Starting phenix.real_space_refine on Tue Feb 11 09:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wop_32654/02_2025/7wop_32654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wop_32654/02_2025/7wop_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_32654/02_2025/7wop_32654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wop_32654/02_2025/7wop_32654.map" model { file = "/net/cci-nas-00/data/ceres_data/7wop_32654/02_2025/7wop_32654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wop_32654/02_2025/7wop_32654.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.08, per 1000 atoms: 0.80 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: 1.27 Conformation dependent library (CDL) restraints added in 578.0 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: 0.61 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: 1.37 Time building geometry restraints manager: 1.50 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: 2.630 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- 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 5235 Z= 0.133 Angle : 0.536 5.738 7116 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP C 98 HIS 0.001 0.000 HIS C 159 PHE 0.005 0.001 PHE C 153 TYR 0.006 0.001 TYR B 51 ARG 0.002 0.000 ARG A 466 *********************** 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 : 0.541 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: 0.8197 (m-80) cc_final: 0.7844 (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: 0.7262 (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: 0.6932 (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: 0.5849 (t) REVERT: B 193 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6774 (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: 0.1898 time to fit residues: 47.0490 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 : 0.596 ------------------------------------------------------------------------------- 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 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151367 restraints weight = 8341.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155766 restraints weight = 4130.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.158581 restraints weight = 2385.728| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5235 Z= 0.233 Angle : 0.646 7.159 7116 Z= 0.334 Chirality : 0.045 0.225 753 Planarity : 0.005 0.049 932 Dihedral : 7.502 56.335 782 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 6.68 % Allowed : 16.97 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.28), residues: 659 helix: -4.10 (0.51), residues: 34 sheet: -1.91 (0.41), residues: 145 loop : -3.42 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 98 HIS 0.005 0.001 HIS B 41 PHE 0.021 0.002 PHE C 192 TYR 0.020 0.002 TYR B 220 ARG 0.004 0.001 ARG B 192 *********************** 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 187 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8480 (m-80) cc_final: 0.7896 (m-80) REVERT: A 403 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7472 (mtp-110) REVERT: A 433 VAL cc_start: 0.8502 (t) cc_final: 0.8274 (t) REVERT: A 453 TYR cc_start: 0.7908 (p90) cc_final: 0.7191 (p90) REVERT: A 474 GLN cc_start: 0.7762 (tt0) cc_final: 0.7517 (tt0) REVERT: A 493 ARG cc_start: 0.7300 (ttt180) cc_final: 0.6907 (ttt180) REVERT: B 60 VAL cc_start: 0.6327 (OUTLIER) cc_final: 0.6064 (m) REVERT: B 185 TYR cc_start: 0.6890 (m-80) cc_final: 0.6580 (m-80) REVERT: B 193 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: B 195 ILE cc_start: 0.7123 (mt) cc_final: 0.6642 (tt) REVERT: B 229 TYR cc_start: 0.7835 (t80) cc_final: 0.7601 (t80) REVERT: C 33 THR cc_start: 0.7724 (p) cc_final: 0.7383 (m) REVERT: C 68 SER cc_start: 0.8700 (t) cc_final: 0.8432 (p) REVERT: C 170 GLU cc_start: 0.7476 (pp20) cc_final: 0.6528 (pp20) REVERT: C 171 TRP cc_start: 0.7559 (t60) cc_final: 0.7141 (t60) REVERT: C 192 PHE cc_start: 0.6861 (m-80) cc_final: 0.6443 (m-10) REVERT: C 236 TYR cc_start: 0.8025 (p90) cc_final: 0.7708 (p90) outliers start: 37 outliers final: 24 residues processed: 179 average time/residue: 0.1734 time to fit residues: 39.4557 Evaluate side-chains 170 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN A 360 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 505 HIS ** 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 = 0.4074 r_free = 0.4074 target = 0.165901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150422 restraints weight = 8391.