Starting phenix.real_space_refine on Thu Sep 10 22:40:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6x_39807/09_2026/8z6x_39807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6x_39807/09_2026/8z6x_39807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z6x_39807/09_2026/8z6x_39807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6x_39807/09_2026/8z6x_39807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z6x_39807/09_2026/8z6x_39807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6x_39807/09_2026/8z6x_39807.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.031 sd= 0.144 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2991 2.51 5 N 781 2.21 5 O 909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4704 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1553 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "C" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1502 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 15, 'TRANS': 187} Chain: "B" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 12, 'TRANS': 206} Time building chain proxies: 1.20, per 1000 atoms: 0.26 Number of scatterers: 4704 At special positions: 0 Unit cell: (97.58, 77.35, 115.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 909 8.00 N 781 7.00 C 2991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 211 " distance=2.03 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: 0.37 Conformation dependent library (CDL) restraints added in 184.5 milliseconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 12 sheets defined 10.7% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.993A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.795A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.809A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.681A pdb=" N GLU C 99 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'B' and resid 69 through 72 removed outlier: 4.124A pdb=" N GLN B 72 " --> pdb=" O PRO B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.727A pdb=" N THR B 99 " --> pdb=" O ALA B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 4.033A pdb=" N LEU B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.961A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.589A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.559A pdb=" N GLY C 13 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN C 43 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 52 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 13 removed outlier: 3.559A pdb=" N GLY C 13 " --> pdb=" O THR C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 24 Processing sheet with id=AA6, first strand: chain 'C' and resid 135 through 139 removed outlier: 3.541A pdb=" N VAL C 154 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 151 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR C 193 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.256A pdb=" N TRP C 169 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.347A pdb=" N ILE B 39 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 55 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TRP B 41 " --> pdb=" O MET B 53 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AB2, first strand: chain 'B' and resid 137 through 139 removed outlier: 5.111A pdb=" N ALA B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 199 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY B 154 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL B 197 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU B 156 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER B 195 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS B 158 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 193 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER B 192 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA B 183 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 194 " --> pdb=" O PHE B 181 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.583A pdb=" N THR B 166 " --> pdb=" O ASN B 214 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1036 1.33 - 1.45: 1157 1.45 - 1.57: 2612 1.57 - 1.69: 1 1.69 - 1.81: 29 Bond restraints: 4835 Sorted by residual: bond pdb=" CA VAL C 30 " pdb=" CB VAL C 30 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" CA TYR C 38 " pdb=" C TYR C 38 " ideal model delta sigma weight residual 1.523 1.493 0.031 1.34e-02 5.57e+03 5.20e+00 bond pdb=" C LEU B 153 " pdb=" O LEU B 153 " ideal model delta sigma weight residual 1.235 1.209 0.025 1.18e-02 7.18e+03 4.66e+00 bond pdb=" C ALA B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.332 1.356 -0.025 1.32e-02 5.74e+03 3.51e+00 bond pdb=" N VAL C 30 " pdb=" CA VAL C 30 " ideal model delta sigma weight residual 1.461 1.481 -0.021 1.19e-02 7.06e+03 3.02e+00 ... (remaining 4830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 6531 2.62 - 5.24: 56 5.24 - 7.86: 2 7.86 - 10.48: 0 10.48 - 13.10: 1 Bond angle restraints: 6590 Sorted by residual: angle pdb=" N TYR C 38 " pdb=" CA TYR C 38 " pdb=" C TYR C 38 " ideal model delta sigma weight residual 110.80 97.70 13.10 2.13e+00 2.20e-01 3.78e+01 angle pdb=" N VAL C 30 " pdb=" CA VAL C 30 " pdb=" C VAL C 30 " ideal model delta sigma weight residual 110.62 114.10 -3.48 1.02e+00 9.61e-01 1.16e+01 angle pdb=" C VAL C 30 " pdb=" CA VAL C 30 " pdb=" CB VAL C 30 " ideal model delta sigma weight residual 112.14 107.59 4.55 1.35e+00 