Starting phenix.real_space_refine on Tue Mar 11 14:28:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wik_21684/03_2025/6wik_21684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wik_21684/03_2025/6wik_21684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2025/6wik_21684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2025/6wik_21684.map" model { file = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2025/6wik_21684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2025/6wik_21684_neut.cif" } resolution = 3.4 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= 0.002 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 33 5.16 5 C 3889 2.51 5 N 1029 2.21 5 O 1127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6078 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1348 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1437 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3293 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.36, per 1000 atoms: 0.55 Number of scatterers: 6078 At special positions: 0 Unit cell: (127.33, 115.56, 83.46, 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 33 16.00 O 1127 8.00 N 1029 7.00 C 3889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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: 1.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 45.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.524A pdb=" N ARG C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 209' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.729A pdb=" N TYR A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 33 " --> pdb=" O TYR A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 86 removed outlier: 3.971A pdb=" N GLY A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.722A pdb=" N ILE A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.519A pdb=" N ALA A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 200 Proline residue: A 189 - end of helix removed outlier: 3.507A pdb=" N TYR A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.839A pdb=" N GLN A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.922A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 removed outlier: 3.528A pdb=" N GLY A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 484 Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.667A pdb=" N ILE A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.800A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 4.154A pdb=" N THR C 117 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.809A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 87 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.580A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 211 through 216 removed outlier: 3.685A pdb=" N TYR C 212 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.491A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.773A pdb=" N VAL D 167 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 179 389 hydrogen bonds defined for protein. 1092 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: 1.61 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1392 1.33 - 1.45: 1395 1.45 - 1.57: 3348 1.57 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6189 Sorted by residual: bond pdb=" N ILE A 203 " pdb=" CA ILE A 203 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.16e-02 7.43e+03 1.17e+01 bond pdb=" N ILE C 126 " pdb=" CA ILE C 126 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 9.99e+00 bond pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.73e+00 bond pdb=" N GLU C 128 " pdb=" CA GLU C 128 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.35e+00 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 7099 1.76 - 3.52: 1207 3.52 - 5.28: 113 5.28 - 7.04: 20 7.04 - 8.80: 3 Bond angle restraints: 8442 Sorted by residual: angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 111.43 -8.18 1.05e+00 9.07e-01 6.07e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 109.48 -6.17 8.90e-01 1.26e+00 4.81e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 