Starting phenix.real_space_refine on Sun Apr 27 05:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6x_39807/04_2025/8z6x_39807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6x_39807/04_2025/8z6x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z6x_39807/04_2025/8z6x_39807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6x_39807/04_2025/8z6x_39807.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6x_39807/04_2025/8z6x_39807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6x_39807/04_2025/8z6x_39807.cif" } resolution = 2.96 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= -0.031 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.28, per 1000 atoms: 1.12 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: 1.15 Conformation dependent library (CDL) restraints added in 651.3 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: 0.61 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: 1.45 Time building geometry restraints manager: 1.38 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: 10.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.500 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:14.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 4.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (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 TRP 0.007 0.001 TRP B 52 HIS 0.001 0.000 HIS C 45 PHE 0.004 0.001 PHE C 139 TYR 0.010 0.001 TYR C 38 ARG 0.002 0.000 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.26525 ( 145) hydrogen bonds : angle 9.28888 ( 357) SS BOND : bond 0.00122 ( 8) SS BOND : angle 0.51190 ( 16) covalent geometry : bond 0.00281 ( 4835) covalent geometry : angle 0.54406 ( 6590) *********************** 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 : 0.529 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: 1.1631 time to fit residues: 115.0288 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 : 0.533 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.0170 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN C 6 GLN C 95 GLN C 190 ASN C 191 ASN B 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.044592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.038874 restraints weight = 17616.229| |-----------------------------------------------------------------------------| r_work (start): 0.2563 rms_B_bonded: 2.34 r_work: 0.2491 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4843 Z= 0.221 Angle : 0.711 8.443 6606 Z= 0.366 Chirality : 0.049 0.148 719 Planarity : 0.005 0.041 843 Dihedral : 8.038 83.304 685 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.03 % Allowed : 12.28 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.46 (0.33), residues: 612 helix: -2.86 (0.65), residues: 34 sheet: -0.03 (0.35), residues: 211 loop : -1.39 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 52 HIS 0.005 0.001 HIS B 215 PHE 0.010 0.002 PHE B 71 TYR 0.013 0.002 TYR C 38 ARG 0.005 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 145) hydrogen bonds : angle 6.83401 ( 357) SS BOND : bond 0.00578 ( 8) SS BOND : angle 1.21991 ( 16) covalent geometry : bond 0.00512 ( 4835) covalent geometry : angle 0.70953 ( 6590) *********************** 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 73 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.551 Fit side-chains REVERT: C 36 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8134 (t80) REVERT: C 150 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8975 (mtpp) outliers start: 21 outliers final: 9 residues processed: 68 average time/residue: 1.1001 time to fit residues: 78.3802 Evaluate side-chains 56 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 21 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS 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 = 0.041928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.036464 restraints weight = 18003.005| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 2.28 r_work: 0.2416 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2331 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4843 Z= 0.254 Angle : 0.726 8.380 6606 Z= 0.373 Chirality : 0.049 0.151 719 Planarity : 0.005 0.039 843 Dihedral : 6.637 56.671 677 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % 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 (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: -1.21 (0.33), residues: 612 helix: -2.44 (0.71), residues: 36 sheet: 0.12 (0.34), residues: 215 loop : -1.23 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 52 HIS 0.005 0.001 HIS B 215 PHE 0.011 0.002 PHE B 71 TYR 0.018 0.002 TYR C 38 ARG 0.005 0.001 ARG B 106 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 145) hydrogen bonds : angle 6.67402 ( 357) SS BOND : bond 0.00525 ( 8) SS BOND : angle 1.48473 ( 16) covalent geometry : bond 0.00597 ( 4835) covalent geometry : angle 0.72281 ( 6590) *********************** 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 69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.485 Fit side-chains REVERT: C 36 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8353 (t80) REVERT: C 150 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8980 (mtmm) REVERT: B 110 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9250 (pp) outliers start: 22 outliers final: 12 residues processed: 66 average time/residue: 0.9702 time to fit residues: 67.3814 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 : 0.482 ------------------------------------------------------------------------------- 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 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 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 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.041199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.035994 restraints weight = 18224.023| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 2.23 r_work: 0.2403 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 4843 Z= 0.248 Angle : 0.745 9.477 6606 Z= 0.383 Chirality : 0.049 0.298 719 Planarity : 0.005 0.043 843 Dihedral : 6.753 56.995 677 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.99 % Allowed : 13.24 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.09 (0.33), residues: 612 helix: -2.33 (0.70), residues: 36 sheet: 0.23 (0.35), residues: 211 loop : -1.15 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 52 HIS 0.005 0.001 HIS B 215 PHE 0.009 0.001 PHE C 139 TYR 0.012 0.002 TYR C 38 ARG 0.008 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 145) hydrogen bonds : angle 6.58871 ( 357) SS BOND : bond 0.00386 ( 8) SS BOND : angle 2.71851 ( 16) covalent geometry : bond 0.00584 ( 4835) covalent geometry : angle 0.73425 ( 6590) *********************** 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 72 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 465 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8783 (mt-10) REVERT: C 36 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8363 (t80) REVERT: C 150 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9037 (mtmm) REVERT: C 170 