Starting phenix.real_space_refine on Tue Feb 11 14:34:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wik_21684/02_2025/6wik_21684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wik_21684/02_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_21684/02_2025/6wik_21684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wik_21684/02_2025/6wik_21684.map" model { file = "/net/cci-nas-00/data/ceres_data/6wik_21684/02_2025/6wik_21684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wik_21684/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.06, per 1000 atoms: 0.67 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: 1.59 Conformation dependent library (CDL) restraints added in 983.7 milliseconds 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: 0.78 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: 2.05 Time building geometry restraints manager: 1.82 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: 0.010 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.160 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.440 ------------------------------------------------------------------------------- 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 : 0.695 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: 0.1888 time to fit residues: 70.2598 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 : 0.699 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.092923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.073956 restraints weight = 19839.280| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 5.36 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3666 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= 0.237 Angle : 0.770 10.586 8442 Z= 0.394 Chirality : 0.044 0.179 1008 Planarity : 0.004 0.042 1070 Dihedral : 4.652 26.787 911 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.40 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: -1.61 (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 : 0.641 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: 0.7889 (OUTLIER) cc_final: 0.7681 (mmm) REVERT: C 26 GLN cc_start: 0.6560 (mt0) cc_final: 0.6281 (mt0) REVERT: C 62 GLN cc_start: 0.7703 (mp10) cc_final: 0.7369 (mp10) REVERT: C 74 ARG cc_start: 0.8438 (ttt180) cc_final: 0.8203 (ttt180) REVERT: C 101 GLU cc_start: 0.8989 (mp0) cc_final: 0.8524 (pm20) REVERT: C 102 ASP cc_start: 0.8557 (m-30) cc_final: 0.7952 (m-30) REVERT: D 30 LEU cc_start: 0.9465 (mp) cc_final: 0.9113 (tt) REVERT: D 32 ARG cc_start: 0.9307 (mmm-85) cc_final: 0.8932 (tpp80) REVERT: D 83 PHE cc_start: 0.8499 (m-80) cc_final: 0.8251 (m-10) REVERT: D 86 LYS cc_start: 0.8418 (ptmm) cc_final: 0.7835 (ptmt) REVERT: D 127 ASP cc_start: 0.8809 (t0) cc_final: 0.8599 (t0) REVERT: A 42 TRP cc_start: 0.9108 (t-100) cc_final: 0.8892 (t-100) REVERT: A 112 MET cc_start: 0.8120 (mmm) cc_final: 0.7857 (tmm) REVERT: A 119 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8697 (tp30) REVERT: A 366 LYS cc_start: 0.8573 (tttt) cc_final: 0.8095 (tptt) REVERT: A 393 MET cc_start: 0.8817 (mtt) cc_final: 0.8554 (mpp) REVERT: A 474 ASP cc_start: 0.9086 (t0) cc_final: 0.8872 (t0) REVERT: A 511 MET cc_start: 0.8470 (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: 0.8843 (ttp) cc_final: 0.8388 (ttp) outliers start: 36 outliers final: 22 residues processed: 238 average time/residue: 0.1723 time to fit residues: 53.4288 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 : 0.700 ------------------------------------------------------------------------------- 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: 10.0000 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: 4.9990 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 overall best weight: 2.3884 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.089823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.071252 