110.29 -7.04 1.05e+00 9.07e-01 4.50e+01 angle pdb=" N PRO D 144 " pdb=" CA PRO D 144 " pdb=" CB PRO D 144 " ideal model delta sigma weight residual 102.85 110.34 -7.49 1.13e+00 7.83e-01 4.40e+01 angle pdb=" N PRO D 237 " pdb=" CA PRO D 237 " pdb=" CB PRO D 237 " ideal model delta sigma weight residual 103.25 110.18 -6.93 1.05e+00 9.07e-01 4.35e+01 ... (remaining 8437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 3270 16.56 - 33.12: 247 33.12 - 49.69: 58 49.69 - 66.25: 12 66.25 - 82.81: 7 Dihedral angle restraints: 3594 sinusoidal: 1136 harmonic: 2458 Sorted by residual: dihedral pdb=" CA GLY D 27 " pdb=" C GLY D 27 " pdb=" N ALA D 28 " pdb=" CA ALA D 28 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU D 30 " pdb=" C LEU D 30 " pdb=" N VAL D 31 " pdb=" CA VAL D 31 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL D 161 " pdb=" C VAL D 161 " pdb=" N THR D 162 " pdb=" CA THR D 162 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 596 0.061 - 0.121: 273 0.121 - 0.182: 108 0.182 - 0.242: 30 0.242 - 0.303: 1 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA TYR D 121 " pdb=" N TYR D 121 " pdb=" C TYR D 121 " pdb=" CB TYR D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA THR D 110 " pdb=" N THR D 110 " pdb=" C THR D 110 " pdb=" CB THR D 110 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL D 112 " pdb=" N VAL D 112 " pdb=" C VAL D 112 " pdb=" CB VAL D 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1005 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C GLU A 165 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 166 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 364 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ARG A 364 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG A 364 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 365 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 63 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO C 64 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.031 5.00e-02 4.00e+02 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 153 2.64 - 3.21: 6067 3.21 - 3.77: 9202 3.77 - 4.34: 11554 4.34 - 4.90: 19877 Nonbonded interactions: 46853 Sorted by model distance: nonbonded pdb=" O ASN A 549 " pdb=" ND2 ASN A 549 " model vdw 2.078 3.120 nonbonded pdb=" O CYS A 387 " pdb=" OG SER A 390 " model vdw 2.254 3.040 nonbonded pdb=" O PHE A 114 " pdb=" OD2 ASP A 118 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 379 " pdb=" OG SER A 382 " model vdw 2.304 3.040 nonbonded pdb=" O LEU A 322 " pdb=" CD1 LEU A 322 " model vdw 2.315 3.460 ... (remaining 46848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.560 Find NCS groups from input model: 0.090 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 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 : 0.012 0.086 6189 Z= 0.801 Angle : 1.274 8.804 8442 Z= 0.933 Chirality : 0.080 0.303 1008 Planarity : 0.005 0.056 1070 Dihedral : 13.633 82.811 2016 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 2.24 % Allowed : 10.48 % Favored : 87.28 % Rotamer: Outliers : 2.55 % Allowed : 16.03 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.88 (0.26), residues: 849 helix: -2.15 (0.25), residues: 354 sheet: -1.58 (0.36), residues: 188 loop : -3.58 (0.29), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 69 HIS 0.008 0.002 HIS A 116 PHE 0.021 0.002 PHE D 126 TYR 0.018 0.002 TYR C 111 ARG 0.015 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 285 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 74 ASN cc_start: 0.6497 (p0) cc_final: 0.6236 (p0) REVERT: A 44 PHE cc_start: 0.8550 (t80) cc_final: 0.8163 (t80) REVERT: A 112 MET cc_start: 0.8045 (mmm) cc_final: 0.7716 (tmm) REVERT: A 119 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8704 (tp30) REVERT: A 297 ASP cc_start: 0.9226 (m-30) cc_final: 0.8660 (m-30) REVERT: A 299 TRP cc_start: 0.7513 (t60) cc_final: 0.7299 (t60) REVERT: A 312 MET cc_start: 0.8444 (mmm) cc_final: 0.8095 (mmm) REVERT: A 321 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7230 (p) REVERT: A 366 LYS cc_start: 0.8560 (tttt) cc_final: 0.7946 (tptt) REVERT: A 393 MET cc_start: 0.8798 (mtt) cc_final: 0.8552 (mpp) REVERT: A 474 ASP cc_start: 0.8918 (t0) cc_final: 0.8607 (t0) REVERT: A 504 LEU cc_start: 0.9246 (mm) cc_final: 0.8710 (mm) outliers start: 14 outliers final: 2 residues processed: 292 average time/residue: 0.1929 time to fit residues: 71.8210 Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 321 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN A 125 HIS A 141 ASN ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN A 498 ASN A 544 GLN A 549 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.092922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073963 restraints weight = 19838.760| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 5.34 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6189 Z= 0.236 Angle : 0.771 10.610 8442 Z= 0.394 Chirality : 0.044 0.179 1008 Planarity : 0.004 0.042 1070 Dihedral : 4.654 26.823 911 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.24 % Favored : 92.93 % Rotamer: Outliers : 6.56 % Allowed : 26.59 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.62 (0.28), residues: 849 helix: 0.22 (0.25), residues: 377 sheet: -0.99 (0.37), residues: 187 loop : -2.84 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 69 HIS 0.008 0.002 HIS A 536 PHE 0.027 0.002 PHE A 460 TYR 0.016 0.002 TYR D 121 ARG 0.005 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: C 26 GLN cc_start: 0.6559 (mt0) cc_final: 0.6278 (mt0) REVERT: C 62 GLN cc_start: 0.7705 (mp10) cc_final: 0.7372 (mp10) REVERT: C 74 ARG cc_start: 0.8440 (ttt180) cc_final: 0.8209 (ttt180) REVERT: C 101 GLU cc_start: 0.8989 (mp0) cc_final: 0.8523 (pm20) REVERT: C 102 ASP cc_start: 0.8557 (m-30) cc_final: 0.7949 (m-30) REVERT: D 30 LEU cc_start: 0.9466 (mp) cc_final: 0.9114 (tt) REVERT: D 32 ARG cc_start: 0.9305 (mmm-85) cc_final: 0.8931 (tpp80) REVERT: D 83 PHE cc_start: 0.8498 (m-80) cc_final: 0.8250 (m-10) REVERT: D 86 LYS cc_start: 0.8417 (ptmm) cc_final: 0.7834 (ptmt) REVERT: D 127 ASP cc_start: 0.8806 (t0) cc_final: 0.8596 (t0) REVERT: A 42 TRP cc_start: 0.9108 (t-100) cc_final: 0.8893 (t-100) REVERT: A 112 MET cc_start: 0.8120 (mmm) cc_final: 0.7857 (tmm) REVERT: A 119 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8697 (tp30) REVERT: A 366 LYS cc_start: 0.8573 (tttt) cc_final: 0.8096 (tptt) REVERT: A 393 MET cc_start: 0.8818 (mtt) cc_final: 0.8553 (mpp) REVERT: A 474 ASP cc_start: 0.9084 (t0) cc_final: 0.8870 (t0) REVERT: A 511 MET cc_start: 0.8469 (mmp) cc_final: 0.8196 (mmm) REVERT: A 534 MET cc_start: 0.9027 (mtm) cc_final: 0.8638 (ttp) REVERT: A 538 MET cc_start: 0.8842 (ttp) cc_final: 0.8387 (ttp) outliers start: 36 outliers final: 22 residues processed: 238 average time/residue: 0.1748 time to fit residues: 54.1834 Evaluate side-chains 210 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 69 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 40.0000 chunk 64 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.0030 overall best weight: 2.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.089135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070571 restraints weight = 20744.670| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 5.21 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6189 Z= 0.297 Angle : 0.737 8.685 8442 Z= 0.381 Chirality : 0.044 0.174 1008 Planarity : 0.004 0.040 1070 Dihedral : 4.353 22.049 907 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.24 % Favored : 92.93 % Rotamer: Outliers : 7.29 % Allowed : 28.60 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.54 (0.29), residues: 849 helix: 1.23 (0.27), residues: 376 sheet: -0.48 (0.38), residues: 190 loop : -2.49 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 158 HIS 0.012 0.003 HIS A 536 PHE 0.014 0.002 PHE A 473 TYR 0.019 0.002 TYR A 502 ARG 0.005 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8763 (tppt) REVERT: C 62 GLN cc_start: 0.7776 (mp10) cc_final: 0.7400 (mp10) REVERT: C 99 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8542 (tp40) REVERT: C 101 GLU cc_start: 0.8956 (mp0) cc_final: 0.8642 (pm20) REVERT: C 102 ASP cc_start: 0.8515 (m-30) cc_final: 0.8046 (m-30) REVERT: D 32 ARG cc_start: 0.9303 (mmm-85) cc_final: 0.9036 (tpp80) REVERT: D 59 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8164 (mtt-85) REVERT: D 71 ASP cc_start: 0.8272 (t0) cc_final: 0.7537 (t0) REVERT: D 74 ASN cc_start: 0.8492 (p0) cc_final: 0.7624 (p0) REVERT: D 76 ASN cc_start: 0.8152 (m110) cc_final: 0.7256 (m110) REVERT: D 82 LYS cc_start: 0.9202 (ptpt) cc_final: 0.8970 (pttt) REVERT: D 86 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8085 (ptmt) REVERT: D 99 TYR cc_start: 0.8583 (m-80) cc_final: 0.8285 (m-10) REVERT: A 309 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 366 LYS cc_start: 0.8596 (tttt) cc_final: 0.8097 (tptt) REVERT: A 393 MET cc_start: 0.8801 (mtt) cc_final: 0.8205 (mmt) REVERT: A 467 ARG cc_start: 0.8945 (mmm-85) cc_final: 0.8710 (mmm160) REVERT: A 511 MET cc_start: 0.8580 (mmp) cc_final: 0.8297 (mmm) REVERT: A 538 MET cc_start: 0.8891 (ttp) cc_final: 0.8539 (ttp) outliers start: 40 outliers final: 29 residues processed: 222 average time/residue: 0.1768 time to fit residues: 51.0614 Evaluate side-chains 214 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 17 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN C 47 GLN A 125 HIS A 182 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.087732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069363 restraints weight = 21141.605| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 5.19 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6189 Z= 0.295 Angle : 0.719 8.205 8442 Z= 0.372 Chirality : 0.043 0.177 1008 Planarity : 0.004 0.039 1070 Dihedral : 4.297 25.546 907 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.89 % Favored : 93.29 % Rotamer: Outliers : 10.75 % Allowed : 28.05 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.33 (0.30), residues: 849 helix: 1.27 (0.27), residues: 380 sheet: -0.27 (0.38), residues: 190 loop : -2.31 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 127 HIS 0.012 0.003 HIS A 536 PHE 0.015 0.002 PHE C 30 TYR 0.014 0.002 TYR A 502 ARG 0.003 0.001 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7667 (mmm) cc_final: 0.6717 (ttm) REVERT: C 44 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8877 (tppt) REVERT: C 62 GLN cc_start: 0.7895 (mp10) cc_final: 0.7517 (mp10) REVERT: C 99 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8272 (tp-100) REVERT: C 101 GLU cc_start: 0.9023 (mp0) cc_final: 0.8710 (pm20) REVERT: C 102 ASP cc_start: 0.8463 (m-30) cc_final: 0.7846 (m-30) REVERT: D 32 ARG cc_start: 0.9372 (mmm-85) cc_final: 0.9087 (tpp80) REVERT: D 59 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8139 (mtt-85) REVERT: D 69 TRP cc_start: 0.7831 (p-90) cc_final: 0.7404 (p-90) REVERT: D 71 ASP cc_start: 0.8263 (t0) cc_final: 0.7974 (t0) REVERT: D 74 ASN cc_start: 0.8316 (p0) cc_final: 0.8089 (p0) REVERT: D 86 LYS cc_start: 0.8465 (ptmm) cc_final: 0.8025 (ptmt) REVERT: D 99 TYR cc_start: 0.8584 (m-80) cc_final: 0.8241 (m-10) REVERT: A 75 LEU cc_start: 0.9388 (tp) cc_final: 0.8985 (tp) REVERT: A 309 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7531 (mm) REVERT: A 312 MET cc_start: 0.8347 (mmm) cc_final: 0.7925 (mmm) REVERT: A 366 LYS cc_start: 0.8566 (tttt) cc_final: 0.8064 (tptt) REVERT: A 393 MET cc_start: 0.8843 (mtt) cc_final: 0.8248 (mmt) REVERT: A 508 HIS cc_start: 0.8663 (t-90) cc_final: 0.8332 (t-90) REVERT: A 511 MET cc_start: 0.8715 (mmp) cc_final: 0.8373 (mmm) REVERT: A 538 MET cc_start: 0.8939 (ttp) cc_final: 0.8550 (ttp) outliers start: 59 outliers final: 46 residues processed: 221 average time/residue: 0.1757 time to fit residues: 50.7098 Evaluate side-chains 223 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 ASN A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.089049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070611 restraints weight = 20794.566| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 5.16 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6189 Z= 0.225 Angle : 0.703 8.715 8442 Z= 0.357 Chirality : 0.042 0.175 1008 Planarity : 0.004 0.041 1070 Dihedral : 4.097 20.341 907 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.42 % Favored : 93.76 % Rotamer: Outliers : 7.83 % Allowed : 32.79 % Favored : 59.