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.154875 restraints weight = 4128.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157717 restraints weight = 2377.519| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5235 Z= 0.209 Angle : 0.628 7.839 7116 Z= 0.325 Chirality : 0.046 0.163 753 Planarity : 0.005 0.048 932 Dihedral : 7.091 58.393 777 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 7.22 % Allowed : 18.77 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.29), residues: 659 helix: -3.67 (0.62), residues: 34 sheet: -1.66 (0.41), residues: 152 loop : -3.18 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 98 HIS 0.004 0.001 HIS B 41 PHE 0.029 0.002 PHE C 153 TYR 0.017 0.001 TYR C 236 ARG 0.003 0.000 ARG A 454 *********************** 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 190 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8468 (m-80) cc_final: 0.7740 (m-80) REVERT: A 378 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8180 (ttmt) REVERT: A 433 VAL cc_start: 0.8396 (t) cc_final: 0.8178 (t) REVERT: A 453 TYR cc_start: 0.7874 (p90) cc_final: 0.7146 (p90) REVERT: A 458 LYS cc_start: 0.8011 (tppt) cc_final: 0.7689 (tppt) REVERT: A 474 GLN cc_start: 0.7783 (tt0) cc_final: 0.7527 (tt0) REVERT: A 493 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6853 (ttt180) REVERT: B 49 MET cc_start: 0.6625 (tpp) cc_final: 0.6353 (mpp) REVERT: B 60 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6286 (m) REVERT: B 163 VAL cc_start: 0.8415 (m) cc_final: 0.8077 (p) REVERT: B 193 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: B 195 ILE cc_start: 0.7177 (mt) cc_final: 0.6565 (tt) REVERT: B 227 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6673 (tp-100) REVERT: C 33 THR cc_start: 0.7701 (p) cc_final: 0.7354 (m) REVERT: C 158 MET cc_start: 0.8299 (mmm) cc_final: 0.8010 (mmt) REVERT: C 170 GLU cc_start: 0.7657 (pp20) cc_final: 0.6681 (pp20) REVERT: C 171 TRP cc_start: 0.7463 (t60) cc_final: 0.7043 (t60) REVERT: C 236 TYR cc_start: 0.8055 (p90) cc_final: 0.7494 (p90) outliers start: 40 outliers final: 26 residues processed: 180 average time/residue: 0.1717 time to fit residues: 39.2298 Evaluate side-chains 176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 388 ASN 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 60 VAL Chi-restraints excluded: chain B residue 68 LYS 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 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 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 3 optimal weight: 0.0970 chunk 54 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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** A 477 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.166421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150671 restraints weight = 8504.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155222 restraints weight = 4160.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.158057 restraints weight = 2390.416| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5235 Z= 0.181 Angle : 0.606 6.417 7116 Z= 0.314 Chirality : 0.045 0.144 753 Planarity : 0.005 0.045 932 Dihedral : 7.073 59.648 776 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 5.96 % Allowed : 21.48 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.30), residues: 659 helix: -3.16 (0.75), residues: 34 sheet: -1.46 (0.41), residues: 157 loop : -3.09 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.032 0.002 PHE C 153 TYR 0.018 0.001 TYR B 185 ARG 0.003 0.000 ARG A 454 *********************** 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 181 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7246 (ptp-110) cc_final: 0.6984 (ptp-110) REVERT: A 378 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8143 (ttmt) REVERT: A 403 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7741 (mtp-110) REVERT: A 453 TYR cc_start: 0.7806 (p90) cc_final: 0.7267 (p90) REVERT: A 458 LYS cc_start: 0.7944 (tppt) cc_final: 0.7718 (tppt) REVERT: A 493 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6856 (ttt180) REVERT: B 60 VAL cc_start: 0.6682 (OUTLIER) cc_final: 0.6480 (m) REVERT: B 163 VAL cc_start: 0.8461 (m) cc_final: 0.8142 (p) REVERT: B 185 TYR cc_start: 0.6815 (m-80) cc_final: 0.6298 (m-80) REVERT: B 195 ILE cc_start: 0.7122 (mt) cc_final: 0.6901 (tt) REVERT: B 227 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6708 (tp-100) REVERT: C 33 THR cc_start: 0.7690 (p) cc_final: 0.7323 (m) REVERT: C 158 MET cc_start: 0.8316 (mmm) cc_final: 0.7868 (mmt) REVERT: C 170 GLU cc_start: 0.7704 (pp20) cc_final: 0.6768 (pp20) REVERT: C 171 TRP cc_start: 0.7498 (t60) cc_final: 0.6940 (t60) REVERT: C 207 MET cc_start: 0.6771 (mmt) cc_final: 0.6449 (mmt) REVERT: C 236 TYR cc_start: 0.7982 (p90) cc_final: 0.7469 (p90) outliers start: 33 outliers final: 24 residues processed: 170 average time/residue: 0.1747 time to fit residues: 37.9947 Evaluate side-chains 173 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 60 VAL Chi-restraints excluded: chain B residue 68 LYS 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 43 THR Chi-restraints excluded: chain C residue 174 VAL 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 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 0.0070 chunk 19 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 159 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.165237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149322 restraints weight = 8409.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.153796 restraints weight = 4136.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.156677 restraints weight = 2410.808| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5235 Z= 0.193 Angle : 0.620 6.370 7116 Z= 0.322 Chirality : 0.045 0.149 753 Planarity : 0.005 0.044 932 Dihedral : 6.743 46.104 774 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 7.40 % Allowed : 20.04 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.30), residues: 659 helix: -2.91 (0.79), residues: 34 sheet: -1.63 (0.41), residues: 165 loop : -3.02 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.032 0.002 PHE C 153 TYR 0.025 0.001 TYR B 93 ARG 0.004 0.000 ARG A 454 *********************** 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 183 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7248 (ptp-110) cc_final: 0.6903 (ptp-110) REVERT: A 365 TYR cc_start: 0.8433 (m-80) cc_final: 0.7686 (m-80) REVERT: A 378 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8105 (ttmt) REVERT: A 453 TYR cc_start: 0.7794 (p90) cc_final: 0.7302 (p90) REVERT: A 474 GLN cc_start: 0.7802 (tt0) cc_final: 0.7455 (tt0) REVERT: A 493 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6823 (ttt180) REVERT: B 25 THR cc_start: 0.7017 (OUTLIER) cc_final: 0.6704 (p) REVERT: B 34 SER cc_start: 0.7165 (t) cc_final: 0.6960 (p) REVERT: B 60 VAL cc_start: 0.6651 (OUTLIER) cc_final: 0.6403 (m) REVERT: B 85 GLU cc_start: 0.5472 (OUTLIER) cc_final: 0.4982 (pm20) REVERT: B 163 VAL cc_start: 0.8462 (m) cc_final: 0.8173 (p) REVERT: B 185 TYR cc_start: 0.6775 (m-80) cc_final: 0.6340 (m-80) REVERT: B 195 ILE cc_start: 0.7214 (mt) cc_final: 0.6889 (tt) REVERT: B 227 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6393 (tp-100) REVERT: C 33 THR cc_start: 0.7716 (p) cc_final: 0.7339 (m) REVERT: C 54 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7110 (mm-40) REVERT: C 98 TRP cc_start: 0.7447 (t-100) cc_final: 0.6417 (t-100) REVERT: C 158 MET cc_start: 0.8172 (mmm) cc_final: 0.7672 (mmt) REVERT: C 170 GLU cc_start: 0.7773 (pp20) cc_final: 0.6958 (pp20) REVERT: C 171 TRP cc_start: 0.7566 (t60) cc_final: 0.7047 (t60) REVERT: C 207 MET cc_start: 0.6088 (mmt) cc_final: 0.5618 (mmm) REVERT: C 236 TYR cc_start: 0.7847 (p90) cc_final: 0.7268 (p90) outliers start: 41 outliers final: 24 residues processed: 171 average time/residue: 0.1748 time to fit residues: 38.4679 Evaluate side-chains 168 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 388 ASN 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 60 VAL 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 109 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 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 C residue 5 THR Chi-restraints excluded: chain C residue 43 THR 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 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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** B 33 ASN ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.146636 restraints weight = 8436.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151028 restraints weight = 4167.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153921 restraints weight = 2438.155| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5235 Z= 0.253 Angle : 0.683 7.037 7116 Z= 0.357 Chirality : 0.047 0.175 753 Planarity : 0.005 0.044 932 Dihedral : 6.810 45.738 771 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 7.04 % Allowed : 20.22 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.30), residues: 659 helix: -3.13 (0.71), residues: 40 sheet: -1.91 (0.38), residues: 180 loop : -2.97 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 98 HIS 0.004 0.001 HIS B 41 PHE 0.033 0.002 PHE C 153 TYR 0.044 0.002 TYR B 93 ARG 0.009 0.001 ARG A 346 *********************** 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 191 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.6702 (tmt90) REVERT: A 357 ARG cc_start: 0.7251 (ptp-110) cc_final: 0.6871 (ptp-110) REVERT: A 365 TYR cc_start: 0.8445 (m-80) cc_final: 0.7673 (m-80) REVERT: A 374 PHE cc_start: 0.7724 (m-10) cc_final: 0.7512 (m-10) REVERT: A 378 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (ttmt) REVERT: A 453 TYR cc_start: 0.7870 (p90) cc_final: 0.7312 (p90) REVERT: A 493 ARG cc_start: 0.7212 (ttt180) cc_final: 0.6868 (ttt180) REVERT: B 25 THR cc_start: 0.7149 (OUTLIER) cc_final: 0.6846 (p) REVERT: B 34 SER cc_start: 0.7260 (t) cc_final: 0.7026 (p) REVERT: B 60 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.6182 (m) REVERT: B 85 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.5066 (pm20) REVERT: B 163 VAL cc_start: 0.8574 (m) cc_final: 0.8318 (p) REVERT: B 185 TYR cc_start: 0.6731 (m-80) cc_final: 0.6359 (m-80) REVERT: B 193 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7447 (m-80) REVERT: B 195 ILE cc_start: 0.7266 (mt) cc_final: 0.6953 (tt) REVERT: B 227 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6377 (tp-100) REVERT: B 231 TYR cc_start: 0.6518 (t80) cc_final: 0.6263 (t80) REVERT: C 33 THR cc_start: 0.7711 (p) cc_final: 0.7333 (m) REVERT: C 68 SER cc_start: 0.8589 (t) cc_final: 0.8319 (p) REVERT: C 158 MET cc_start: 0.8158 (mmm) cc_final: 0.7616 (mmt) REVERT: C 170 GLU cc_start: 0.7847 (pp20) cc_final: 0.7405 (pp20) REVERT: C 207 MET cc_start: 0.5983 (mmt) cc_final: 0.5678 (mmm) REVERT: C 236 TYR cc_start: 0.7808 (p90) cc_final: 0.7286 (p90) outliers start: 39 outliers final: 25 residues processed: 180 average time/residue: 0.1961 time to fit residues: 45.0187 Evaluate side-chains 183 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 395 VAL Chi-restraints excluded: chain A residue 402 ILE 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 60 VAL 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 109 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 43 optimal weight: 0.0040 chunk 21 optimal weight: 0.0870 chunk 16 optimal weight: 0.0370 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 overall best weight: 0.1648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.166678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150839 restraints weight = 8379.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155270 restraints weight = 4183.