restraints weight = 20720.196| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 5.25 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6189 Z= 0.286 Angle : 0.726 8.289 8442 Z= 0.376 Chirality : 0.043 0.198 1008 Planarity : 0.004 0.041 1070 Dihedral : 4.314 21.873 907 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.71 % Favored : 92.46 % Rotamer: Outliers : 6.74 % Allowed : 28.78 % Favored : 64.48 % 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: -0.52 (0.29), residues: 849 helix: 1.26 (0.27), residues: 376 sheet: -0.45 (0.39), residues: 184 loop : -2.48 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 158 HIS 0.011 0.002 HIS A 536 PHE 0.013 0.002 PHE A 324 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 247 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.739 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: C 44 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8757 (tppt) REVERT: C 62 GLN cc_start: 0.7745 (mp10) cc_final: 0.7370 (mp10) REVERT: C 99 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8517 (tp40) REVERT: C 101 GLU cc_start: 0.8935 (mp0) cc_final: 0.8618 (pm20) REVERT: C 102 ASP cc_start: 0.8497 (m-30) cc_final: 0.8019 (m-30) REVERT: D 71 ASP cc_start: 0.8220 (t0) cc_final: 0.7344 (t0) REVERT: D 74 ASN cc_start: 0.8451 (p0) cc_final: 0.7704 (p0) REVERT: D 76 ASN cc_start: 0.8142 (m110) cc_final: 0.7228 (m110) REVERT: D 82 LYS cc_start: 0.9165 (ptpt) cc_final: 0.8957 (pttt) REVERT: D 83 PHE cc_start: 0.8706 (m-80) cc_final: 0.8351 (m-10) REVERT: D 86 LYS cc_start: 0.8484 (ptmm) cc_final: 0.8083 (ptmt) REVERT: A 309 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7561 (mm) REVERT: A 366 LYS cc_start: 0.8628 (tttt) cc_final: 0.8110 (tptt) REVERT: A 393 MET cc_start: 0.8790 (mtt) cc_final: 0.8204 (mmt) REVERT: A 474 ASP cc_start: 0.9092 (t0) cc_final: 0.8886 (t0) REVERT: A 511 MET cc_start: 0.8505 (mmp) cc_final: 0.8259 (mmm) REVERT: A 538 MET cc_start: 0.8898 (ttp) cc_final: 0.8539 (ttp) outliers start: 37 outliers final: 27 residues processed: 222 average time/residue: 0.1810 time to fit residues: 51.9730 Evaluate side-chains 211 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 D residue 73 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU 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 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 375 ILE 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 536 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 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 26 GLN C 47 GLN A 125 HIS ** 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 = 0.3588 r_free = 0.3588 target = 0.086492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067855 restraints weight = 21231.406| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 5.23 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 6189 Z= 0.360 Angle : 0.752 9.016 8442 Z= 0.392 Chirality : 0.043 0.173 1008 Planarity : 0.004 0.038 1070 Dihedral : 4.418 25.898 907 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.36 % Favored : 92.82 % Rotamer: Outliers : 10.75 % Allowed : 27.50 % Favored : 61.75 % 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: -0.44 (0.30), residues: 849 helix: 1.16 (0.26), residues: 380 sheet: -0.33 (0.38), residues: 189 loop : -2.30 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 127 HIS 0.013 0.003 HIS A 536 PHE 0.017 0.002 PHE A 473 TYR 0.015 0.002 TYR D 99 ARG 0.004 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 248 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 0.616 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: 0.8500 (mmm) cc_final: 0.8266 (mmt) REVERT: C 62 GLN cc_start: 0.7911 (mp10) cc_final: 0.7527 (mp10) REVERT: C 99 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8292 (tp-100) REVERT: C 101 GLU cc_start: 0.9000 (mp0) cc_final: 0.8683 (pm20) REVERT: C 102 ASP cc_start: 0.8522 (m-30) cc_final: 0.7858 (m-30) REVERT: D 69 TRP cc_start: 0.7888 (p-90) cc_final: 0.7513 (p-90) REVERT: D 71 ASP cc_start: 0.8309 (t0) cc_final: 0.8058 (t0) REVERT: D 74 ASN cc_start: 0.8298 (p0) cc_final: 0.8022 (p0) REVERT: D 86 LYS cc_start: 0.8477 (ptmm) cc_final: 0.8054 (ptmt) REVERT: A 27 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8984 (tt) REVERT: A 85 LYS cc_start: 0.8740 (pttt) cc_final: 0.8507 (mtmt) REVERT: A 309 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 312 MET cc_start: 0.8390 (mmm) cc_final: 0.7999 (mmm) REVERT: A 366 LYS cc_start: 0.8604 (tttt) cc_final: 0.8085 (tptt) REVERT: A 393 MET cc_start: 0.8821 (mtt) cc_final: 0.8241 (mmt) REVERT: A 508 HIS cc_start: 0.8666 (t-90) cc_final: 0.8309 (t-90) REVERT: A 511 MET cc_start: 0.8769 (mmp) cc_final: 0.8464 (mmm) REVERT: A 534 MET cc_start: 0.9132 (mtm) cc_final: 0.8656 (ttp) REVERT: A 538 MET cc_start: 0.8945 (ttp) cc_final: 0.8580 (ttp) outliers start: 59 outliers final: 47 residues processed: 217 average time/residue: 0.1829 time to fit residues: 51.5353 Evaluate side-chains 223 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.677 ------------------------------------------------------------------------------- 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 92 THR Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 27 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 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 110 LEU 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 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 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 Chi-restraints excluded: chain A residue 547 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.089243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.070779 restraints weight = 20616.451| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 5.16 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6189 Z= 0.210 Angle : 0.703 8.752 8442 Z= 0.357 Chirality : 0.042 0.149 1008 Planarity : 0.004 0.043 1070 Dihedral : 4.118 21.300 907 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.30 % Favored : 93.88 % Rotamer: Outliers : 6.56 % Allowed : 32.42 % Favored : 61.02 % 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: 0.09 (0.30), residues: 849 helix: 1.55 (0.27), residues: 379 sheet: 0.02 (0.39), residues: 183 loop : -1.99 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 127 HIS 0.010 0.002 HIS A 536 PHE 0.012 0.001 PHE C 118 TYR 0.019 0.001 TYR D 99 ARG 0.010 0.001 ARG D 59 *********************** 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 231 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 MET cc_start: 0.8452 (mmm) cc_final: 0.8164 (mmt) REVERT: C 44 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8874 (tppt) REVERT: C 62 GLN cc_start: 0.7718 (mp10) cc_final: 0.7388 (mp10) REVERT: C 99 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8244 (tp-100) REVERT: C 101 GLU cc_start: 0.9117 (mp0) cc_final: 0.8826 (pm20) REVERT: C 102 ASP cc_start: 0.8487 (m-30) cc_final: 0.7673 (m-30) REVERT: D 32 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.9079 (tpp80) REVERT: D 36 LEU cc_start: 0.9184 (tp) cc_final: 0.8974 (tt) REVERT: D 69 TRP cc_start: 0.8010 (p-90) cc_final: 0.7518 (p-90) REVERT: D 74 ASN cc_start: 0.8180 (p0) cc_final: 0.7696 (p0) REVERT: D 78 ILE cc_start: 0.8726 (mp) cc_final: 0.8390 (tp) REVERT: D 86 LYS cc_start: 0.8476 (ptmm) cc_final: 0.7974 (ptmt) REVERT: D 101 GLN cc_start: 0.8836 (tp40) cc_final: 0.8593 (tp40) REVERT: D 109 ASP cc_start: 0.8809 (m-30) cc_final: 0.8442 (m-30) REVERT: A 309 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7434 (mm) REVERT: A 312 MET cc_start: 0.8323 (mmm) cc_final: 0.7858 (mmm) REVERT: A 321 VAL cc_start: 0.8259 (m) cc_final: 0.7856 (m) REVERT: A 366 LYS cc_start: 