80) REVERT: B 277 ASP cc_start: 0.9548 (m-30) cc_final: 0.9066 (p0) REVERT: B 319 ASN cc_start: 0.9550 (m-40) cc_final: 0.9110 (t0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.5754 time to fit residues: 88.5302 Evaluate side-chains 110 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.062954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.047524 restraints weight = 148142.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050027 restraints weight = 78389.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051796 restraints weight = 50049.113| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6973 Z= 0.163 Angle : 0.575 4.339 9788 Z= 0.351 Chirality : 0.037 0.139 1080 Planarity : 0.004 0.042 959 Dihedral : 24.454 86.874 1664 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.73 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: 0.89 (0.33), residues: 607 helix: 1.40 (0.26), residues: 386 sheet: -0.91 (0.69), residues: 29 loop : -0.76 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 55 HIS 0.003 0.001 HIS A 196 PHE 0.009 0.001 PHE B 163 TYR 0.012 0.001 TYR A 168 ARG 0.004 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 407) hydrogen bonds : angle 4.30371 ( 1102) covalent geometry : bond 0.00331 ( 6973) covalent geometry : angle 0.57468 ( 9788) *********************** 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 125 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.797 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 108 SER cc_start: 0.7906 (m) cc_final: 0.7577 (p) REVERT: A 130 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8405 (ppt170) REVERT: A 265 PHE cc_start: 0.9606 (m-80) cc_final: 0.9158 (m-80) REVERT: B 64 PHE cc_start: 0.8751 (t80) cc_final: 0.8441 (t80) REVERT: B 74 TYR cc_start: 0.9410 (t80) cc_final: 0.8866 (t80) REVERT: B 77 TYR cc_start: 0.9642 (t80) cc_final: 0.9204 (t80) REVERT: B 256 LEU cc_start: 0.9570 (tp) cc_final: 0.9166 (mm) REVERT: B 273 TYR cc_start: 0.9066 (m-80) cc_final: 0.8658 (m-80) REVERT: B 277 ASP cc_start: 0.9601 (m-30) cc_final: 0.9107 (p0) REVERT: B 319 ASN cc_start: 0.9541 (m-40) cc_final: 0.9123 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.5459 time to fit residues: 83.2987 Evaluate side-chains 107 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.068243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.054397 restraints weight = 185913.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056858 restraints weight = 101045.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.058566 restraints weight = 65521.979| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6973 Z= 0.167 Angle : 0.587 6.030 9788 Z= 0.356 Chirality : 0.038 0.140 1080 Planarity : 0.007 0.193 959 Dihedral : 24.438 87.402 1664 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.13 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: 0.93 (0.33), residues: 607 helix: 1.41 (0.26), residues: 387 sheet: -0.96 (0.69), residues: 29 loop : -0.70 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 315 HIS 0.006 0.001 HIS B 91 PHE 0.009 0.001 PHE B 163 TYR 0.011 0.001 TYR A 168 ARG 0.028 0.001 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 407) hydrogen bonds : angle 4.24346 ( 1102) covalent geometry : bond 0.00338 ( 6973) covalent geometry : angle 0.58677 ( 9788) *********************** 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 122 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.958 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: A 108 SER cc_start: 0.7936 (m) cc_final: 0.7590 (p) REVERT: A 130 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8431 (ppt170) REVERT: A 173 ARG cc_start: 0.8972 (ttt180) cc_final: 0.8687 (ttt180) REVERT: A 265 PHE cc_start: 0.9610 (m-80) cc_final: 0.9151 (m-80) REVERT: B 64 PHE cc_start: 0.8755 (t80) cc_final: 0.8451 (t80) REVERT: B 74 TYR cc_start: 0.9326 (t80) cc_final: 0.8585 (t80) REVERT: B 77 TYR cc_start: 0.9650 (t80) cc_final: 0.9232 (t80) REVERT: B 176 GLU cc_start: 0.9432 (mp0) cc_final: 0.9186 (mp0) REVERT: B 256 LEU cc_start: 0.9561 (tp) cc_final: 0.9121 (mm) REVERT: B 273 TYR cc_start: 0.9058 (m-80) cc_final: 0.8661 (m-80) REVERT: B 277 ASP cc_start: 0.9603 (m-30) cc_final: 0.9114 (p0) REVERT: B 319 ASN cc_start: 0.9539 (m-40) cc_final: 0.9121 (t0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.5530 time to fit residues: 82.7894 Evaluate side-chains 109 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.067730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054122 restraints weight = 187593.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056549 restraints weight = 101507.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.058248 restraints weight = 65856.234| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6973 Z= 0.176 Angle : 0.588 5.438 9788 Z= 0.359 Chirality : 0.038 0.166 1080 Planarity : 0.006 0.151 959 Dihedral : 24.447 88.031 1664 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.88 (0.34), residues: 607 helix: 1.39 (0.26), residues: 387 sheet: -1.05 (0.72), residues: 29 loop : -0.75 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP B 224 HIS 0.004 0.001 HIS A 196 PHE 0.009 0.001 PHE B 64 TYR 0.011 0.001 TYR A 168 ARG 0.026 0.001 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 407) hydrogen bonds : angle 4.34398 ( 1102) covalent geometry : bond 0.00358 ( 6973) covalent geometry : angle 0.58757 ( 9788) ********************** 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 121 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 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: symmetry clash revert: symmetry clash REVERT: A 108 SER cc_start: 0.7709 (m) cc_final: 0.7393 (p) REVERT: A 130 ARG cc_start: 0.8880 (mtt180) cc_final: 0.8438 (ppt170) REVERT: A 265 PHE cc_start: 0.9610 (m-80) cc_final: 0.9161 (m-80) REVERT: B 74 TYR cc_start: 0.9390 (t80) cc_final: 0.8795 (t80) REVERT: B 77 TYR cc_start: 0.9663 (t80) cc_final: 0.9254 (t80) REVERT: B 92 LEU cc_start: 0.9480 (mm) cc_final: 0.9185 (mt) REVERT: B 176 GLU cc_start: 0.9440 (mp0) cc_final: 0.9202 (mp0) REVERT: B 256 LEU cc_start: 0.9560 (tp) cc_final: 0.9129 (mm) REVERT: B 273 TYR cc_start: 0.8948 (m-80) cc_final: 0.8513 (m-80) REVERT: B 277 ASP cc_start: 0.9607 (m-30) cc_final: 0.9121 (p0) REVERT: B 319 ASN cc_start: 0.9543 (m-40) cc_final: 0.9122 (t0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.5546 time to fit residues: 81.6353 Evaluate side-chains 107 residues out of total 511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.062831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.047410 restraints weight = 143610.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049934 restraints weight = 75183.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051718 restraints weight = 47670.559| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6973 Z= 0.160 Angle : 0.574 5.243 9788 Z= 0.350 Chirality : 0.037 0.140 1080 Planarity : 0.006 0.128 959 Dihedral : 24.384 88.699 1664 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: 1.05 (0.34), residues: 607 helix: 1.54 (0.27), residues: 387 sheet: -0.92 (0.77), residues: 29 loop : -0.73 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 224 HIS 0.007 0.001 HIS B 91 PHE 0.009 0.001 PHE B 163 TYR 0.009 0.001 TYR A 168 ARG 0.023 0.001 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 407) hydrogen bonds : angle 4.24738 ( 1102) covalent geometry : bond 0.00328 ( 6973) covalent geometry : angle 0.57364 ( 9788) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5309.76 seconds wall clock time: 92 minutes 10.49 seconds (5530.49 seconds total)