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8265 (ptpp) REVERT: B 110 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9222 (pp) outliers start: 26 outliers final: 13 residues processed: 69 average time/residue: 0.9028 time to fit residues: 65.6934 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 : 0.482 ------------------------------------------------------------------------------- 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 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 110 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 178 VAL 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 31 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.041349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.036185 restraints weight = 18433.721| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 2.23 r_work: 0.2408 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2326 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4843 Z= 0.221 Angle : 0.707 8.675 6606 Z= 0.362 Chirality : 0.049 0.254 719 Planarity : 0.005 0.042 843 Dihedral : 6.676 56.802 677 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.57 % Allowed : 13.82 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.01 (0.33), residues: 612 helix: -2.24 (0.77), residues: 29 sheet: 0.38 (0.35), residues: 213 loop : -1.22 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 52 HIS 0.004 0.001 HIS B 215 PHE 0.008 0.001 PHE B 71 TYR 0.011 0.002 TYR C 161 ARG 0.006 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 145) hydrogen bonds : angle 6.45579 ( 357) SS BOND : bond 0.00386 ( 8) SS BOND : angle 2.24113 ( 16) covalent geometry : bond 0.00520 ( 4835) covalent geometry : angle 0.69956 ( 6590) *********************** 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: 29 poor density : 43 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: C 36 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8356 (t80) REVERT: C 66 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8142 (mttp) REVERT: C 150 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9054 (mtmm) REVERT: C 170 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8294 (ptpp) REVERT: B 110 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9216 (pp) outliers start: 29 outliers final: 19 residues processed: 68 average time/residue: 0.9677 time to fit residues: 69.3447 Evaluate side-chains 64 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 40 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 37 ASN Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 66 LYS 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 178 VAL 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 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 44 optimal weight: 0.0970 chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2677 r_free = 0.2677 target = 0.042007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.036843 restraints weight = 18157.284| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 2.23 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: 0.9119 moved from start: 0.3456 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= 0.172 Angle : 0.662 8.548 6606 Z= 0.337 Chirality : 0.047 0.235 719 Planarity : 0.005 0.042 843 Dihedral : 6.499 56.450 677 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.18 % Allowed : 15.36 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.86 (0.33), residues: 612 helix: -2.07 (0.79), residues: 29 sheet: 0.79 (0.36), residues: 204 loop : -1.29 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.003 0.001 HIS B 215 PHE 0.008 0.001 PHE B 71 TYR 0.009 0.001 TYR C 161 ARG 0.006 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 145) hydrogen bonds : angle 6.28205 ( 357) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.95818 ( 16) covalent geometry : bond 0.00403 ( 4835) covalent geometry : angle 0.65552 ( 6590) *********************** 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 71 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 44 time to evaluate : 0.886 Fit side-chains REVERT: C 36 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8319 (t80) REVERT: C 150 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9079 (mtmm) REVERT: C 170 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8241 (ptpp) REVERT: C 215 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: B 110 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9210 (pp) outliers start: 27 outliers final: 16 residues processed: 67 average time/residue: 0.9782 time to fit residues: 68.9820 Evaluate side-chains 64 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2637 r_free = 0.2637 target = 0.040739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.035698 restraints weight = 18164.624| |-----------------------------------------------------------------------------| r_work (start): 0.2466 rms_B_bonded: 2.19 r_work: 0.2394 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2311 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4843 Z= 0.240 Angle : 0.715 9.827 6606 Z= 0.366 Chirality : 0.049 0.251 719 Planarity : 0.005 0.043 843 Dihedral : 6.744 56.418 677 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.80 % Allowed : 16.12 % 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 (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 (0.33), residues: 612 helix: -2.13 (0.83), residues: 28 sheet: 0.59 (0.36), residues: 211 loop : -1.21 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 52 HIS 0.003 0.001 HIS B 215 PHE 0.010 0.001 PHE C 139 TYR 0.014 0.002 TYR C 161 ARG 0.007 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 145) hydrogen bonds : angle 6.46355 ( 357) SS BOND : bond 0.00437 ( 8) SS BOND : angle 2.20030 ( 16) covalent geometry : bond 0.00568 ( 4835) covalent geometry : angle 0.70766 ( 6590) *********************** 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 69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 44 time to evaluate : 0.495 Fit side-chains REVERT: C 36 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8369 (t80) REVERT: C 37 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.8987 (m-40) REVERT: C 150 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9099 (mtmm) REVERT: C 170 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8206 (ptpp) REVERT: C 207 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7836 (tptt) REVERT: C 215 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: B 110 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9224 (pp) outliers start: 25 outliers final: 14 residues processed: 66 average time/residue: 0.9286 time to fit residues: 64.7617 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 : 0.537 ------------------------------------------------------------------------------- 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 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 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 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 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 44 