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.158165 restraints weight = 2445.804| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5235 Z= 0.166 Angle : 0.644 6.882 7116 Z= 0.333 Chirality : 0.046 0.148 753 Planarity : 0.005 0.045 932 Dihedral : 6.525 44.906 771 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 5.96 % Allowed : 21.48 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.31), residues: 659 helix: -2.59 (0.85), residues: 34 sheet: -1.46 (0.42), residues: 169 loop : -2.94 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 98 HIS 0.002 0.001 HIS C 159 PHE 0.034 0.002 PHE C 153 TYR 0.035 0.001 TYR B 93 ARG 0.005 0.000 ARG A 346 *********************** 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 180 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.7672 (m) cc_final: 0.7406 (p) REVERT: A 357 ARG cc_start: 0.7230 (ptp-110) cc_final: 0.6787 (ptp-110) REVERT: A 365 TYR cc_start: 0.8405 (m-80) cc_final: 0.7802 (m-80) REVERT: A 378 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8082 (ttmt) REVERT: A 451 TYR cc_start: 0.7214 (m-80) cc_final: 0.6921 (m-80) REVERT: A 453 TYR cc_start: 0.7784 (p90) cc_final: 0.7500 (p90) REVERT: A 474 GLN cc_start: 0.7622 (tt0) cc_final: 0.7353 (tp40) REVERT: B 25 THR cc_start: 0.7113 (OUTLIER) cc_final: 0.6793 (p) REVERT: B 60 VAL cc_start: 0.6594 (OUTLIER) cc_final: 0.6353 (m) REVERT: B 85 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.5044 (pm20) REVERT: B 102 PHE cc_start: 0.8417 (m-80) cc_final: 0.8131 (m-10) REVERT: B 163 VAL cc_start: 0.8544 (m) cc_final: 0.8300 (p) REVERT: B 185 TYR cc_start: 0.6379 (m-80) cc_final: 0.6091 (m-80) REVERT: B 193 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7120 (m-80) REVERT: B 195 ILE cc_start: 0.7155 (mt) cc_final: 0.6692 (tt) REVERT: B 208 MET cc_start: 0.3672 (OUTLIER) cc_final: 0.3290 (mpp) REVERT: B 227 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6368 (tp-100) REVERT: B 231 TYR cc_start: 0.6428 (t80) cc_final: 0.6207 (t80) REVERT: C 33 THR cc_start: 0.7634 (p) cc_final: 0.7304 (m) REVERT: C 54 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7028 (mm-40) REVERT: C 68 SER cc_start: 0.8686 (t) cc_final: 0.8422 (p) REVERT: C 149 SER cc_start: 0.7405 (p) cc_final: 0.7177 (m) REVERT: C 158 MET cc_start: 0.8193 (mmm) cc_final: 0.7664 (mmt) REVERT: C 170 GLU cc_start: 0.7910 (pp20) cc_final: 0.7511 (pp20) REVERT: C 236 TYR cc_start: 0.7670 (p90) cc_final: 0.7360 (p90) outliers start: 33 outliers final: 23 residues processed: 171 average time/residue: 0.1751 time to fit residues: 38.3253 Evaluate side-chains 176 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 395 VAL Chi-restraints excluded: chain A residue 402 ILE 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 60 VAL 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 193 PHE Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 208 MET 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 174 VAL 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 28 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 0.0270 chunk 30 optimal weight: 0.0000 chunk 48 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4109 r_free = 0.4109 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.151791 restraints weight = 8469.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156368 restraints weight = 4258.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159216 restraints weight = 2500.632| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5235 Z= 0.157 Angle : 0.630 7.229 7116 Z= 0.321 Chirality : 0.045 0.144 753 Planarity : 0.005 0.046 932 Dihedral : 6.317 44.942 770 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 5.05 % Allowed : 25.27 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.31), residues: 659 helix: -2.80 (0.76), residues: 40 sheet: -1.34 (0.42), residues: 169 loop : -2.87 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 98 HIS 0.002 0.000 HIS B 41 PHE 0.031 0.002 PHE C 153 TYR 0.033 0.001 TYR B 93 ARG 0.004 0.000 ARG A 346 *********************** 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 171 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7245 (ptp-110) cc_final: 0.6899 (ptp-110) REVERT: A 365 TYR cc_start: 0.8478 (m-80) cc_final: 0.7873 (m-80) REVERT: A 378 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8048 (ttmt) REVERT: A 474 GLN cc_start: 0.7601 (tt0) cc_final: 0.7349 (tp40) REVERT: B 25 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6882 (p) REVERT: B 49 MET cc_start: 0.5888 (mmm) cc_final: 0.5592 (mtt) REVERT: B 60 VAL cc_start: 0.6285 (OUTLIER) cc_final: 0.5969 (m) REVERT: B 85 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.5072 (pm20) REVERT: B 102 PHE cc_start: 0.8342 (m-80) cc_final: 0.8065 (m-10) REVERT: B 163 VAL cc_start: 0.8541 (m) cc_final: 0.8326 (p) REVERT: B 174 VAL cc_start: 0.8197 (p) cc_final: 0.7954 (m) REVERT: B 227 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6358 (tp-100) REVERT: C 33 THR cc_start: 0.7618 (p) cc_final: 0.7295 (m) REVERT: C 54 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7027 (mm-40) REVERT: C 68 SER cc_start: 0.8621 (t) cc_final: 0.8352 (p) REVERT: C 158 MET cc_start: 0.8216 (mmm) cc_final: 0.7713 (mmt) REVERT: C 170 GLU cc_start: 0.7936 (pp20) cc_final: 0.7541 (pp20) REVERT: C 236 TYR cc_start: 0.7616 (p90) cc_final: 0.7304 (p90) outliers start: 28 outliers final: 19 residues processed: 164 average time/residue: 0.1743 time to fit residues: 36.6721 Evaluate side-chains 165 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 60 VAL 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 155 VAL Chi-restraints excluded: chain B residue 172 GLU 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 C residue 71 SER 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 40 optimal weight: 0.6980 chunk 54 optimal weight: 0.0170 chunk 19 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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** A 477 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.165027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149115 restraints weight = 8295.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153595 restraints weight = 4097.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.156485 restraints weight = 2374.739| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5235 Z= 0.232 Angle : 0.682 8.078 7116 Z= 0.352 Chirality : 0.046 0.159 753 Planarity : 0.005 0.045 932 Dihedral : 6.567 45.339 770 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.57 % Favored : 85.43 % Rotamer: Outliers : 5.78 % Allowed : 24.19 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.32), residues: 659 helix: -3.13 (0.89), residues: 28 sheet: -1.43 (0.40), residues: 183 loop : -2.70 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.035 0.002 PHE C 153 TYR 0.039 0.002 TYR B 93 ARG 0.004 0.000 ARG A 403 *********************** 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 172 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: A 456 PHE cc_start: 0.8297 (m-80) cc_final: 0.8087 (m-10) REVERT: A 474 GLN cc_start: 0.7673 (tt0) cc_final: 0.7416 (tt0) REVERT: A 493 ARG cc_start: 0.7198 (ttt180) cc_final: 0.6975 (ttt180) REVERT: B 25 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6901 (p) REVERT: B 49 MET cc_start: 0.6071 (mmm) cc_final: 0.5647 (mtp) REVERT: B 85 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.5085 (pm20) REVERT: B 102 PHE cc_start: 0.8391 (m-80) cc_final: 0.8127 (m-10) REVERT: B 111 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.4097 (tm) REVERT: B 163 VAL cc_start: 0.8535 (m) cc_final: 0.8331 (p) REVERT: B 185 TYR cc_start: 0.6755 (m-80) cc_final: 0.6416 (m-80) REVERT: B 195 ILE cc_start: 0.7816 (tt) cc_final: 0.7188 (tt) REVERT: B 227 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6444 (tp-100) REVERT: C 33 THR cc_start: 0.7693 (p) cc_final: 0.7335 (m) REVERT: C 54 GLN cc_start: 0.7510 (mm-40) cc_final: 0.6945 (mm-40) REVERT: C 68 SER cc_start: 0.8683 (t) cc_final: 0.8424 (p) REVERT: C 158 MET cc_start: 0.8145 (mmm) cc_final: 0.7599 (mmt) REVERT: C 170 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7611 (pp20) REVERT: C 236 TYR cc_start: 0.7718 (p90) cc_final: 