Starting phenix.real_space_refine on Tue Mar 3 13:23:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wop_32654/03_2026/7wop_32654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wop_32654/03_2026/7wop_32654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_2026/7wop_32654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_2026/7wop_32654.map" model { file = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_2026/7wop_32654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wop_32654/03_2026/7wop_32654.cif" } resolution = 3.51 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= 0.000 sd= 0.016 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 3212 2.51 5 N 863 2.21 5 O 1009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5107 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1588 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 185} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1754 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1765 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 1.23, per 1000 atoms: 0.24 Number of scatterers: 5107 At special positions: 0 Unit cell: (86.184, 78.736, 102.144, 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 1009 8.00 N 863 7.00 C 3212 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 B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 220 " 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: 0.26 Conformation dependent library (CDL) restraints added in 328.7 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1190 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 5.5% alpha, 17.3% 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 342 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.655A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.830A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.546A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.500A pdb=" N GLU C 84 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 removed outlier: 3.500A pdb=" N HIS C 156 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.502A pdb=" N TRP B 37 " --> pdb=" O MET B 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 106 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 69 removed outlier: 5.110A pdb=" N SER B 65 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 67 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 172 through 177 removed outlier: 5.785A pdb=" N TRP B 173 " --> pdb=" O ARG B 164 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG B 164 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 160 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.716A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 87 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB1, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.696A pdb=" N TYR C 183 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL C 174 " --> pdb=" O MET C 158 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N MET C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 195 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: 0.71 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1663 1.35 - 1.46: 1355 1.46 - 1.58: 2187 1.58 - 1.70: 0 1.70 - 1.81: 30 Bond restraints: 5235 Sorted by residual: bond pdb=" N GLY C 237 " pdb=" CA GLY C 237 " ideal model delta sigma weight residual 1.458 1.447 0.011 9.20e-03 1.18e+04 1.34e+00 bond pdb=" CA PRO B 228 " pdb=" C PRO B 228 " ideal model delta sigma weight residual 1.526 1.518 0.008 8.50e-03 1.38e+04 8.29e-01 bond pdb=" C ILE B 226 " pdb=" O ILE B 226 " ideal model delta sigma weight residual 1.232 1.242 -0.010 1.15e-02 7.56e+03 7.95e-01 bond pdb=" CA GLY A 476 " pdb=" C GLY A 476 " ideal model delta sigma weight residual 1.514 1.527 -0.012 1.41e-02 5.03e+03 7.51e-01 bond pdb=" N THR B 19 " pdb=" CA THR B 19 " ideal model delta sigma weight residual 1.460 1.470 -0.011 1.42e-02 4.96e+03 5.62e-01 ... (remaining 5230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 6811 1.15 - 2.30: 229 2.30 - 3.44: 61 3.44 - 4.59: 12 4.59 - 5.74: 3 Bond angle restraints: 7116 Sorted by residual: angle pdb=" C SER C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.25e+00 angle pdb=" N ASN A 481 " pdb=" CA ASN A 481 " pdb=" C ASN A 481 " ideal model delta sigma weight residual 113.15 109.85 3.30 1.19e+00 7.06e-01 7.69e+00 angle pdb=" N GLY A 504 " pdb=" CA GLY A 504 " pdb=" C GLY A 504 " ideal model delta sigma weight residual 113.79 110.74 3.05 1.17e+00 7.31e-01 6.81e+00 angle pdb=" N GLY B 95 " pdb=" CA GLY B 95 " pdb=" C GLY B 95 " ideal model delta sigma weight residual 