5.49e-01 1.14e+01 angle pdb=" C ALA B 140 " pdb=" N PRO B 141 " pdb=" CA PRO B 141 " ideal model delta sigma weight residual 119.76 116.93 2.83 1.00e+00 1.00e+00 8.01e+00 angle pdb=" N VAL C 30 " pdb=" CA VAL C 30 " pdb=" CB VAL C 30 " ideal model delta sigma weight residual 110.54 114.21 -3.67 1.36e+00 5.41e-01 7.27e+00 ... (remaining 6585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2763 17.69 - 35.37: 78 35.37 - 53.06: 21 53.06 - 70.75: 3 70.75 - 88.43: 1 Dihedral angle restraints: 2866 sinusoidal: 1083 harmonic: 1783 Sorted by residual: dihedral pdb=" CA GLU C 56 " pdb=" C GLU C 56 " pdb=" N VAL C 57 " pdb=" CA VAL C 57 " ideal model delta harmonic sigma weight residual -180.00 -153.19 -26.81 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" C THR B 150 " pdb=" N THR B 150 " pdb=" CA THR B 150 " pdb=" CB THR B 150 " ideal model delta harmonic sigma weight residual -122.00 -130.45 8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" N THR B 150 " pdb=" C THR B 150 " pdb=" CA THR B 150 " pdb=" CB THR B 150 " ideal model delta harmonic sigma weight residual 123.40 131.42 -8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 2863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 628 0.065 - 0.129: 84 0.129 - 0.194: 5 0.194 - 0.258: 1 0.258 - 0.323: 1 Chirality restraints: 719 Sorted by residual: chirality pdb=" CA THR B 150 " pdb=" N THR B 150 " pdb=" C THR B 150 " pdb=" CB THR B 150 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB VAL C 30 " pdb=" CA VAL C 30 " pdb=" CG1 VAL C 30 " pdb=" CG2 VAL C 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CA TYR C 38 " pdb=" N TYR C 38 " pdb=" C TYR C 38 " pdb=" CB TYR C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 716 not shown) Planarity restraints: 843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 29 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASP C 29 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP C 29 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL C 30 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 184 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO C 185 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 337 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.015 5.00e-02 4.00e+02 ... (remaining 840 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 290 2.73 - 3.27: 4607 3.27 - 3.81: 7188 3.81 - 4.36: 9060 4.36 - 4.90: 15812 Nonbonded interactions: 36957 Sorted by model distance: nonbonded pdb=" O ASP C 172 " pdb=" OG SER C 173 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR C 42 " pdb=" O LEU B 114 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" N ASN A 334 " model vdw 2.272 3.120 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.283 3.040 nonbonded pdb=" O GLU C 56 " pdb=" N LYS C 66 " model vdw 2.311 3.120 ... (remaining 36952 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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 : 0.003 0.033 4843 Z= 0.153 Angle : 0.544 13.099 6606 Z= 0.293 Chirality : 0.046 0.323 719 Planarity : 0.003 0.033 843 Dihedral : 9.206 88.434 1712 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.19 % Favored : 92.65 % Rotamer: Outliers : 3.07 % Allowed : 5.57 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.31), residues: 612 helix: -4.14 (0.43), residues: 46 sheet: -0.68 (0.34), residues: 196 loop : -2.05 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 75 TYR 0.010 0.001 TYR C 38 PHE 0.004 0.001 PHE C 139 TRP 0.007 0.001 TRP B 52 HIS 0.001 0.000 HIS C 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 ( 4835) covalent geometry : angle 0.54406 / 0.29 ( 6590) SS BOND : bond 0.00122 / 0.06 ( 8) SS BOND : angle 0.51190 / 0.31 ( 16) hydrogen bonds : bond 0.26525 / 17.20 ( 145) hydrogen bonds : angle 9.28888 / 6.45 ( 357) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: C 150 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8495 (mtpp) REVERT: C 215 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6763 (mp10) REVERT: B 2 MET cc_start: 0.8525 (mtm) cc_final: 0.8235 (mtm) REVERT: B 212 ASN cc_start: 0.7602 (m110) cc_final: 0.7295 (m-40) outliers start: 16 outliers final: 5 residues processed: 95 average time/residue: 0.5543 time to fit residues: 54.7897 Evaluate side-chains 59 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 144 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 56 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.3837 > 50:) chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN C 95 GLN C 190 ASN C 191 ASN B 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.045503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.039705 restraints weight = 17870.912| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 2.38 r_work: 0.2518 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2432 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4843 Z= 0.191 Angle : 0.681 8.309 6606 Z= 0.349 Chirality : 0.048 0.151 719 Planarity : 0.005 0.039 843 Dihedral : 7.958 82.979 685 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.84 % Allowed : 12.09 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.33), residues: 612 helix: -2.31 (0.74), residues: 28 sheet: -0.04 (0.35), residues: 208 loop : -1.40 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 115 TYR 0.012 0.002 TYR B 88 PHE 0.009 0.001 PHE B 71 TRP 0.018 0.002 TRP B 52 HIS 0.005 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 ( 4835) covalent geometry : angle 0.68011 / 0.35 ( 6590) SS BOND : bond 0.00603 / 0.45 ( 8) SS BOND : angle 0.97735 / 0.53 ( 16) hydrogen bonds : bond 0.03904 / 2.55 ( 145) hydrogen bonds : angle 6.78934 / 4.76 ( 357) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.194 Fit side-chains REVERT: C 36 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8107 (t80) REVERT: C 150 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8875 (mtmm) outliers start: 20 outliers final: 9 residues processed: 65 average time/residue: 0.5034 time to fit residues: 34.2099 Evaluate side-chains 57 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN C 45 HIS C 188 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.042009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.036567 restraints weight = 18020.009| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.27 r_work: 0.2417 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2333 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 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 : 0.006 0.037 4843 Z= 0.267 Angle : 0.744 8.542 6606 Z= 0.382 Chirality : 0.049 0.151 719 Planarity : 0.005 0.040 843 Dihedral : 6.695 56.783 677 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.22 % Allowed : 13.44 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.33), residues: 612 helix: -2.48 (0.70), residues: 36 sheet: 0.12 (0.35), residues: 211 loop : -1.20 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 115 TYR 0.020 0.002 TYR C 38 PHE 0.011 0.002 PHE B 71 TRP 0.018 0.002 TRP B 52 HIS 0.006 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 ( 4835) covalent geometry : angle 0.74016 / 0.38 ( 6590) SS BOND : bond 0.00434 / 0.33 ( 8) SS BOND : angle 1.67947 / 0.95 ( 16) hydrogen bonds : bond 0.04362 / 2.83 ( 145) hydrogen bonds : angle 6.71065 / 4.69 ( 357) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.182 Fit side-chains REVERT: C 36 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8356 (t80) REVERT: C 150 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8958 (mtmm) REVERT: C 215 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7210 (mp10) REVERT: B 110 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9237 (pp) outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.4643 time to fit residues: 33.1528 Evaluate side-chains 60 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 188 GLN ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.042424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.037123 restraints weight = 17977.829| |-----------------------------------------------------------------------------| r_work (start): 0.2512 rms_B_bonded: 2.24 r_work: 0.2440 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2357 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9192 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4843 Z= 0.184 Angle : 0.687 9.473 6606 Z= 0.352 Chirality : 0.048 0.292 719 Planarity : 0.005 0.040 843 Dihedral : 6.518 56.509 677 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.41 % Allowed : 13.63 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.33), residues: 612 helix: -2.14 (0.79), residues: 29 sheet: 0.24 (0.35), residues: 215 loop : -1.21 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 115 TYR 0.009 0.002 TYR A 489 PHE 0.008 0.001 PHE B 71 TRP 0.014 0.001 TRP B 52 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 4835) covalent geometry : angle 0.67644 / 0.35 ( 6590) SS BOND : bond 0.00364 / 0.22 ( 8) SS BOND : angle 2.48694 / 1.17 ( 16) hydrogen bonds : bond 0.03710 / 2.39 ( 145) hydrogen bonds : angle 6.43367 / 4.51 ( 357) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 48 time to evaluate : 0.185 Fit side-chains REVERT: C 36 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8319 (t80) REVERT: C 150 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9092 (mtmm) REVERT: C 170 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8242 (ptpp) REVERT: C 215 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: B 110 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9206 (pp) outliers start: 23 outliers final: 10 residues processed: 68 average time/residue: 0.4334 time to fit residues: 31.0217 Evaluate side-chains 57 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 0.0010 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.041655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.036476 restraints weight = 18115.326| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 2.22 r_work: 0.2418 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2336 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4843 Z= 0.215 Angle : 0.706 8.654 6606 Z= 0.360 Chirality : 0.048 0.255 719 Planarity : 0.005 0.041 843 Dihedral : 6.612 56.321 677 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.37 % Allowed : 13.24 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.33), residues: 612 helix: -2.18 (0.77), residues: 29 sheet: 0.37 (0.35), residues: 211 loop : -1.18 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 115 TYR 0.011 0.002 TYR C 161 PHE 0.008 0.001 PHE C 139 TRP 0.013 0.001 TRP B 52 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 4835) covalent geometry : angle 0.69842 / 0.36 ( 6590) SS BOND : bond 0.00378 / 0.24 ( 8) SS BOND : angle 2.20374 / 1.12 ( 16) hydrogen bonds : bond 0.03797 / 2.46 ( 145) hydrogen bonds : angle 6.42747 / 4.50 ( 357) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 44 time to evaluate : 0.187 Fit side-chains REVERT: C 36 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8319 (t80) REVERT: C 150 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9054 (mtmm) REVERT: C 170 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8285 (ptpp) REVERT: C 215 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: B 110 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9209 (pp) outliers start: 28 outliers final: 15 residues processed: 69 average time/residue: 0.4212 time to fit residues: 30.6728 Evaluate side-chains 62 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 0.9990 chunk 29 optimal weight: 0.0010 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 214 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.042396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.037193 restraints weight = 18367.446| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 2.24 r_work: 0.2445 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2363 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4843 Z= 0.161 Angle : 0.652 8.139 6606 Z= 0.332 Chirality : 0.047 0.236 719 Planarity : 0.005 0.041 843 Dihedral : 6.407 55.962 677 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.80 % Allowed : 14.97 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.34), residues: 612 helix: -0.99 (0.97), residues: 21 sheet: 0.80 (0.36), residues: 204 loop : -1.23 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.009 0.001 TYR C 161 PHE 0.008 0.001 PHE B 71 TRP 0.012 0.001 TRP B 52 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 4835) covalent geometry : angle 0.64604 / 0.33 ( 6590) SS BOND : bond 0.00370 / 0.21 ( 8) SS BOND : angle 1.96863 / 1.03 ( 16) hydrogen bonds : bond 0.03474 / 2.24 ( 145) hydrogen bonds : angle 6.22093 / 4.36 ( 357) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.178 Fit side-chains REVERT: C 36 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.8332 (t80) REVERT: C 150 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9097 (mtmm) REVERT: C 170 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8261 (ptpp) REVERT: C 215 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: B 110 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9219 (pp) outliers start: 25 outliers final: 15 residues processed: 68 average time/residue: 0.4334 time to fit residues: 31.0289 Evaluate side-chains 66 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 0.0170 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.041872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.036775 restraints weight = 18260.571| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 2.21 r_work: 0.2432 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2349 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4843 Z= 0.181 Angle : 0.670 8.526 6606 Z= 0.342 Chirality : 0.047 0.236 719 Planarity : 0.005 0.041 843 Dihedral : 6.394 51.662 677 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.18 % Allowed : 14.97 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.34), residues: 612 helix: -0.87 (1.01), residues: 20 sheet: 0.92 (0.37), residues: 204 loop : -1.24 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 115 TYR 0.010 0.002 TYR C 161 PHE 0.008 0.001 PHE C 139 TRP 0.011 0.001 TRP B 52 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 4835) covalent geometry : angle 0.66306 / 0.34 ( 6590) SS BOND : bond 0.00416 / 0.26 ( 8) SS BOND : angle 2.01278 / 1.06 ( 16) hydrogen bonds : bond 0.03554 / 2.30 ( 145) hydrogen bonds : angle 6.27062 / 4.40 ( 357) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 45 time to evaluate : 0.200 Fit side-chains REVERT: C 150 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9108 (mtmm) REVERT: C 170 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8271 (ptpp) REVERT: C 215 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7005 (mp10) REVERT: B 110 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9234 (pp) outliers start: 27 outliers final: 14 residues processed: 68 average time/residue: 0.4508 time to fit residues: 32.2327 Evaluate side-chains 61 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain C residue 36 TYR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 23 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.041369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.036289 restraints weight = 18691.626| |-----------------------------------------------------------------------------| r_work (start): 0.2488 rms_B_bonded: 2.21 r_work: 0.2415 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2332 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4843 Z= 0.205 Angle : 0.702 8.791 6606 Z= 0.357 Chirality : 0.048 0.243 719 Planarity : 0.005 0.041 843 Dihedral : 6.356 51.707 675 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.84 % Allowed : 17.08 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.34), residues: 612 helix: -2.40 (0.74), residues: 28 sheet: 0.84 (0.37), residues: 207 loop : -1.20 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 115 TYR 0.011 0.002 TYR C 161 PHE 0.008 0.001 PHE C 139 TRP 0.012 0.001 TRP B 52 HIS 0.003 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 4835) covalent geometry : angle 0.69560 / 0.35 ( 6590) SS BOND : bond 0.00447 / 0.29 ( 8) SS BOND : angle 2.09470 / 1.10 ( 16) hydrogen bonds : bond 