0.7281 (p90) outliers start: 32 outliers final: 24 residues processed: 164 average time/residue: 0.1772 time to fit residues: 36.9450 Evaluate side-chains 169 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 205 TYR 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 170 GLU Chi-restraints excluded: chain C residue 174 VAL 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 37 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.0170 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4058 r_free = 0.4058 target = 0.164370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148391 restraints weight = 8341.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152923 restraints weight = 4081.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155840 restraints weight = 2351.403| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5235 Z= 0.251 Angle : 0.705 7.774 7116 Z= 0.366 Chirality : 0.047 0.227 753 Planarity : 0.005 0.045 932 Dihedral : 6.677 44.707 769 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer: Outliers : 5.05 % Allowed : 25.27 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.31), residues: 659 helix: -3.51 (0.70), residues: 34 sheet: -1.24 (0.42), residues: 171 loop : -2.80 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 171 HIS 0.003 0.001 HIS B 41 PHE 0.034 0.002 PHE C 153 TYR 0.041 0.002 TYR B 93 ARG 0.005 0.001 ARG A 357 ********************** 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 169 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8050 (ttmt) REVERT: A 394 ASN cc_start: 0.7529 (p0) cc_final: 0.7288 (p0) REVERT: A 454 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7778 (tpp-160) REVERT: A 474 GLN cc_start: 0.7617 (tt0) cc_final: 0.7098 (tt0) REVERT: A 493 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6983 (ttt180) REVERT: B 25 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6899 (p) REVERT: B 85 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5098 (pm20) REVERT: B 102 PHE cc_start: 0.8404 (m-80) cc_final: 0.8105 (m-10) REVERT: B 111 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.4108 (tm) REVERT: B 185 TYR cc_start: 0.6976 (m-80) cc_final: 0.6595 (m-80) REVERT: B 195 ILE cc_start: 0.7789 (tt) cc_final: 0.7209 (tt) REVERT: B 227 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6527 (tp-100) REVERT: C 33 THR cc_start: 0.7685 (p) cc_final: 0.7364 (m) REVERT: C 68 SER cc_start: 0.8551 (t) cc_final: 0.8282 (p) REVERT: C 158 MET cc_start: 0.8131 (mmm) cc_final: 0.7578 (mmt) REVERT: C 170 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: C 236 TYR cc_start: 0.7676 (p90) cc_final: 0.7296 (p90) outliers start: 28 outliers final: 22 residues processed: 162 average time/residue: 0.1919 time to fit residues: 39.7883 Evaluate side-chains 167 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 205 TYR 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 96 LEU Chi-restraints excluded: chain C residue 170 GLU 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 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.0470 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.164339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148190 restraints weight = 8430.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.152712 restraints weight = 4098.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.155705 restraints weight = 2373.572| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5235 Z= 0.215 Angle : 0.689 7.442 7116 Z= 0.356 Chirality : 0.047 0.201 753 Planarity : 0.005 0.044 932 Dihedral : 6.641 44.706 769 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 5.23 % Allowed : 25.99 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.31), residues: 659 helix: -3.36 (0.74), residues: 34 sheet: -1.51 (0.40), residues: 185 loop : -2.69 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP C 171 HIS 0.003 0.001 HIS B 41 PHE 0.034 0.002 PHE C 153 TYR 0.038 0.002 TYR B 93 ARG 0.004 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.41 seconds wall clock time: 40 minutes 52.90 seconds (2452.90 seconds total)