Starting phenix.real_space_refine on Sun Mar 10 21:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/03_2024/7wop_32654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/03_2024/7wop_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/03_2024/7wop_32654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/03_2024/7wop_32654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/03_2024/7wop_32654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wop_32654/03_2024/7wop_32654.pdb" } 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 Residue "A ARG 346": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.24, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.75 Conformation dependent library (CDL) restraints added in 903.7 milliseconds 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1190 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 5.5% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 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: 1.12 Time building geometry restraints manager: 1.91 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: 100.51 - 107.20: 166 107.20 - 113.89: 2745 113.89 - 120.58: 1949 120.58 - 127.27: 2199 127.27 - 133.97: 57 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 2.440 nonbonded pdb=" O THR C 33 " pdb=" OH TYR C 236 " model vdw 2.233 2.440 nonbonded pdb=" OG SER C 27 " pdb=" OD1 ASP C 94 " model vdw 2.235 2.440 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 159 " model vdw 2.306 2.440 nonbonded pdb=" OG SER B 147 " pdb=" OG1 THR B 203 " model vdw 2.328 2.440 ... (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 ========== 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.580 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.180 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 0.553 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: 0.1722 time to fit residues: 42.8745 Evaluate side-chains 162 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 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 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: 2.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.0040 overall best weight: 0.4550 ------------------------------------------------------------------------------- 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 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 16 GLN C 39 GLN C 80 GLN C 97 ASN C 137 GLN C 206 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5235 Z= 0.221 Angle : 0.622 7.099 7116 Z= 0.319 Chirality : 0.045 0.223 753 Planarity : 0.005 0.049 932 Dihedral : 7.420 55.391 782 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.57 % Favored : 85.43 % Rotamer: Outliers : 7.40 % Allowed : 15.88 % Favored : 76.71 % 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: -4.36 (0.28), residues: 659 helix: -4.08 (0.52), residues: 34 sheet: -1.88 (0.41), residues: 145 loop : -3.42 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 241 HIS 0.005 0.001 HIS B 41 PHE 0.022 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 197 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8347 (m-80) cc_final: 0.7871 (m-80) REVERT: A 375 PHE cc_start: 0.7783 (m-10) cc_final: 0.7492 (m-10) REVERT: A 453 TYR cc_start: 0.7857 (p90) cc_final: 0.7250 (p90) REVERT: A 474 GLN cc_start: 0.7580 (tt0) cc_final: 0.7282 (tt0) REVERT: A 493 ARG cc_start: 0.7092 (ttt180) cc_final: 0.6789 (ttt180) REVERT: B 60 VAL cc_start: 0.6419 (OUTLIER) cc_final: 0.6114 (m) REVERT: B 185 TYR cc_start: 0.6958 (m-80) cc_final: 0.6655 (m-80) REVERT: B 195 ILE cc_start: 0.7219 (mt) cc_final: 0.6770 (tt) REVERT: B 227 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6563 (tp-100) REVERT: B 231 TYR cc_start: 0.6267 (t80) cc_final: 0.6055 (t80) REVERT: C 33 THR cc_start: 0.7626 (p) cc_final: 0.7348 (m) REVERT: C 68 SER cc_start: 0.8663 (t) cc_final: 0.8436 (p) REVERT: C 98 TRP cc_start: 0.7404 (t-100) cc_final: 0.6999 (t-100) REVERT: C 170 GLU cc_start: 0.7081 (pp20) cc_final: 0.6811 (pp20) REVERT: C 171 TRP cc_start: 0.7577 (t60) cc_final: 0.7335 (t60) REVERT: C 173 SER cc_start: 0.7724 (t) cc_final: 0.7372 (p) REVERT: C 236 TYR cc_start: 0.7844 (p90) cc_final: 0.7557 (p90) outliers start: 41 outliers final: 26 residues processed: 188 average time/residue: 0.1656 time to fit residues: 39.6821 Evaluate side-chains 180 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 225 SER Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 360 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 GLN C 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5235 Z= 0.284 Angle : 0.659 8.481 7116 Z= 0.344 Chirality : 0.047 0.187 753 Planarity : 0.005 0.048 932 Dihedral : 7.032 46.042 775 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 8.12 % Allowed : 