0.03700 / 2.39 ( 145) hydrogen bonds : angle 6.38642 / 4.48 ( 357) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.116 Fit side-chains REVERT: C 170 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8279 (ptpp) REVERT: C 215 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: B 110 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9234 (pp) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.4728 time to fit residues: 30.6834 Evaluate side-chains 61 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.0570 chunk 12 optimal weight: 0.3980 chunk 25 optimal weight: 0.0970 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.042765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.037665 restraints weight = 18172.156| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 2.21 r_work: 0.2464 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4843 Z= 0.139 Angle : 0.636 7.935 6606 Z= 0.323 Chirality : 0.046 0.222 719 Planarity : 0.005 0.041 843 Dihedral : 5.401 41.106 669 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.84 % Allowed : 17.66 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.34), residues: 612 helix: -1.63 (0.89), residues: 20 sheet: 0.97 (0.38), residues: 206 loop : -1.19 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 115 TYR 0.009 0.001 TYR C 107 PHE 0.006 0.001 PHE C 139 TRP 0.011 0.001 TRP B 52 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 4835) covalent geometry : angle 0.63018 / 0.32 ( 6590) SS BOND : bond 0.00396 / 0.23 ( 8) SS BOND : angle 1.84084 / 0.98 ( 16) hydrogen bonds : bond 0.03280 / 2.12 ( 145) hydrogen bonds : angle 6.14039 / 4.31 ( 357) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.192 Fit side-chains REVERT: A 465 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8456 (mt-10) REVERT: C 115 ARG cc_start: 0.9082 (ttm-80) cc_final: 0.8843 (mtm110) REVERT: C 170 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8225 (ptpp) REVERT: C 215 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: B 110 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9232 (pp) outliers start: 20 outliers final: 13 residues processed: 63 average time/residue: 0.4543 time to fit residues: 30.0512 Evaluate side-chains 60 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 56 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.4441 > 50:) chunk 3 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.042488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.037362 restraints weight = 18395.731| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 2.22 r_work: 0.2453 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4843 Z= 0.148 Angle : 0.653 7.890 6606 Z= 0.329 Chirality : 0.046 0.219 719 Planarity : 0.005 0.040 843 Dihedral : 5.389 40.756 669 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.45 % Allowed : 18.04 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.34), residues: 612 helix: -1.55 (0.92), residues: 20 sheet: 1.03 (0.38), residues: 206 loop : -1.16 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 115 TYR 0.009 0.001 TYR C 107 PHE 0.007 0.001 PHE B 71 TRP 0.011 0.001 TRP B 52 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4835) covalent geometry : angle 0.64736 / 0.33 ( 6590) SS BOND : bond 0.00384 / 0.24 ( 8) SS BOND : angle 1.85131 / 1.00 ( 16) hydrogen bonds : bond 0.03308 / 2.13 ( 145) hydrogen bonds : angle 6.14585 / 4.31 ( 357) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.198 Fit side-chains REVERT: A 465 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8444 (mt-10) REVERT: C 115 ARG cc_start: 0.9091 (ttm-80) cc_final: 0.8853 (mtm110) REVERT: C 207 LYS cc_start: 0.8161 (ptmt) cc_final: 0.7904 (tppt) REVERT: C 215 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: B 110 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9215 (pp) outliers start: 18 outliers final: 14 residues processed: 59 average time/residue: 0.4582 time to fit residues: 28.4037 Evaluate side-chains 59 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 215 GLN Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.0670 chunk 19 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.041896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.036806 restraints weight = 18527.962| |-----------------------------------------------------------------------------| r_work (start): 0.2504 rms_B_bonded: 2.22 r_work: 0.2432 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2351 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4843 Z= 0.177 Angle : 0.678 8.261 6606 Z= 0.345 Chirality : 0.047 0.231 719 Planarity : 0.005 0.041 843 Dihedral : 5.557 41.514 669 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.26 % Allowed : 18.43 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.34), residues: 612 helix: -1.58 (0.94), residues: 20 sheet: 1.01 (0.38), residues: 206 loop : -1.19 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 115 TYR 0.011 0.001 TYR A 489 PHE 0.008 0.001 PHE C 139 TRP 0.011 0.001 TRP B 52 HIS 0.002 0.001 HIS B 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 4835) covalent geometry : angle 0.67150 / 0.34 ( 6590) SS BOND : bond 0.00412 / 0.26 ( 8) SS BOND : angle 1.95293 / 1.04 ( 16) hydrogen bonds : bond 0.03479 / 2.24 ( 145) hydrogen bonds : angle 6.26072 / 4.38 ( 357) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1824.86 seconds wall clock time: 32 minutes 5.75 seconds (1925.75 seconds total)