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.05 (0.30), residues: 849 helix: 1.44 (0.27), residues: 379 sheet: -0.11 (0.38), residues: 184 loop : -2.02 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 127 HIS 0.011 0.002 HIS A 536 PHE 0.017 0.001 PHE C 30 TYR 0.017 0.001 TYR C 56 ARG 0.002 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 MET cc_start: 0.8270 (mmm) cc_final: 0.7959 (mmm) REVERT: C 44 LYS cc_start: 0.9211 (ttmm) cc_final: 0.8876 (tppt) REVERT: C 62 GLN cc_start: 0.7777 (mp10) cc_final: 0.7421 (mp10) REVERT: C 65 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7705 (ptmm) REVERT: C 102 ASP cc_start: 0.8477 (m-30) cc_final: 0.7836 (m-30) REVERT: D 32 ARG cc_start: 0.9363 (mmm-85) cc_final: 0.9106 (tpp80) REVERT: D 59 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7962 (mtt-85) REVERT: D 69 TRP cc_start: 0.7978 (p-90) cc_final: 0.7468 (p-90) REVERT: D 71 ASP cc_start: 0.8144 (t0) cc_final: 0.7917 (t70) REVERT: D 74 ASN cc_start: 0.8180 (p0) cc_final: 0.7726 (p0) REVERT: D 78 ILE cc_start: 0.8663 (mp) cc_final: 0.8325 (tp) REVERT: D 86 LYS cc_start: 0.8470 (ptmm) cc_final: 0.7815 (ptmt) REVERT: D 99 TYR cc_start: 0.8573 (m-80) cc_final: 0.8246 (m-10) REVERT: D 108 GLU cc_start: 0.9387 (pm20) cc_final: 0.9119 (pm20) REVERT: A 85 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8300 (mtmm) REVERT: A 309 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 312 MET cc_start: 0.8343 (mmm) cc_final: 0.7897 (mmm) REVERT: A 366 LYS cc_start: 0.8535 (tttt) cc_final: 0.8017 (tptt) REVERT: A 508 HIS cc_start: 0.8632 (t-90) cc_final: 0.8272 (t-90) REVERT: A 511 MET cc_start: 0.8694 (mmp) cc_final: 0.8290 (mmm) REVERT: A 538 MET cc_start: 0.8895 (ttp) cc_final: 0.8518 (ttp) outliers start: 43 outliers final: 35 residues processed: 212 average time/residue: 0.1671 time to fit residues: 46.8170 Evaluate side-chains 216 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 546 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 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 = 0.3555 r_free = 0.3555 target = 0.084051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065759 restraints weight = 21277.218| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 5.07 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 6189 Z= 0.442 Angle : 0.799 9.373 8442 Z= 0.419 Chirality : 0.044 0.162 1008 Planarity : 0.004 0.037 1070 Dihedral : 4.388 20.309 907 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.48 % Favored : 92.82 % Rotamer: Outliers : 9.84 % Allowed : 33.15 % Favored : 57.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.45 (0.30), residues: 849 helix: 1.01 (0.26), residues: 379 sheet: -0.23 (0.37), residues: 201 loop : -2.22 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 127 HIS 0.012 0.002 HIS A 536 PHE 0.015 0.002 PHE C 30 TYR 0.017 0.002 TYR C 111 ARG 0.004 0.001 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 179 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6951 (ttp) REVERT: C 31 MET cc_start: 0.8282 (mmm) cc_final: 0.8054 (mmm) REVERT: C 62 GLN cc_start: 0.7920 (mp10) cc_final: 0.7517 (mp10) REVERT: C 101 GLU cc_start: 0.8727 (pm20) cc_final: 0.8418 (pm20) REVERT: C 102 ASP cc_start: 0.8709 (m-30) cc_final: 0.8290 (m-30) REVERT: D 32 ARG cc_start: 0.9365 (mmm-85) cc_final: 0.9077 (tpp80) REVERT: D 59 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8125 (mtt-85) REVERT: D 71 ASP cc_start: 0.8211 (t0) cc_final: 0.7964 (t0) REVERT: D 74 ASN cc_start: 0.8301 (p0) cc_final: 0.7902 (p0) REVERT: D 86 LYS cc_start: 0.8470 (ptmm) cc_final: 0.7654 (ptmt) REVERT: D 101 GLN cc_start: 0.8807 (tp40) cc_final: 0.8569 (tp40) REVERT: A 217 CYS cc_start: 0.9243 (t) cc_final: 0.8870 (m) REVERT: A 309 