111.36 114.27 -2.91 1.17e+00 7.31e-01 6.17e+00 angle pdb=" N THR B 25 " pdb=" CA THR B 25 " pdb=" C THR B 25 " ideal model delta sigma weight residual 114.09 110.45 3.64 1.55e+00 4.16e-01 5.51e+00 ... (remaining 7111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 2847 16.21 - 32.42: 166 32.42 - 48.63: 36 48.63 - 64.84: 8 64.84 - 81.05: 4 Dihedral angle restraints: 3061 sinusoidal: 1163 harmonic: 1898 Sorted by residual: dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual 79.00 20.34 58.66 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PRO B 228 " pdb=" C PRO B 228 " pdb=" N TYR B 229 " pdb=" CA TYR B 229 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N PHE B 193 " pdb=" CA PHE B 193 " pdb=" CB PHE B 193 " pdb=" CG PHE B 193 " ideal model delta sinusoidal sigma weight residual 180.00 -120.02 -59.98 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 425 0.029 - 0.057: 221 0.057 - 0.086: 65 0.086 - 0.115: 36 0.115 - 0.143: 6 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA VAL A 483 " pdb=" N VAL A 483 " pdb=" C VAL A 483 " pdb=" CB VAL A 483 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 750 not shown) Planarity restraints: 932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 7 " -0.032 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO B 8 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 166 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 167 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 167 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 167 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 6 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO C 7 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.025 5.00e-02 4.00e+02 ... (remaining 929 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 413 2.74 - 3.28: 5253 3.28 - 3.82: 8454 3.82 - 4.36: 9662 4.36 - 4.90: 16798 Nonbonded interactions: 40580 Sorted by model distance: nonbonded pdb=" OG SER B 36 " pdb=" OG SER B 91 " model vdw 2.203 3.040 nonbonded pdb=" O THR C 33 " pdb=" OH TYR C 236 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 27 " pdb=" OD1 ASP C 94 " model vdw 2.235 3.040 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 159 " model vdw 2.306 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG1 THR B 203 " model vdw 2.328 3.040 ... (remaining 40575 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.130 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 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 : 0.002 0.037 5243 Z= 0.101 Angle : 0.536 5.738 7132 Z= 0.311 Chirality : 0.040 0.143 753 Planarity : 0.004 0.049 932 Dihedral : 10.828 81.052 1847 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 9.21 % Allowed : 8.48 % Favored : 82.31 % 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: -4.81 (0.27), residues: 659 helix: -4.90 (0.33), residues: 26 sheet: -2.57 (0.38), residues: 157 loop : -3.60 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.006 0.001 TYR B 51 PHE 0.005 0.001 PHE C 153 TRP 0.011 0.001 TRP C 98 HIS 0.001 0.000 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 5235) covalent geometry : angle 0.53586 ( 7116) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.61254 ( 16) hydrogen bonds : bond 0.19869 ( 78) hydrogen bonds : angle 10.35855 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.8461 (m110) cc_final: 0.8186 (m-40) REVERT: A 365 TYR cc_start: 0.8196 (m-80) cc_final: 0.7845 (m-80) REVERT: A 395 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7770 (m) REVERT: A 399 SER cc_start: 0.8050 (m) cc_final: 0.7261 (t) REVERT: A 453 TYR cc_start: 0.7655 (p90) cc_final: 0.7269 (p90) REVERT: A 454 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7978 (tpp-160) REVERT: A 493 ARG cc_start: 0.6931 (ttt180) cc_final: 0.6692 (ttt180) REVERT: B 60 VAL cc_start: 0.6133 (OUTLIER) cc_final: 0.5759 (m) REVERT: B 108 VAL cc_start: 0.6482 (OUTLIER) cc_final: 0.5848 (t) REVERT: B 193 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6773 (m-80) REVERT: C 36 TRP cc_start: 0.7702 (m100) cc_final: 0.7418 (m100) REVERT: C 195 SER cc_start: 0.7910 (p) cc_final: 0.7658 (m) outliers start: 51 outliers final: 19 residues processed: 197 average time/residue: 0.0761 time to fit residues: 19.1547 Evaluate side-chains 162 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.0060 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 409 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 487 ASN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 40 GLN B 129 GLN B 165 GLN B 199 ASN B 202 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 80 GLN C 97 ASN C 137 GLN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.168202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.152501 restraints weight = 8490.