0.8555 (tttt) cc_final: 0.8035 (tptt) REVERT: A 508 HIS cc_start: 0.8619 (t-90) cc_final: 0.8141 (t-90) REVERT: A 511 MET cc_start: 0.8673 (mmp) cc_final: 0.8344 (mmm) REVERT: A 538 MET cc_start: 0.8893 (ttp) cc_final: 0.8526 (ttp) outliers start: 36 outliers final: 26 residues processed: 213 average time/residue: 0.1658 time to fit residues: 47.0003 Evaluate side-chains 204 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 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 50 LEU Chi-restraints excluded: chain A residue 68 VAL 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 162 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 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 326 CYS 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: 9.9990 chunk 39 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.083472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065069 restraints weight = 21299.558| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 5.02 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 6189 Z= 0.510 Angle : 0.838 10.271 8442 Z= 0.446 Chirality : 0.046 0.173 1008 Planarity : 0.004 0.036 1070 Dihedral : 4.626 19.979 907 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.07 % Favored : 92.23 % Rotamer: Outliers : 10.02 % Allowed : 32.24 % Favored : 57.74 % 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: 0.95 (0.26), residues: 376 sheet: -0.22 (0.38), residues: 195 loop : -2.27 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 127 HIS 0.012 0.003 HIS A 536 PHE 0.013 0.002 PHE A 540 TYR 0.031 0.002 TYR D 99 ARG 0.007 0.001 ARG D 59 *********************** 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 227 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6996 (ttp) REVERT: C 31 MET cc_start: 0.8371 (mmm) cc_final: 0.8156 (mmt) REVERT: C 47 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 62 GLN cc_start: 0.8051 (mp10) cc_final: 0.7644 (mp10) REVERT: C 102 ASP cc_start: 0.8689 (m-30) cc_final: 0.7796 (m-30) REVERT: D 32 ARG cc_start: 0.9349 (mmm-85) cc_final: 0.9047 (tpp80) REVERT: D 86 LYS cc_start: 0.8518 (ptmm) cc_final: 0.8049 (ptmt) REVERT: D 101 GLN cc_start: 0.8803 (tp40) cc_final: 0.8562 (tp40) REVERT: D 109 ASP cc_start: 0.9006 (m-30) cc_final: 0.8639 (m-30) REVERT: D 118 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7306 (ttmm) REVERT: A 217 CYS cc_start: 0.9254 (t) cc_final: 0.8868 (m) REVERT: A 309 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 366 LYS cc_start: 0.8563 (tttt) cc_final: 0.8018 (tptt) REVERT: A 508 HIS cc_start: 0.8730 (t-90) cc_final: 0.8207 (t-90) REVERT: A 511 MET cc_start: 0.9068 (mmp) cc_final: 0.8521 (mmp) REVERT: A 538 MET cc_start: 0.9002 (ttp) cc_final: 0.8597 (ttp) outliers start: 55 outliers final: 40 residues processed: 202 average time/residue: 0.1592 time to fit residues: 42.5351 Evaluate side-chains 203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL 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 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 89 ILE Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 ILE 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 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 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 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 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 529 VAL Chi-restraints excluded: chain A residue 536 HIS 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: 1.9990 chunk 14 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 11 optimal weight: 40.0000 chunk 71 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.084928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066814 restraints weight = 21071.035| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 5.00 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 