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.041831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.036731 restraints weight = 18213.481| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.20 r_work: 0.2429 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4843 Z= 0.170 Angle : 0.666 8.844 6606 Z= 0.336 Chirality : 0.047 0.230 719 Planarity : 0.005 0.042 843 Dihedral : 6.388 55.750 675 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.61 % Allowed : 17.08 % 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 (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: -0.68 (0.34), residues: 612 helix: -1.41 (0.91), residues: 20 sheet: 0.95 (0.37), residues: 204 loop : -1.25 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.002 0.001 HIS B 215 PHE 0.008 0.001 PHE C 139 TYR 0.009 0.001 TYR A 453 ARG 0.008 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 145) hydrogen bonds : angle 6.28021 ( 357) SS BOND : bond 0.00385 ( 8) SS BOND : angle 1.91897 ( 16) covalent geometry : bond 0.00400 ( 4835) covalent geometry : angle 0.66050 ( 6590) *********************** 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 69 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 45 time to evaluate : 0.538 Fit side-chains REVERT: C 36 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8330 (t80) REVERT: C 170 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8237 (ptpp) REVERT: C 215 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: B 110 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9214 (pp) outliers start: 24 outliers final: 14 residues processed: 65 average time/residue: 1.0374 time to fit residues: 70.9117 Evaluate side-chains 62 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 36 TYR 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 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** 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 = 0.2638 r_free = 0.2638 target = 0.040777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.035761 restraints weight = 18499.379| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 2.20 r_work: 0.2396 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2313 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4843 Z= 0.222 Angle : 0.705 9.676 6606 Z= 0.360 Chirality : 0.048 0.243 719 Planarity : 0.005 0.042 843 Dihedral : 6.209 51.105 671 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.03 % Allowed : 17.66 % 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 (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: -0.84 (0.34), residues: 612 helix: -2.57 (0.75), residues: 28 sheet: 0.72 (0.36), residues: 211 loop : -1.21 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.003 0.001 HIS B 215 PHE 0.009 0.001 PHE C 139 TYR 0.013 0.002 TYR C 161 ARG 0.007 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 145) hydrogen bonds : angle 6.44752 ( 357) SS BOND : bond 0.00402 ( 8) SS BOND : angle 2.13529 ( 16) covalent geometry : bond 0.00523 ( 4835) covalent geometry : angle 0.69842 ( 6590) *********************** 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 67 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.761 Fit side-chains REVERT: C 66 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8096 (mttp) REVERT: C 170 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (ptpp) REVERT: C 207 LYS cc_start: 0.8147 (ptmt) cc_final: 0.7868 (tptt) REVERT: C 215 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: B 110 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9217 (pp) outliers start: 21 outliers final: 13 residues processed: 64 average time/residue: 1.6620 time to fit residues: 111.8946 Evaluate side-chains 59 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 66 LYS 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 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.0770 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2679 r_free = 0.2679 target = 0.042044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036956 restraints weight = 18167.423| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 2.19 r_work: 0.2438 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2356 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4843 Z= 0.155 Angle : 0.667 7.983 6606 Z= 0.337 Chirality : 0.046 0.223 719 Planarity : 0.005 0.042 843 Dihedral : 5.536 42.961 669 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.65 % Allowed : 18.43 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.34), residues: 612 helix: -2.13 (0.84), residues: 20 sheet: 1.05 (0.37), residues: 204 loop : -1.21 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.002 0.001 HIS B 215 PHE 0.007 0.001 PHE B 71 TYR 0.009 0.001 TYR C 107 ARG 0.008 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 145) hydrogen bonds : angle 6.25219 ( 357) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.86632 ( 16) covalent geometry : bond 0.00364 ( 4835) covalent geometry : angle 0.66097 ( 6590) ********************** 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 65 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.568 Fit side-chains REVERT: C 170 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8263 (ptpp) REVERT: C 207 LYS cc_start: 0.8055 (ptmt) cc_final: 0.7775 (tppt) REVERT: C 215 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: B 110 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9209 (pp) outliers start: 19 outliers final: 15 residues processed: 61 average time/residue: 1.0720 time to fit residues: 68.5713 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 : 0.561 ------------------------------------------------------------------------------- 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 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 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 26 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.041177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.036158 restraints weight = 18406.563| |-----------------------------------------------------------------------------| r_work (start): 0.2481 rms_B_bonded: 2.19 r_work: 0.2409 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2327 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4843 Z= 0.197 Angle : 0.688 8.475 6606 Z= 0.352 Chirality : 0.047 0.233 719 Planarity : 0.005 0.042 843 Dihedral : 5.697 43.565 669 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.84 % Allowed : 18.23 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.34), residues: 612 helix: -2.68 (0.72), residues: 28 sheet: 0.90 (0.36), residues: 211 loop : -1.22 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 52 HIS 0.002 0.001 HIS B 215 PHE 0.009 0.001 PHE C 139 TYR 0.011 0.002 TYR C 161 ARG 0.008 0.001 ARG C 115 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 145) hydrogen bonds : angle 6.36753 ( 357) SS BOND : bond 0.00388 ( 8) SS BOND : angle 1.99479 ( 16) covalent geometry : bond 0.00464 ( 4835) covalent geometry : angle 0.68214 ( 6590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4425.90 seconds wall clock time: 78 minutes 36.85 seconds (4716.85 seconds total)