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156992 restraints weight = 4187.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159774 restraints weight = 2406.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161641 restraints weight = 1549.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162844 restraints weight = 1075.449| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5243 Z= 0.142 Angle : 0.635 7.326 7132 Z= 0.326 Chirality : 0.045 0.217 753 Planarity : 0.005 0.049 932 Dihedral : 7.437 56.433 782 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.26 % Favored : 85.74 % Rotamer: Outliers : 6.68 % Allowed : 16.79 % Favored : 76.53 % 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: -4.33 (0.28), residues: 659 helix: -4.06 (0.53), residues: 34 sheet: -1.99 (0.40), residues: 157 loop : -3.36 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 192 TYR 0.020 0.002 TYR B 220 PHE 0.021 0.002 PHE C 192 TRP 0.015 0.002 TRP C 98 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5235) covalent geometry : angle 0.63461 ( 7116) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.74277 ( 16) hydrogen bonds : bond 0.02993 ( 78) hydrogen bonds : angle 7.01314 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8453 (m-80) cc_final: 0.7899 (m-80) REVERT: A 378 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8229 (ttmt) REVERT: A 403 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.7437 (mtp-110) REVERT: A 423 TYR cc_start: 0.7907 (t80) cc_final: 0.7656 (t80) REVERT: A 433 VAL cc_start: 0.8476 (t) cc_final: 0.8269 (t) REVERT: A 453 TYR cc_start: 0.7870 (p90) cc_final: 0.7140 (p90) REVERT: A 493 ARG cc_start: 0.7305 (ttt180) cc_final: 0.6889 (ttt180) REVERT: B 60 VAL cc_start: 0.6291 (OUTLIER) cc_final: 0.6024 (m) REVERT: B 185 TYR cc_start: 0.6801 (m-80) cc_final: 0.6472 (m-80) REVERT: B 193 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: B 195 ILE cc_start: 0.7052 (mt) cc_final: 0.6569 (tt) REVERT: B 229 TYR cc_start: 0.7760 (t80) cc_final: 0.7514 (t80) REVERT: C 33 THR cc_start: 0.7707 (p) cc_final: 0.7336 (m) REVERT: C 40 LEU cc_start: 0.8196 (mm) cc_final: 0.7992 (mp) REVERT: C 68 SER cc_start: 0.8660 (t) cc_final: 0.8380 (p) REVERT: C 171 TRP cc_start: 0.7490 (t60) cc_final: 0.7262 (t60) REVERT: C 192 PHE cc_start: 0.6798 (m-80) cc_final: 0.6292 (m-10) REVERT: C 236 TYR cc_start: 0.8050 (p90) cc_final: 0.7757 (p90) outliers start: 37 outliers final: 24 residues processed: 175 average time/residue: 0.0733 time to fit residues: 16.4302 Evaluate side-chains 168 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 354 ASN A 360 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146429 restraints weight = 8338.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.150790 restraints weight = 4165.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153527 restraints weight = 2426.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155363 restraints weight = 1571.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.156609 restraints weight = 1102.268| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5243 Z= 0.194 Angle : 0.665 6.819 7132 Z= 0.348 Chirality : 0.047 0.192 753 Planarity : 0.005 0.048 932 Dihedral : 7.376 59.197 777 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 7.58 % Allowed : 18.95 % Favored : 73.47 % 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: -4.16 (0.29), residues: 659 helix: -3.68 (0.61), residues: 34 sheet: -1.91 (0.38), residues: 171 loop : -3.26 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 454 TYR 0.015 0.002 TYR B 220 PHE 0.030 0.002 PHE C 153 TRP 0.015 0.002 TRP C 98 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 5235) covalent geometry : angle 0.66516 ( 7116) SS BOND : bond 0.00417 ( 8) SS BOND : angle 0.77807 ( 16) hydrogen bonds : bond 0.03471 ( 78) hydrogen bonds : angle 6.89039 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7716 (m-10) cc_final: 0.7447 (m-10) REVERT: A 378 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8175 (ttmt) REVERT: A 453 TYR cc_start: 0.7953 (p90) cc_final: 0.7205 (p90) REVERT: A 454 ARG cc_start: 0.8364 (ttm110) cc_final: 0.8157 (ttm170) REVERT: A 458 LYS cc_start: 0.8130 (tppt) cc_final: 0.7843 (tppt) REVERT: A 493 ARG cc_start: 0.7222 (ttt180) cc_final: 0.6878 (ttt180) REVERT: B 49 MET cc_start: 0.6606 (tpp) cc_final: 0.6348 (mpp) REVERT: B 60 VAL cc_start: 0.6714 (OUTLIER) cc_final: 0.6457 (m) REVERT: B 88 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5755 (m-80) REVERT: B 193 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: B 195 ILE cc_start: 0.7226 (mt) cc_final: 0.6614 (tt) REVERT: B 208 MET cc_start: 0.3703 (tpp) cc_final: 0.3480 (tpp) REVERT: B 227 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6859 (tp-100) REVERT: B 231 TYR cc_start: 0.6514 (t80) cc_final: 0.6221 (t80) REVERT: C 29 ILE cc_start: 0.8731 (mt) cc_final: 0.8475 (tt) REVERT: C 33 THR cc_start: 0.7790 (p) cc_final: 0.7427 (m) REVERT: C 68 SER cc_start: 0.8564 (t) cc_final: 0.8308 (p) REVERT: C 158 MET cc_start: 0.8160 (mmm) cc_final: 0.7682 (mmt) REVERT: C 170 GLU cc_start: 0.7633 (pp20) cc_final: 0.6660 (pp20) REVERT: C 171 TRP cc_start: 0.7592 (t60) cc_final: 0.7152 (t60) REVERT: C 173 SER cc_start: 0.7655 (t) cc_final: 0.7434 (p) REVERT: C 236 TYR cc_start: 0.8074 (p90) cc_final: 0.7457 (p90) outliers start: 42 outliers final: 28 residues processed: 184 average time/residue: 0.0719 time to fit residues: 17.0512 Evaluate side-chains 182 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145463 restraints weight = 8373.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149853 restraints weight = 4159.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152591 restraints weight = 2420.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154387 restraints weight = 1566.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.155496 restraints weight = 1105.938| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5243 Z= 0.177 Angle : 0.658 6.192 7132 Z= 0.343 Chirality : 0.047 0.158 753 Planarity : 0.005 0.045 932 Dihedral : 7.394 58.869 776 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 7.04 % Allowed : 20.76 % Favored : 72.20 % 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: -4.04 (0.29), residues: 659 helix: -3.24 (0.74), residues: 34 sheet: -1.86 (0.39), residues: 170 loop : -3.20 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 454 TYR 0.021 0.002 TYR B 93 PHE 0.031 0.002 PHE C 153 TRP 0.015 0.002 TRP C 98 HIS 0.004 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5235) covalent geometry : angle 0.65797 ( 7116) SS BOND : bond 0.00305 ( 8) SS BOND : angle 0.74352 ( 16) hydrogen bonds : bond 0.03282 ( 78) hydrogen bonds : angle 6.84308 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7255 (ptp-110) cc_final: 0.6983 (ptp-110) REVERT: A 365 TYR cc_start: 0.8400 (m-80) cc_final: 0.7829 (m-80) REVERT: A 378 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8126 (ttmt) REVERT: A 403 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7758 (mtp-110) REVERT: A 453 TYR cc_start: 0.7982 (p90) cc_final: 0.7313 (p90) REVERT: A 458 LYS cc_start: 0.8027 (tppt) cc_final: 0.7611 (mmmt) REVERT: A 493 ARG cc_start: 0.7217 (ttt180) cc_final: 0.6876 (ttt180) REVERT: B 85 GLU cc_start: 0.5494 (OUTLIER) cc_final: 0.4985 (pm20) REVERT: B 102 PHE cc_start: 0.8554 (m-80) cc_final: 0.8210 (m-10) REVERT: B 185 TYR cc_start: 0.6997 (m-80) cc_final: 0.6501 (m-80) REVERT: B 193 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: B 195 ILE cc_start: 0.7161 (mt) cc_final: 0.6897 (tt) REVERT: B 227 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6720 (tp-100) REVERT: B 230 TYR cc_start: 0.7426 (t80) cc_final: 0.7148 (t80) REVERT: B 231 TYR cc_start: 0.6810 (t80) cc_final: 0.6448 (t80) REVERT: C 28 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7685 (p0) REVERT: C 29 ILE cc_start: 0.8747 (mt) cc_final: 0.8481 (tt) REVERT: C 33 THR cc_start: 0.7682 (p) cc_final: 0.7248 (m) REVERT: C 68 SER cc_start: 0.8590 (t) cc_final: 0.8345 (p) REVERT: C 158 MET cc_start: 0.8188 (mmm) cc_final: 0.7608 (mmt) REVERT: C 170 GLU cc_start: 0.7660 (pp20) cc_final: 0.6759 (pp20) REVERT: C 171 TRP cc_start: 0.7604 (t60) cc_final: 0.7209 (t60) REVERT: C 173 SER cc_start: 0.7701 (t) cc_final: 0.7445 (p) REVERT: C 236 TYR cc_start: 0.8064 (p90) cc_final: 0.7346 (p90) outliers start: 39 outliers final: 27 residues processed: 178 average time/residue: 0.0754 time to fit residues: 17.1181 Evaluate side-chains 179 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 43 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.160955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145062 restraints weight = 8610.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149516 restraints weight = 4267.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152340 restraints weight = 2481.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.154167 restraints weight = 1606.