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7675 (mm) REVERT: A 366 LYS cc_start: 0.8616 (tttt) cc_final: 0.8082 (tptt) REVERT: A 506 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8803 (mm) REVERT: A 508 HIS cc_start: 0.8726 (t-90) cc_final: 0.8147 (t-90) REVERT: A 534 MET cc_start: 0.9146 (mtm) cc_final: 0.8795 (ttt) REVERT: A 538 MET cc_start: 0.8956 (ttp) cc_final: 0.8570 (ttp) outliers start: 54 outliers final: 46 residues processed: 203 average time/residue: 0.1675 time to fit residues: 44.6549 Evaluate side-chains 216 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 546 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 11 optimal weight: 40.0000 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069103 restraints weight = 20822.934| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 5.13 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6189 Z= 0.218 Angle : 0.726 10.320 8442 Z= 0.369 Chirality : 0.042 0.161 1008 Planarity : 0.003 0.041 1070 Dihedral : 4.193 22.461 907 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.83 % Favored : 94.46 % Rotamer: Outliers : 7.65 % Allowed : 34.24 % Favored : 58.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.02 (0.30), residues: 849 helix: 1.35 (0.27), residues: 379 sheet: -0.02 (0.38), residues: 191 loop : -1.94 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 127 HIS 0.011 0.002 HIS A 536 PHE 0.013 0.001 PHE C 30 TYR 0.013 0.001 TYR A 502 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7658 (mmm) cc_final: 0.7177 (ttm) REVERT: C 31 MET cc_start: 0.8215 (mmm) cc_final: 0.7992 (mmm) REVERT: C 44 LYS cc_start: 0.9227 (ttmm) cc_final: 0.8932 (tppt) REVERT: C 62 GLN cc_start: 0.7878 (mp10) cc_final: 0.7626 (mp10) REVERT: C 90 ASP cc_start: 0.8985 (m-30) cc_final: 0.8246 (m-30) REVERT: C 102 ASP cc_start: 0.8771 (m-30) cc_final: 0.8291 (m-30) REVERT: D 32 ARG cc_start: 0.9367 (mmm-85) cc_final: 0.9099 (tpp80) REVERT: D 59 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7947 (mtt-85) REVERT: D 74 ASN cc_start: 0.8238 (p0) cc_final: 0.7867 (p0) REVERT: D 79 TYR cc_start: 0.8629 (m-80) cc_final: 0.8245 (m-80) REVERT: D 86 LYS cc_start: 0.8530 (ptmm) cc_final: 0.7757 (ptmt) REVERT: D 99 TYR cc_start: 0.8712 (m-80) cc_final: 0.8434 (m-10) REVERT: D 101 GLN cc_start: 0.8886 (tp40) cc_final: 0.8570 (tp40) REVERT: D 108 GLU cc_start: 0.9407 (pm20) cc_final: 0.9161 (pm20) REVERT: A 196 MET cc_start: 0.8616 (ptt) cc_final: 0.8366 (ppp) REVERT: A 217 CYS cc_start: 0.9223 (t) cc_final: 0.8884 (m) REVERT: A 309 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7431 (mm) REVERT: A 312 MET cc_start: 0.8239 (mmm) cc_final: 0.7860 (mmm) REVERT: A 366 LYS cc_start: 0.8577 (tttt) cc_final: 0.8049 (tptt) REVERT: A 508 HIS cc_start: 0.8547 (t70) cc_final: 0.8235 (t-90) REVERT: A 511 MET cc_start: 0.8874 (mmp) cc_final: 0.8475 (mmm) REVERT: A 534 MET cc_start: 0.9053 (mtm) cc_final: 0.8615 (ttp) REVERT: A 538 MET cc_start: 0.8903 (ttp) cc_final: 0.8500 (ttp) outliers start: 42 outliers final: 35 residues processed: 212 average time/residue: 0.1692 time to fit residues: 46.8826 Evaluate side-chains 222 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 546 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 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 = 0.3543 r_free = 0.3543 target = 0.083521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.065771 restraints weight = 21061.484| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.97 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 6189 Z= 0.372 Angle : 0.780 9.824 8442 Z= 0.405 Chirality : 0.044 0.163 1008 Planarity : 0.004 0.036 1070 Dihedral : 4.380 21.606 907 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.71 % Favored : 92.82 % Rotamer: Outliers : 8.74 % Allowed : 34.43 % Favored : 56.