18.59 % Favored : 73.29 % 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: -4.24 (0.29), residues: 659 helix: -3.83 (0.57), residues: 34 sheet: -2.06 (0.38), residues: 171 loop : -3.27 (0.25), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 98 HIS 0.005 0.001 HIS B 41 PHE 0.029 0.002 PHE C 153 TYR 0.016 0.002 TYR B 185 ARG 0.003 0.000 ARG C 224 *********************** 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 197 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.6158 (t80) REVERT: A 365 TYR cc_start: 0.8368 (m-80) cc_final: 0.7771 (m-80) REVERT: A 423 TYR cc_start: 0.7867 (t80) cc_final: 0.7634 (t80) REVERT: A 453 TYR cc_start: 0.7916 (p90) cc_final: 0.7270 (p90) REVERT: A 493 ARG cc_start: 0.7066 (ttt180) cc_final: 0.6839 (ttt180) REVERT: B 32 TYR cc_start: 0.7675 (m-80) cc_final: 0.7463 (m-80) REVERT: B 195 ILE cc_start: 0.7440 (mt) cc_final: 0.6899 (tt) REVERT: B 227 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6442 (tp-100) REVERT: B 231 TYR cc_start: 0.6706 (t80) cc_final: 0.6347 (t80) REVERT: C 33 THR cc_start: 0.7634 (p) cc_final: 0.7271 (m) REVERT: C 40 LEU cc_start: 0.8412 (mm) cc_final: 0.8197 (mp) REVERT: C 68 SER cc_start: 0.8629 (t) cc_final: 0.8358 (p) REVERT: C 236 TYR cc_start: 0.7889 (p90) cc_final: 0.7478 (p90) outliers start: 45 outliers final: 27 residues processed: 183 average time/residue: 0.1808 time to fit residues: 42.1313 Evaluate side-chains 177 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 88 TYR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 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 225 SER Chi-restraints excluded: chain C residue 248 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 6 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 209 ASN C 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3288 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= 0.184 Angle : 0.617 6.271 7116 Z= 0.317 Chirality : 0.045 0.139 753 Planarity : 0.005 0.045 932 Dihedral : 6.728 45.425 771 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 6.50 % Allowed : 22.92 % Favored : 70.58 % 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 (0.30), residues: 659 helix: -3.34 (0.71), residues: 34 sheet: -1.96 (0.38), residues: 180 loop : -3.11 (0.27), residues: 445 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 0.016 0.001 TYR B 93 ARG 0.007 0.000 ARG C 17 *********************** 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 178 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7159 (ptp-110) cc_final: 0.6921 (ptp-110) REVERT: A 365 TYR cc_start: 0.8312 (m-80) cc_final: 0.7740 (m-80) REVERT: A 433 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8105 (t) REVERT: A 453 TYR cc_start: 0.7823 (p90) cc_final: 0.7263 (p90) REVERT: A 493 ARG cc_start: 0.7033 (ttt180) cc_final: 0.6767 (ttt180) REVERT: B 102 PHE cc_start: 0.8648 (m-80) cc_final: 0.8392 (m-10) REVERT: B 185 TYR cc_start: 0.6944 (m-80) cc_final: 0.6475 (m-80) REVERT: B 193 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: B 227 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6427 (tp-100) REVERT: B 231 TYR cc_start: 0.6675 (t80) cc_final: 0.6301 (t80) REVERT: C 33 THR cc_start: 0.7610 (p) cc_final: 0.7173 (m) REVERT: C 40 LEU cc_start: 0.8341 (mm) cc_final: 0.8129 (mp) REVERT: C 68 SER cc_start: 0.8712 (t) cc_final: 0.8477 (p) REVERT: C 98 TRP cc_start: 0.7394 (t-100) cc_final: 0.7062 (t-100) REVERT: C 236 TYR cc_start: 0.7720 (p90) cc_final: 0.7276 (p90) outliers start: 36 outliers final: 25 residues processed: 166 average time/residue: 0.1676 time to fit residues: 35.3546 Evaluate side-chains 169 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 388 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 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 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 193 PHE Chi-restraints excluded: chain B residue 199 ASN 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 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5235 Z= 0.256 Angle : 0.649 6.032 7116 Z= 0.337 Chirality : 0.046 0.159 753 Planarity : 0.005 0.044 932 Dihedral : 6.947 48.881 771 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.39 % Favored : 83.61 % Rotamer: Outliers : 7.22 % Allowed : 23.29 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.07 (0.30), residues: 659 helix: -3.51 (0.61), residues: 41 sheet: -2.01 (0.38), residues: 166 loop : -3.10 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 171 HIS 0.004 0.001 HIS B 41 PHE 0.031 0.002 PHE C 153 TYR 0.032 0.002 TYR B 93 ARG 0.003 0.001 ARG C 17 *********************** 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 182 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6778 (tmt90) REVERT: A 357 ARG cc_start: 0.7173 (ptp-110) cc_final: 0.6950 (ptp-110) REVERT: A 423 TYR cc_start: 0.7833 (t80) cc_final: 0.7462 (t80) REVERT: A 453 TYR cc_start: 0.7919 (p90) cc_final: 0.7426 (p90) REVERT: A 474 GLN cc_start: 0.7542 (tt0) cc_final: 0.6568 (tt0) REVERT: A 493 ARG cc_start: 0.7062 (ttt180) cc_final: 0.6836 (ttt180) REVERT: B 25 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6932 (p) REVERT: B 102 PHE cc_start: 0.8640 (m-80) cc_final: 0.8366 (m-10) REVERT: B 174 VAL cc_start: 0.8484 (m) cc_final: 0.8264 (p) REVERT: B 185 TYR cc_start: 0.7328 (m-80) cc_final: 0.6900 (m-80) REVERT: B 195 ILE cc_start: 0.7623 (tp) cc_final: 0.7174 (tt) REVERT: B 227 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6330 (tp-100) REVERT: C 33 THR cc_start: 0.7671 (p) cc_final: 0.7106 (m) REVERT: C 40 LEU cc_start: 0.8454 (mm) cc_final: 0.8250 (mp) REVERT: C 68 SER cc_start: 0.8635 (t) cc_final: 0.8375 (p) REVERT: C 100 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: C 158 MET cc_start: 0.8335 (mmm) cc_final: 0.8112 (mmm) REVERT: C 170 GLU cc_start: 0.7416 (pp20) cc_final: 0.7168 (pp20) REVERT: C 236 TYR cc_start: 0.7612 (p90) cc_final: 0.7314 (p90) outliers start: 40 outliers final: 27 residues processed: 168 average time/residue: 0.1748 time to fit residues: 37.2088 Evaluate side-chains 170 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 433 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 88 TYR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 450 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** B 33 ASN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5235 Z= 0.318 Angle : 0.693 5.979 7116 Z= 0.362 Chirality : 0.048 0.163 753 Planarity : 0.005 0.046 932 Dihedral : 7.285 53.523 771 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Rotamer: Outliers : 8.30 % Allowed : 23.83 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.08 (0.29), residues: 659 helix: -3.16 (0.74), residues: 34 sheet: -1.99 (0.38), residues: 166 loop : -3.19 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 171 HIS 0.004 0.001 HIS B 41 PHE 0.032 0.002 PHE C 153 TYR 0.048 0.002 TYR B 93 ARG 0.005 0.001 ARG A 403 *********************** 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 187 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 141 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 355 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6870 (tmt90) REVERT: A 357 ARG cc_start: 0.7201 (ptp-110) cc_final: 0.6932 (ptp-110) REVERT: A 374 PHE cc_start: 0.7767 (m-10) cc_final: 0.7509 (m-10) REVERT: A 453 TYR cc_start: 0.7973 (p90) cc_final: 0.7410 (p90) REVERT: A 493 ARG cc_start: 0.7089 (ttt180) cc_final: 0.6877 (ttt180) REVERT: B 25 THR cc_start: 0.7255 (OUTLIER) cc_final: 0.6952 (p) REVERT: B 85 GLU cc_start: 0.5668 (OUTLIER) cc_final: 0.5197 (pm20) REVERT: B 102 PHE cc_start: 0.8500 (m-80) cc_final: 0.8225 (m-10) REVERT: B 174 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 227 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6414 (tp-100) REVERT: C 33 THR cc_start: 0.7687 (p) cc_final: 0.6890 (t) REVERT: C 68 SER cc_start: 0.8693 (t) cc_final: 0.8460 (p) REVERT: C 170 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7096 (pp20) REVERT: C 171 TRP cc_start: 0.8042 (t60) cc_final: 0.7631 (t60) outliers start: 46 outliers final: 31 residues processed: 169 average time/residue: 0.1779 time to fit residues: 38.0071 Evaluate side-chains 179 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU 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 54 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 88 TYR 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 174 VAL 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 199 ASN Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 170 GLU 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 7 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5235 Z= 0.254 Angle : 0.672 6.465 7116 Z= 0.351 Chirality : 0.047 0.168 753 Planarity : 0.005 0.046 932 Dihedral : 7.183 55.499 771 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 7.76 % Allowed : 25.63 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.29), residues: 659 helix: -3.33 (0.64), residues: 41 sheet: -2.01 (0.38), residues: 167 loop : -3.14 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.033 0.002 PHE C 153 TYR 0.044 0.002 TYR B 93 ARG 0.003 0.000 ARG A 403 *********************** 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 181 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6407 (t80) REVERT: A 355 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6878 (tmt90) REVERT: A 357 ARG cc_start: 0.7118 (ptp-110) cc_final: 0.6862 (ptp-110) REVERT: A 374 PHE cc_start: 0.7754 (m-10) cc_final: 0.7543 (m-10) REVERT: A 453 TYR cc_start: 0.7937 (p90) cc_final: 0.7479 (p90) REVERT: A 454 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7403 (tpp80) REVERT: B 25 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6898 (p) REVERT: B 85 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5176 (pm20) REVERT: B 111 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.4193 (tm) REVERT: B 174 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 185 TYR cc_start: 0.7301 (m-80) cc_final: 0.6971 (m-80) REVERT: B 193 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: B 227 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6311 (tp-100) REVERT: C 33 THR cc_start: 0.7490 (p) cc_final: 0.7089 (m) REVERT: C 68 SER cc_start: 0.8681 (t) cc_final: 0.8458 (p) REVERT: C 100 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: C 215 THR cc_start: 0.7517 (m) cc_final: 0.7259 (p) outliers start: 43 outliers final: 29 residues processed: 167 average time/residue: 0.1669 time to fit residues: 35.5820 Evaluate side-chains 180 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 142 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU 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 54 SER Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 88 TYR 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 174 VAL 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 199 ASN Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE 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 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.0050 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4234 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= 0.208 Angle : 0.652 6.698 7116 Z= 0.337 Chirality : 0.046 0.175 753 Planarity : 0.005 0.045 932 Dihedral : 7.092 57.936 771 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.54 % Favored : 83.46 % Rotamer: Outliers : 6.50 % Allowed : 26.90 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.30), residues: 659 helix: -3.70 (0.67), residues: 35 sheet: -1.90 (0.38), residues: 176 loop : -3.03 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 171 HIS 0.002 0.001 HIS B 41 PHE 0.033 0.002 PHE C 153 TYR 0.039 0.002 TYR B 93 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1318 Ramachandran restraints generated. 659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.6412 (t80) REVERT: A 355 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6886 (tmt90) REVERT: A 357 ARG cc_start: 0.7097 (ptp-110) cc_final: 0.6828 (ptp-110) REVERT: A 433 VAL cc_start: 0.8348 (t) cc_final: 0.8128 (t) REVERT: A 453 TYR cc_start: 0.7900 (p90) cc_final: 0.7476 (p90) REVERT: A 454 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7534 (tpp80) REVERT: B 25 THR cc_start: 0.7246 (OUTLIER) cc_final: 0.6943 (p) REVERT: B 85 GLU cc_start: 0.5567 (OUTLIER) cc_final: 0.5175 (pm20) REVERT: B 111 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4210 (tm) REVERT: B 174 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 185 TYR cc_start: 0.7192 (m-80) cc_final: 0.6824 (m-80) REVERT: B 227 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6216 (tp-100) REVERT: C 33 THR cc_start: 0.7453 (p) cc_final: 0.7051 (m) REVERT: C 68 SER cc_start: 0.8666 (t) cc_final: 0.8446 (p) REVERT: C 100 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7344 (m-10) outliers start: 36 outliers final: 26 residues processed: 165 average time/residue: 0.1709 time to fit residues: 35.8898 Evaluate side-chains 174 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 371 LEU 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 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 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE 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 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 450 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5235 Z= 0.306 Angle : 0.708 6.405 7116 Z= 0.371 Chirality : 0.048 0.197 753 Planarity : 0.005 0.044 932 Dihedral : 7.239 53.370 770 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.66 % Favored : 81.34 % Rotamer: Outliers : 7.04 % Allowed : 26.17 % Favored : 66.79 % 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: -3.97 (0.29), residues: 659 helix: -3.68 (0.65), residues: 35 sheet: -1.83 (0.40), residues: 154 loop : -3.07 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 171 HIS 0.004 0.001 HIS B 41 PHE 0.035 0.002 PHE C 153 TYR 0.046 0.002 TYR B 93 ARG 0.004 0.001 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 182 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.6665 (t80) REVERT: A 355 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.6914 (tmt90) REVERT: A 357 ARG cc_start: 0.7186 (ptp-110) cc_final: 0.6924 (ptp-110) REVERT: A 374 PHE cc_start: 0.7777 (m-10) cc_final: 0.7524 (m-10) REVERT: A 453 