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155014 restraints weight = 1130.319| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5243 Z= 0.165 Angle : 0.659 7.065 7132 Z= 0.346 Chirality : 0.046 0.154 753 Planarity : 0.005 0.045 932 Dihedral : 7.401 56.126 775 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 7.94 % Allowed : 20.04 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.96 (0.30), residues: 659 helix: -2.96 (0.81), residues: 34 sheet: -1.74 (0.40), residues: 168 loop : -3.19 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 454 TYR 0.032 0.002 TYR B 93 PHE 0.032 0.002 PHE C 153 TRP 0.014 0.002 TRP C 98 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5235) covalent geometry : angle 0.65914 ( 7116) SS BOND : bond 0.00254 ( 8) SS BOND : angle 0.68874 ( 16) hydrogen bonds : bond 0.03226 ( 78) hydrogen bonds : angle 6.76830 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.6304 (t80) REVERT: A 350 VAL cc_start: 0.7921 (m) cc_final: 0.7554 (p) REVERT: A 357 ARG cc_start: 0.7237 (ptp-110) cc_final: 0.6901 (ptp-110) REVERT: A 365 TYR cc_start: 0.8402 (m-80) cc_final: 0.7796 (m-80) REVERT: A 378 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8123 (ttmt) REVERT: A 453 TYR cc_start: 0.7966 (p90) cc_final: 0.7558 (p90) REVERT: B 25 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6937 (p) REVERT: B 85 GLU cc_start: 0.5446 (OUTLIER) cc_final: 0.4957 (pm20) REVERT: B 102 PHE cc_start: 0.8500 (m-80) cc_final: 0.8189 (m-10) REVERT: B 185 TYR cc_start: 0.6846 (m-80) cc_final: 0.6437 (m-80) REVERT: B 195 ILE cc_start: 0.7212 (mt) cc_final: 0.6904 (tt) REVERT: B 227 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6590 (tp-100) REVERT: B 230 TYR cc_start: 0.7429 (t80) cc_final: 0.7183 (t80) REVERT: B 231 TYR cc_start: 0.6932 (t80) cc_final: 0.6470 (t80) REVERT: C 29 ILE cc_start: 0.8743 (mt) cc_final: 0.8506 (tt) REVERT: C 33 THR cc_start: 0.7708 (p) cc_final: 0.7253 (m) REVERT: C 68 SER cc_start: 0.8608 (t) cc_final: 0.8346 (p) REVERT: C 158 MET cc_start: 0.8161 (mmm) cc_final: 0.7543 (mmt) REVERT: C 170 GLU cc_start: 0.7710 (pp20) cc_final: 0.7191 (pp20) REVERT: C 171 TRP cc_start: 0.7651 (t60) cc_final: 0.7312 (t60) REVERT: C 173 SER cc_start: 0.7671 (t) cc_final: 0.7391 (p) REVERT: C 207 MET cc_start: 0.6327 (mmp) cc_final: 0.6108 (mmm) REVERT: C 236 TYR cc_start: 0.7919 (p90) cc_final: 0.7214 (p90) outliers start: 44 outliers final: 27 residues processed: 178 average time/residue: 0.0635 time to fit residues: 14.7584 Evaluate side-chains 173 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN C 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144434 restraints weight = 8491.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148794 restraints weight = 4221.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151643 restraints weight = 2469.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153515 restraints weight = 1603.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.154424 restraints weight = 1135.649| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5243 Z= 0.171 Angle : 0.680 6.077 7132 Z= 0.356 Chirality : 0.047 0.159 753 Planarity : 0.005 0.045 932 Dihedral : 7.060 45.760 772 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.63 % Favored : 84.37 % Rotamer: Outliers : 7.58 % Allowed : 21.66 % Favored : 70.76 % 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: -3.88 (0.30), residues: 659 helix: -2.91 (0.83), residues: 34 sheet: -1.67 (0.41), residues: 168 loop : -3.14 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 346 TYR 0.046 0.002 TYR B 93 PHE 0.033 0.002 PHE C 153 TRP 0.015 0.002 TRP C 98 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5235) covalent geometry : angle 0.67998 ( 7116) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.70501 ( 16) hydrogen bonds : bond 0.03228 ( 78) hydrogen bonds : angle 6.81157 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6544 (OUTLIER) cc_final: 0.6324 (t80) REVERT: A 350 VAL cc_start: 0.7822 (m) cc_final: 0.7512 (p) REVERT: A 355 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6767 (tmt90) REVERT: A 357 ARG cc_start: 0.7233 (ptp-110) cc_final: 0.6867 (ptp-110) REVERT: A 365 TYR cc_start: 0.8398 (m-80) cc_final: 0.7863 (m-80) REVERT: A 378 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: A 453 TYR cc_start: 0.7984 (p90) cc_final: 0.7658 (p90) REVERT: A 454 ARG cc_start: 0.8222 (tpp80) cc_final: 0.7701 (tpp80) REVERT: B 25 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6953 (p) REVERT: B 85 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.4971 (pm20) REVERT: B 102 PHE cc_start: 0.8483 (m-80) cc_final: 0.8215 (m-10) REVERT: B 106 THR cc_start: 0.6897 (p) cc_final: 0.6697 (p) REVERT: B 185 TYR cc_start: 0.6759 (m-80) cc_final: 0.6402 (m-80) REVERT: B 195 ILE cc_start: 0.7273 (mt) cc_final: 0.6909 (tt) REVERT: B 227 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6414 (tp-100) REVERT: B 230 TYR cc_start: 0.7421 (t80) cc_final: 0.7173 (t80) REVERT: C 33 THR cc_start: 0.7726 (p) cc_final: 0.7230 (m) REVERT: C 68 SER cc_start: 0.8628 (t) cc_final: 0.8375 (p) REVERT: C 158 MET cc_start: 0.8104 (mmm) cc_final: 0.7485 (mmt) REVERT: C 170 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7317 (pp20) REVERT: C 173 SER cc_start: 0.7620 (t) cc_final: 0.7288 (p) REVERT: C 236 TYR cc_start: 0.7929 (p90) cc_final: 0.7417 (p90) outliers start: 42 outliers final: 28 residues processed: 169 average time/residue: 0.0730 time to fit residues: 15.8841 Evaluate side-chains 176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 0.0970 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 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 = 0.4066 r_free = 0.4066 target = 0.164575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148562 restraints weight = 8381.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153031 restraints weight = 4147.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.155909 restraints weight = 2416.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.157720 restraints weight = 1561.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158929 restraints weight = 1104.197| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5243 Z= 0.118 Angle : 0.644 6.737 7132 Z= 0.337 Chirality : 0.046 0.160 753 Planarity : 0.005 0.046 932 Dihedral : 6.764 45.694 772 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 5.78 % Allowed : 23.83 % Favored : 70.40 % 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: -3.70 (0.31), residues: 659 helix: -2.68 (0.87), residues: 34 sheet: -1.48 (0.42), residues: 168 loop : -3.05 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.039 0.001 TYR B 93 PHE 0.035 0.002 PHE C 153 TRP 0.031 0.002 TRP C 171 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5235) covalent geometry : angle 0.64386 ( 7116) SS BOND : bond 0.00226 ( 8) SS BOND : angle 0.85482 ( 16) hydrogen bonds : bond 0.02965 ( 78) hydrogen bonds : angle 6.55141 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.7769 (m) cc_final: 0.7407 (p) REVERT: A 357 ARG cc_start: 0.7220 (ptp-110) cc_final: 0.6788 (ptp-110) REVERT: A 378 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8073 (ttmt) REVERT: A 453 TYR cc_start: 0.7889 (p90) cc_final: 0.7658 (p90) REVERT: A 454 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7857 (tpp-160) REVERT: B 25 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6907 (p) REVERT: B 85 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.4999 (pm20) REVERT: B 102 PHE cc_start: 0.8368 (m-80) cc_final: 0.8132 (m-10) REVERT: B 185 TYR cc_start: 0.6485 (m-80) cc_final: 0.6284 (m-80) REVERT: B 193 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.7020 (m-80) REVERT: B 195 ILE cc_start: 0.7105 (mt) cc_final: 0.6858 (tp) REVERT: B 227 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6241 (tp-100) REVERT: C 33 THR cc_start: 0.7645 (p) cc_final: 0.7406 (m) REVERT: C 68 SER cc_start: 0.8734 (t) cc_final: 0.8492 (p) REVERT: C 158 MET cc_start: 0.8111 (mmm) cc_final: 0.7541 (mmt) REVERT: C 170 GLU cc_start: 0.7727 (pp20) cc_final: 0.7255 (pp20) REVERT: C 173 SER cc_start: 0.7645 (t) cc_final: 0.7131 (p) outliers start: 32 outliers final: 25 residues processed: 161 average time/residue: 0.0711 time to fit residues: 14.7332 Evaluate side-chains 161 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144401 restraints weight = 8446.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.148871 restraints weight = 4195.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.151768 restraints weight = 2457.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.153576 restraints weight = 1598.