6189 Z= 0.317 Angle : 0.766 10.047 8442 Z= 0.392 Chirality : 0.044 0.143 1008 Planarity : 0.004 0.038 1070 Dihedral : 4.469 22.077 907 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.54 % Favored : 93.99 % Rotamer: Outliers : 6.74 % Allowed : 35.34 % Favored : 57.92 % 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: -0.27 (0.30), residues: 849 helix: 1.12 (0.26), residues: 379 sheet: -0.07 (0.37), residues: 199 loop : -2.15 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 127 HIS 0.012 0.002 HIS A 536 PHE 0.010 0.002 PHE C 118 TYR 0.026 0.002 TYR D 99 ARG 0.009 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 208 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7536 (mmm) cc_final: 0.7002 (ttp) REVERT: C 44 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8852 (tppt) REVERT: C 62 GLN cc_start: 0.7984 (mp10) cc_final: 0.7589 (mp10) REVERT: C 99 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8184 (mm110) REVERT: C 102 ASP cc_start: 0.8612 (m-30) cc_final: 0.8326 (m-30) REVERT: D 32 ARG cc_start: 0.9361 (mmm-85) cc_final: 0.9069 (tpp80) REVERT: D 57 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8286 (ttpt) REVERT: D 76 ASN cc_start: 0.8596 (m110) cc_final: 0.8083 (m110) REVERT: D 86 LYS cc_start: 0.8516 (ptmm) cc_final: 0.7872 (ptmt) REVERT: D 101 GLN cc_start: 0.8836 (tp40) cc_final: 0.8595 (tp40) REVERT: D 109 ASP cc_start: 0.8874 (m-30) cc_final: 0.8371 (m-30) REVERT: A 217 CYS cc_start: 0.9201 (t) cc_final: 0.8874 (m) REVERT: A 309 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7555 (mm) REVERT: A 312 MET cc_start: 0.8356 (mmm) cc_final: 0.7953 (mmm) REVERT: A 366 LYS cc_start: 0.8569 (tttt) cc_final: 0.7998 (tptt) REVERT: A 508 HIS cc_start: 0.8444 (t70) cc_final: 0.8143 (t-90) REVERT: A 511 MET cc_start: 0.9043 (mmp) cc_final: 0.8506 (mmp) REVERT: A 534 MET cc_start: 0.9127 (mtm) cc_final: 0.8768 (ttt) REVERT: A 538 MET cc_start: 0.8847 (ttp) cc_final: 0.8486 (ttp) outliers start: 37 outliers final: 31 residues processed: 191 average time/residue: 0.1756 time to fit residues: 44.1763 Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 VAL 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 D residue 73 GLU Chi-restraints excluded: chain D residue 138 SER 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 29 optimal weight: 8.9990 chunk 14 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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 = 0.3600 r_free = 0.3600 target = 0.086603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.068381 restraints weight = 20393.724| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 5.08 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6189 Z= 0.204 Angle : 0.733 9.951 8442 Z= 0.370 Chirality : 0.042 0.145 1008 Planarity : 0.004 0.040 1070 Dihedral : 4.246 22.066 907 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 5.46 % Allowed : 36.79 % Favored : 57.74 % 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: 0.15 (0.30), residues: 849 helix: 1.44 (0.26), residues: 378 sheet: 0.14 (0.38), residues: 187 loop : -1.79 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 224 HIS 0.010 0.002 HIS A 536 PHE 0.011 0.001 PHE C 118 TYR 0.017 0.001 TYR D 99 ARG 0.005 0.001 ARG D 59 *********************** 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 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7541 (mmm) cc_final: 0.7044 (ttp) REVERT: C 44 LYS cc_start: 0.9238 (ttmm) cc_final: 0.8947 (tppt) REVERT: C 62 GLN cc_start: 0.7897 (mp10) cc_final: 0.7642 (mp10) REVERT: C 90 ASP cc_start: 0.8973 (m-30) cc_final: 0.8218 (m-30) REVERT: C 99 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8486 (mm110) REVERT: C 102 ASP cc_start: 0.8698 (m-30) cc_final: 0.8281 (m-30) REVERT: D 74 ASN cc_start: 0.8589 (p0) cc_final: 0.8253 (p0) REVERT: D 78 ILE cc_start: 0.8403 (mp) cc_final: 