TYR cc_start: 0.8005 (p90) cc_final: 0.7352 (p90) REVERT: A 454 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7632 (tpp80) REVERT: B 25 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.6940 (p) REVERT: B 85 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.5257 (pm20) REVERT: B 111 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4238 (tm) REVERT: B 174 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 185 TYR cc_start: 0.7348 (m-80) cc_final: 0.7035 (m-80) REVERT: B 227 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6358 (tp-100) REVERT: C 33 THR cc_start: 0.7490 (p) cc_final: 0.7086 (m) REVERT: C 68 SER cc_start: 0.8776 (t) cc_final: 0.8529 (p) REVERT: C 100 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7373 (m-10) REVERT: C 215 THR cc_start: 0.7599 (m) cc_final: 0.7342 (p) outliers start: 39 outliers final: 29 residues processed: 170 average time/residue: 0.1679 time to fit residues: 36.5677 Evaluate side-chains 180 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 427 ASP 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 88 TYR 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 174 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE 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 64 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 5 optimal weight: 0.0870 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.0050 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5235 Z= 0.194 Angle : 0.656 7.218 7116 Z= 0.339 Chirality : 0.045 0.169 753 Planarity : 0.005 0.045 932 Dihedral : 6.858 45.675 770 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer: Outliers : 5.42 % Allowed : 28.52 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.30), residues: 659 helix: -3.40 (0.74), residues: 35 sheet: -1.70 (0.39), residues: 168 loop : -2.98 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 171 HIS 0.003 0.001 HIS C 159 PHE 0.033 0.002 PHE C 153 TYR 0.038 0.002 TYR B 93 ARG 0.004 0.000 ARG B 192 ********************** 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 171 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8017 (m) cc_final: 0.7666 (p) REVERT: A 355 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6802 (tmt90) REVERT: A 357 ARG cc_start: 0.7062 (ptp-110) cc_final: 0.6759 (ptp-110) REVERT: A 438 SER cc_start: 0.8607 (p) cc_final: 0.8225 (t) REVERT: A 453 TYR cc_start: 0.7890 (p90) cc_final: 0.7392 (p90) REVERT: B 25 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6846 (p) REVERT: B 71 ASN cc_start: 0.6617 (t0) cc_final: 0.6392 (t0) REVERT: B 85 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5245 (pm20) REVERT: B 111 LEU cc_start: 0.4599 (OUTLIER) cc_final: 0.4190 (tm) REVERT: B 174 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8178 (p) REVERT: B 185 TYR cc_start: 0.6984 (m-80) cc_final: 0.6610 (m-80) REVERT: B 227 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6222 (tp-100) REVERT: C 33 THR cc_start: 0.7327 (p) cc_final: 0.7022 (m) REVERT: C 68 SER cc_start: 0.8682 (t) cc_final: 0.8470 (p) REVERT: C 100 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: C 215 THR cc_start: 0.7485 (m) cc_final: 0.7120 (t) outliers start: 30 outliers final: 22 residues processed: 163 average time/residue: 0.1730 time to fit residues: 35.9698 Evaluate side-chains 169 residues out of total 555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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 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 174 VAL Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE 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 14 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 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 = 0.4001 r_free = 0.4001 target = 0.158881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.142967 restraints weight = 8219.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147357 restraints weight = 4155.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150136 restraints weight = 2449.862| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5235 Z= 0.251 Angle : 0.694 9.101 7116 Z= 0.355 Chirality : 0.046 0.175 753 Planarity : 0.005 0.045 932 Dihedral : 6.671 45.513 766 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.75 % Favored : 82.25 % Rotamer: Outliers : 5.96 % Allowed : 27.44 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.30), residues: 659 helix: -3.43 (0.71), residues: 35 sheet: -1.68 (0.40), residues: 162 loop : -3.00 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 98 HIS 0.003 0.001 HIS B 41 PHE 0.035 0.002 PHE C 153 TYR 0.043 0.002 TYR B 93 ARG 0.005 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.00 seconds wall clock time: 31 minutes 5.29 seconds (1865.29 seconds total)