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.154931 restraints weight = 1144.288| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5243 Z= 0.187 Angle : 0.697 7.064 7132 Z= 0.366 Chirality : 0.048 0.211 753 Planarity : 0.005 0.045 932 Dihedral : 6.994 45.297 769 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 6.32 % Allowed : 24.19 % Favored : 69.49 % 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: -3.79 (0.30), residues: 659 helix: -2.67 (0.83), residues: 34 sheet: -1.44 (0.41), residues: 164 loop : -3.16 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 17 TYR 0.045 0.002 TYR B 93 PHE 0.034 0.002 PHE C 153 TRP 0.041 0.003 TRP C 171 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5235) covalent geometry : angle 0.69641 ( 7116) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.78941 ( 16) hydrogen bonds : bond 0.03056 ( 78) hydrogen bonds : angle 6.52328 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.7628 (m) cc_final: 0.7290 (p) REVERT: A 355 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6829 (tmt90) REVERT: A 357 ARG cc_start: 0.7153 (ptp-110) cc_final: 0.6776 (ptp-110) REVERT: A 378 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8101 (ttmt) REVERT: A 453 TYR cc_start: 0.7919 (p90) cc_final: 0.7690 (p90) REVERT: A 454 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7815 (tpp80) REVERT: B 25 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6950 (p) REVERT: B 85 GLU cc_start: 0.5443 (OUTLIER) cc_final: 0.5000 (pm20) REVERT: B 102 PHE cc_start: 0.8417 (m-80) cc_final: 0.8161 (m-10) REVERT: B 106 THR cc_start: 0.6910 (p) cc_final: 0.6698 (p) REVERT: B 111 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4057 (tm) REVERT: B 185 TYR cc_start: 0.6733 (m-80) cc_final: 0.6503 (m-80) REVERT: B 193 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: B 195 ILE cc_start: 0.7205 (mt) cc_final: 0.6846 (tt) REVERT: B 211 LEU cc_start: 0.5307 (pp) cc_final: 0.5075 (pp) REVERT: B 227 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6414 (tp-100) REVERT: C 33 THR cc_start: 0.7718 (p) cc_final: 0.7428 (m) REVERT: C 68 SER cc_start: 0.8678 (t) cc_final: 0.8409 (p) REVERT: C 158 MET cc_start: 0.8081 (mmm) cc_final: 0.7463 (mmt) REVERT: C 171 TRP cc_start: 0.7755 (t60) cc_final: 0.7512 (t60) REVERT: C 173 SER cc_start: 0.7592 (t) cc_final: 0.7344 (p) outliers start: 35 outliers final: 26 residues processed: 165 average time/residue: 0.0680 time to fit residues: 14.4355 Evaluate side-chains 173 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 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 = 0.4014 r_free = 0.4014 target = 0.159866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143652 restraints weight = 8346.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148030 restraints weight = 4181.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.150853 restraints weight = 2479.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.152704 restraints weight = 1633.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154027 restraints weight = 1163.790| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5243 Z= 0.178 Angle : 0.703 7.482 7132 Z= 0.369 Chirality : 0.048 0.192 753 Planarity : 0.005 0.046 932 Dihedral : 7.014 45.380 769 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.45 % Favored : 82.55 % Rotamer: Outliers : 6.32 % Allowed : 24.73 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.74 (0.30), residues: 659 helix: -3.42 (0.82), residues: 28 sheet: -1.63 (0.42), residues: 164 loop : -2.96 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 17 TYR 0.045 0.002 TYR B 93 PHE 0.034 0.002 PHE C 153 TRP 0.037 0.002 TRP C 171 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5235) covalent geometry : angle 0.70258 ( 7116) SS BOND : bond 0.00236 ( 8) SS BOND : angle 0.73616 ( 16) hydrogen bonds : bond 0.03036 ( 78) hydrogen bonds : angle 6.58497 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7170 (ptp-110) cc_final: 0.6773 (ptp-110) REVERT: A 378 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8104 (ttmt) REVERT: A 453 TYR cc_start: 0.7984 (p90) cc_final: 0.7653 (p90) REVERT: B 25 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6902 (p) REVERT: B 85 GLU cc_start: 0.5426 (OUTLIER) cc_final: 0.5053 (pm20) REVERT: B 102 PHE cc_start: 0.8383 (m-80) cc_final: 0.8155 (m-10) REVERT: B 111 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.4038 (tm) REVERT: B 193 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: B 195 ILE cc_start: 0.7176 (mt) cc_final: 0.6808 (tt) REVERT: B 227 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.6411 (tp-100) REVERT: C 33 THR cc_start: 0.7681 (p) cc_final: 0.7122 (m) REVERT: C 68 SER cc_start: 0.8702 (t) cc_final: 0.8439 (p) REVERT: C 158 MET cc_start: 0.8140 (mmm) cc_final: 0.7526 (mmt) REVERT: C 170 GLU cc_start: 0.7635 (pp20) cc_final: 0.7067 (pp20) REVERT: C 171 TRP cc_start: 0.7781 (t60) cc_final: 0.6701 (t60) REVERT: C 173 SER cc_start: 0.7612 (t) cc_final: 0.7277 (p) REVERT: C 207 MET cc_start: 0.6382 (mmm) cc_final: 0.6142 (mmm) REVERT: C 236 TYR cc_start: 0.7818 (p90) cc_final: 0.7499 (p90) outliers start: 35 outliers final: 28 residues processed: 167 average time/residue: 0.0702 time to fit residues: 15.2668 Evaluate side-chains 176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 61 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 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 = 0.4018 r_free = 0.4018 target = 0.160384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144280 restraints weight = 8445.