0.8158 (tp) REVERT: D 79 TYR cc_start: 0.8604 (m-80) cc_final: 0.8235 (m-80) REVERT: D 86 LYS cc_start: 0.8553 (ptmm) cc_final: 0.8059 (ptmt) REVERT: D 101 GLN cc_start: 0.8781 (tp40) cc_final: 0.8578 (tp40) REVERT: D 109 ASP cc_start: 0.8771 (m-30) cc_final: 0.8311 (m-30) REVERT: A 27 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8920 (tt) REVERT: A 217 CYS cc_start: 0.9186 (t) cc_final: 0.8853 (m) REVERT: A 309 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7444 (mm) REVERT: A 312 MET cc_start: 0.8209 (mmm) cc_final: 0.7812 (mmm) REVERT: A 321 VAL cc_start: 0.8284 (m) cc_final: 0.7651 (m) REVERT: A 366 LYS cc_start: 0.8495 (tttt) cc_final: 0.7960 (tptt) REVERT: A 464 ILE cc_start: 0.8913 (mm) cc_final: 0.8463 (mm) REVERT: A 508 HIS cc_start: 0.8305 (t70) cc_final: 0.7772 (t-90) REVERT: A 511 MET cc_start: 0.8918 (mmp) cc_final: 0.8678 (mmm) REVERT: A 534 MET cc_start: 0.9049 (mtm) cc_final: 0.8611 (ttp) REVERT: A 538 MET cc_start: 0.8906 (ttp) cc_final: 0.8505 (ttp) outliers start: 30 outliers final: 26 residues processed: 201 average time/residue: 0.1728 time to fit residues: 45.5522 Evaluate side-chains 205 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL 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 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 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 546 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 HIS ** 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 = 0.3580 r_free = 0.3580 target = 0.085666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067035 restraints weight = 20752.925| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 5.09 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6189 Z= 0.271 Angle : 0.751 9.008 8442 Z= 0.382 Chirality : 0.042 0.147 1008 Planarity : 0.004 0.039 1070 Dihedral : 4.233 21.341 907 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 5.65 % Allowed : 36.98 % Favored : 57.38 % 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: 0.14 (0.30), residues: 849 helix: 1.47 (0.26), residues: 374 sheet: 0.14 (0.38), residues: 185 loop : -1.81 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 224 HIS 0.002 0.001 HIS A 43 PHE 0.009 0.001 PHE C 118 TYR 0.019 0.001 TYR D 99 ARG 0.005 0.001 ARG D 59 *********************** 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 206 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7615 (mmm) cc_final: 0.7062 (ttp) REVERT: C 44 LYS cc_start: 0.9178 (ttmm) cc_final: 0.8814 (tppt) REVERT: C 62 GLN cc_start: 0.7932 (mp10) cc_final: 0.7670 (mp10) REVERT: C 99 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8483 (mm110) REVERT: C 102 ASP cc_start: 0.8751 (m-30) cc_final: 0.8248 (m-30) REVERT: D 57 LYS cc_start: 0.8598 (ttpp) cc_final: 0.8385 (ttpt) REVERT: D 74 ASN cc_start: 0.8529 (p0) cc_final: 0.8048 (p0) REVERT: D 79 TYR cc_start: 0.8662 (m-80) cc_final: 0.8269 (m-80) REVERT: D 86 LYS cc_start: 0.8563 (ptmm) cc_final: 0.7987 (ptmt) REVERT: D 101 GLN cc_start: 0.8773 (tp40) cc_final: 0.8539 (tp40) REVERT: A 217 CYS cc_start: 0.9246 (t) cc_final: 0.8838 (m) REVERT: A 309 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 312 MET cc_start: 0.8279 (mmm) cc_final: 0.7892 (mmm) REVERT: A 321 VAL cc_start: 0.8320 (m) cc_final: 0.7669 (m) REVERT: A 366 LYS cc_start: 0.8523 (tttt) cc_final: 0.7975 (tptt) REVERT: A 464 ILE cc_start: 0.8930 (mm) cc_final: 0.8499 (mm) REVERT: A 508 HIS cc_start: 0.8327 (t70) cc_final: 0.7729 (t-90) REVERT: A 534 MET cc_start: 0.8989 (mtm) cc_final: 0.8658 (ttt) REVERT: A 538 MET cc_start: 0.8936 (ttp) cc_final: 0.8548 (ttp) outliers start: 31 outliers final: 25 residues processed: 192 average time/residue: 0.1652 time to fit residues: 41.8898 Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 D residue 73 GLU Chi-restraints excluded: chain D residue 138 SER 