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.25 (0.30), residues: 849 helix: 1.19 (0.26), residues: 378 sheet: -0.14 (0.37), residues: 197 loop : -2.11 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP D 69 HIS 0.011 0.002 HIS A 536 PHE 0.013 0.002 PHE C 30 TYR 0.019 0.002 TYR D 122 ARG 0.005 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7581 (mmm) cc_final: 0.6875 (ttp) REVERT: C 31 MET cc_start: 0.8237 (mmm) cc_final: 0.7987 (mmm) REVERT: C 62 GLN cc_start: 0.8033 (mp10) cc_final: 0.7623 (mp10) REVERT: C 102 ASP cc_start: 0.8939 (m-30) cc_final: 0.8542 (m-30) REVERT: D 32 ARG cc_start: 0.9369 (mmm-85) cc_final: 0.9138 (tpp80) REVERT: D 59 ARG cc_start: 0.8302 (mtp85) cc_final: 0.8073 (mtt-85) REVERT: D 71 ASP cc_start: 0.7926 (t0) cc_final: 0.7713 (t0) REVERT: D 74 ASN cc_start: 0.8324 (p0) cc_final: 0.8111 (p0) REVERT: D 86 LYS cc_start: 0.8571 (ptmm) cc_final: 0.7773 (ptmt) REVERT: D 101 GLN cc_start: 0.8844 (tp40) cc_final: 0.8495 (tp40) REVERT: A 196 MET cc_start: 0.8625 (ptt) cc_final: 0.8375 (ppp) REVERT: A 309 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7542 (mm) REVERT: A 312 MET cc_start: 0.8348 (mmm) cc_final: 0.7942 (mmm) REVERT: A 366 LYS cc_start: 0.8512 (tttt) cc_final: 0.7960 (tptt) REVERT: A 506 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8735 (mm) REVERT: A 508 HIS cc_start: 0.8526 (t70) cc_final: 0.8036 (t-90) REVERT: A 511 MET cc_start: 0.9011 (mmp) cc_final: 0.8604 (mmm) REVERT: A 534 MET cc_start: 0.9135 (mtm) cc_final: 0.8779 (ttt) REVERT: A 538 MET cc_start: 0.8947 (ttp) cc_final: 0.8533 (ttp) outliers start: 48 outliers final: 39 residues processed: 195 average time/residue: 0.1740 time to fit residues: 44.5561 Evaluate side-chains 212 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 546 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 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 = 0.3581 r_free = 0.3581 target = 0.085601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067722 restraints weight = 20800.118| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 5.01 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6189 Z= 0.247 Angle : 0.762 10.618 8442 Z= 0.384 Chirality : 0.043 0.173 1008 Planarity : 0.004 0.038 1070 Dihedral : 4.279 22.457 907 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.01 % Favored : 93.52 % Rotamer: Outliers : 7.47 % Allowed : 35.34 % Favored : 57.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.00 (0.30), residues: 849 helix: 1.43 (0.26), residues: 378 sheet: -0.24 (0.37), residues: 194 loop : -1.81 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 69 HIS 0.011 0.002 HIS A 536 PHE 0.041 0.002 PHE A 460 TYR 0.030 0.002 TYR D 52 ARG 0.003 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7667 (mmm) cc_final: 0.6997 (ttp) REVERT: C 31 MET cc_start: 0.8229 (mmm) cc_final: 0.7999 (mmm) REVERT: C 44 LYS cc_start: 0.9168 (ttmm) cc_final: 0.8821 (tppt) REVERT: C 62 GLN cc_start: 0.7952 (mp10) cc_final: 0.7688 (mp10) REVERT: C 102 ASP cc_start: 0.8911 (m-30) cc_final: 0.8460 (m-30) REVERT: D 32 ARG cc_start: 0.9360 (mmm-85) cc_final: 0.9105 (tpp80) REVERT: D 59 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8081 (mtt-85) REVERT: D 74 ASN cc_start: 0.8266 (p0) cc_final: 0.8057 (p0) REVERT: D 84 GLN cc_start: 0.9273 (tt0) cc_final: 0.8672 (mm110) REVERT: D 86 LYS cc_start: 0.8554 (ptmm) cc_final: 0.7896 (ptmt) REVERT: D 99 TYR cc_start: 0.8747 (m-80) cc_final: 0.8469 (m-10) REVERT: D 101 GLN cc_start: 0.8840 (tp40) cc_final: 0.8578 (tp40) REVERT: A 165 GLU cc_start: 0.9101 (mp0) cc_final: 0.8206 (mp0) REVERT: A 196 MET cc_start: 0.8622 (ptt) cc_final: 0.8381 (ppp) REVERT: A 217 CYS cc_start: 0.9194 (t) cc_final: 0.8843 (m) REVERT: A 309 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7407 (mm) REVERT: A 312 MET cc_start: 0.8229 (mmm) cc_final: 0.7835 (mmm) REVERT: A 321 VAL cc_start: 0.8203 (m) cc_final: 0.7820 (m) REVERT: A 366 LYS cc_start: 0.8520 (tttt) cc_final: 0.7990 (tptt) REVERT: A 464 ILE cc_start: 0.8934 (mm) cc_final: 0.8472 (mm) REVERT: A 508 HIS cc_start: 0.8545 (t70) cc_final: 0.8179 (t-90) REVERT: A 511 MET cc_start: 0.8962 (mmp) cc_final: 0.8628 (mmm) REVERT: A 534 MET cc_start: 0.9087 (mtm) cc_final: 0.8635 (ttp) REVERT: A 538 MET cc_start: 0.8936 (ttp) cc_final: 0.8513 (ttp) outliers start: 41 outliers