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148751 restraints weight = 4222.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.151539 restraints weight = 2473.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153426 restraints weight = 1614.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.154604 restraints weight = 1140.703| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 5243 Z= 0.190 Angle : 0.749 15.380 7132 Z= 0.389 Chirality : 0.049 0.262 753 Planarity : 0.005 0.046 932 Dihedral : 7.107 45.764 769 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.24 % Favored : 83.76 % Rotamer: Outliers : 6.14 % Allowed : 25.99 % Favored : 67.87 % 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: -3.68 (0.31), residues: 659 helix: -3.36 (0.83), residues: 28 sheet: -1.59 (0.42), residues: 164 loop : -2.92 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 17 TYR 0.044 0.002 TYR B 93 PHE 0.035 0.002 PHE C 153 TRP 0.035 0.002 TRP C 171 HIS 0.003 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 5235) covalent geometry : angle 0.74278 ( 7116) SS BOND : bond 0.00746 ( 8) SS BOND : angle 2.09460 ( 16) hydrogen bonds : bond 0.03051 ( 78) hydrogen bonds : angle 6.58871 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7166 (ptp-110) cc_final: 0.6763 (ptp-110) REVERT: A 378 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7462 (ttmp) REVERT: A 453 TYR cc_start: 0.8023 (p90) cc_final: 0.7647 (p90) REVERT: B 25 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6964 (p) REVERT: B 85 GLU cc_start: 0.5423 (OUTLIER) cc_final: 0.5060 (pm20) REVERT: B 102 PHE cc_start: 0.8381 (m-80) cc_final: 0.8152 (m-10) REVERT: B 111 LEU cc_start: 0.4449 (OUTLIER) cc_final: 0.4050 (tm) REVERT: B 185 TYR cc_start: 0.7025 (m-80) cc_final: 0.6615 (m-80) REVERT: B 193 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 227 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6506 (tp-100) REVERT: C 33 THR cc_start: 0.7701 (p) cc_final: 0.7117 (m) REVERT: C 68 SER cc_start: 0.8706 (t) cc_final: 0.8445 (p) REVERT: C 158 MET cc_start: 0.8114 (mmm) cc_final: 0.7612 (mmt) REVERT: C 170 GLU cc_start: 0.7600 (pp20) cc_final: 0.7030 (pp20) REVERT: C 171 TRP cc_start: 0.7817 (t60) cc_final: 0.6775 (t60) REVERT: C 173 SER cc_start: 0.7639 (t) cc_final: 0.7289 (p) REVERT: C 236 TYR cc_start: 0.7817 (p90) cc_final: 0.7516 (p90) outliers start: 34 outliers final: 28 residues processed: 162 average time/residue: 0.0700 time to fit residues: 14.6930 Evaluate side-chains 173 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 247 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 23 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 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 = 0.4093 r_free = 0.4093 target = 0.166799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150725 restraints weight = 8496.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155291 restraints weight = 4258.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158161 restraints weight = 2471.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160078 restraints weight = 1592.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.161274 restraints weight = 1112.850| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5243 Z= 0.127 Angle : 0.698 12.736 7132 Z= 0.358 Chirality : 0.046 0.180 753 Planarity : 0.005 0.046 932 Dihedral : 6.742 46.091 769 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.96 % Favored : 86.04 % Rotamer: Outliers : 5.78 % Allowed : 26.71 % Favored : 67.51 % 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: -3.48 (0.31), residues: 659 helix: -3.07 (0.90), residues: 28 sheet: -1.43 (0.43), residues: 163 loop : -2.80 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 17 TYR 0.037 0.002 TYR B 93 PHE 0.033 0.002 PHE C 153 TRP 0.025 0.002 TRP C 171 HIS 0.002 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5235) covalent geometry : angle 0.69467 ( 7116) SS BOND : bond 0.00892 ( 8) SS BOND : angle 1.50235 ( 16) hydrogen bonds : bond 0.02711 ( 78) hydrogen bonds : angle 6.32765 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1112.50 seconds wall clock time: 19 minutes 50.87 seconds (1190.87 seconds total)