final: 35 residues processed: 207 average time/residue: 0.1734 time to fit residues: 46.8361 Evaluate side-chains 215 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 546 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 19 optimal weight: 0.0370 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 380 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 = 0.3580 r_free = 0.3580 target = 0.085623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067741 restraints weight = 21002.861| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.02 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.6491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6189 Z= 0.261 Angle : 0.772 10.299 8442 Z= 0.389 Chirality : 0.044 0.174 1008 Planarity : 0.004 0.038 1070 Dihedral : 4.382 24.316 907 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.71 % Favored : 92.93 % Rotamer: Outliers : 7.10 % Allowed : 36.07 % Favored : 56.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.02 (0.30), residues: 849 helix: 1.40 (0.26), residues: 378 sheet: -0.21 (0.37), residues: 194 loop : -1.77 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP D 69 HIS 0.011 0.002 HIS A 536 PHE 0.012 0.001 PHE C 30 TYR 0.036 0.002 TYR D 52 ARG 0.004 0.001 ARG D 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1698 Ramachandran restraints generated. 849 Oldfield, 0 Emsley, 849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7714 (mmm) cc_final: 0.7062 (ttp) REVERT: C 31 MET cc_start: 0.8251 (mmm) cc_final: 0.7968 (mmm) REVERT: C 44 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8866 (tppt) REVERT: C 62 GLN cc_start: 0.7945 (mp10) cc_final: 0.7683 (mp10) REVERT: C 102 ASP cc_start: 0.9010 (m-30) cc_final: 0.8588 (m-30) REVERT: D 32 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.9134 (tpp80) REVERT: D 59 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7860 (mtt-85) REVERT: D 86 LYS cc_start: 0.8578 (ptmm) cc_final: 0.8171 (ptmt) REVERT: D 99 TYR cc_start: 0.8748 (m-80) cc_final: 0.8459 (m-10) REVERT: D 101 GLN cc_start: 0.8847 (tp40) cc_final: 0.8540 (tp40) REVERT: D 108 GLU cc_start: 0.9459 (pm20) cc_final: 0.8942 (pm20) REVERT: A 217 CYS cc_start: 0.9224 (t) cc_final: 0.8864 (m) REVERT: A 309 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7467 (mm) REVERT: A 312 MET cc_start: 0.8250 (mmm) cc_final: 0.7864 (mmm) REVERT: A 321 VAL cc_start: 0.8120 (m) cc_final: 0.7761 (m) REVERT: A 366 LYS cc_start: 0.8503 (tttt) cc_final: 0.7978 (tptt) REVERT: A 464 ILE cc_start: 0.8942 (mm) cc_final: 0.8490 (mm) REVERT: A 508 HIS cc_start: 0.8390 (t70) cc_final: 0.8045 (t-90) REVERT: A 511 MET cc_start: 0.9005 (mmp) cc_final: 0.8608 (mmm) REVERT: A 534 MET cc_start: 0.9060 (mtm) cc_final: 0.8592 (ttp) REVERT: A 538 MET cc_start: 0.8946 (ttp) cc_final: 0.8521 (ttp) outliers start: 39 outliers final: 34 residues processed: 205 average time/residue: 0.1771 time to fit residues: 47.7333 Evaluate side-chains 213 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN A 100 ASN A 141 ASN A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.087186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068983 restraints weight = 21166.581| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 5.08 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.6638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6189 Z= 0.228 Angle : 0.796 12.631 8442 Z= 0.395 Chirality : 0.044 0.183 1008 Planarity : 0.004 0.037 1070 Dihedral : 4.377 25.345 907 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.54 % Favored : 94.11 % Rotamer: Outliers : 7.10 % Allowed : 36.07 % Favored : 56.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.07 (0.30), residues: 849 helix: 1.44 (0.26), residues: 378 sheet: -0.04 (0.37), residues: 190 loop : -1.83 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 69 HIS 0.010 0.002 HIS A 536 PHE 0.015 0.001 PHE C 30 TYR 0.019 0.001 TYR D 52 ARG 0.004 0.000 ARG D 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.21 seconds wall clock time: 58 minutes 16.47 seconds (3496.47 seconds total)