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 96 LEU Chi-restraints excluded: chain A residue 105 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 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 504 LEU Chi-restraints excluded: chain A residue 512 VAL 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: 0.9990 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 42 optimal weight: 0.0970 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 ASN A 100 ASN A 174 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 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 = 0.3614 r_free = 0.3614 target = 0.087476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.069509 restraints weight = 20447.485| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 5.06 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6189 Z= 0.206 Angle : 0.784 11.488 8442 Z= 0.386 Chirality : 0.043 0.173 1008 Planarity : 0.004 0.039 1070 Dihedral : 4.183 22.697 907 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.65 % Favored : 93.99 % Rotamer: Outliers : 5.83 % Allowed : 36.79 % Favored : 57.38 % 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: 0.26 (0.30), residues: 849 helix: 1.64 (0.27), residues: 374 sheet: 0.14 (0.39), residues: 180 loop : -1.77 (0.38), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 69 HIS 0.003 0.001 HIS A 536 PHE 0.011 0.001 PHE C 118 TYR 0.014 0.001 TYR D 99 ARG 0.004 0.001 ARG D 59 ********************** 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 217 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 MET cc_start: 0.7674 (mmm) cc_final: 0.7054 (ttp) REVERT: C 44 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8909 (tppt) REVERT: C 62 GLN cc_start: 0.7775 (mp10) cc_final: 0.7523 (mp10) REVERT: C 65 LYS cc_start: 0.8175 (ptmm) cc_final: 0.7810 (ptmm) REVERT: C 90 ASP cc_start: 0.8995 (m-30) cc_final: 0.8136 (m-30) REVERT: C 102 ASP cc_start: 0.9032 (m-30) cc_final: 0.8657 (m-30) REVERT: D 79 TYR cc_start: 0.8592 (m-80) cc_final: 0.8196 (m-80) REVERT: D 86 LYS cc_start: 0.8573 (ptmm) cc_final: 0.7817 (ptmt) REVERT: D 101 GLN cc_start: 0.8806 (tp40) cc_final: 0.8407 (tp40) REVERT: A 217 CYS cc_start: 0.9224 (t) cc_final: 0.8835 (m) REVERT: A 309 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7414 (mm) REVERT: A 312 MET cc_start: 0.8183 (mmm) cc_final: 0.7791 (mmm) REVERT: A 321 VAL cc_start: 0.8188 (m) cc_final: 0.7438 (m) REVERT: A 366 LYS cc_start: 0.8383 (tttt) cc_final: 0.7868 (tptt) REVERT: A 464 ILE cc_start: 0.8933 (mm) cc_final: 0.8519 (mm) REVERT: A 508 HIS cc_start: 0.8264 (t70) cc_final: 0.7586 (t-90) REVERT: A 534 MET cc_start: 0.8967 (mtm) cc_final: 0.8611 (ttt) REVERT: A 538 MET cc_start: 0.8937 (ttp) cc_final: 0.8670 (ttp) outliers start: 32 outliers final: 25 residues processed: 204 average time/residue: 0.1757 time to fit residues: 46.4862 Evaluate side-chains 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 78 VAL Chi-restraints excluded: chain D residue 73 GLU 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 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 137 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 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 481 LEU 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 546 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 536 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 = 0.3577 r_free = 0.3577 target = 0.085564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067602 restraints weight = 21181.896| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 5.03 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6189 Z= 0.291 Angle : 0.808 11.168 8442 Z= 0.409 Chirality : 0.044 0.186 1008 Planarity : 0.004 0.038 1070 Dihedral : 4.323 23.903 907 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.01 % Favored : 93.64 % Rotamer: Outliers : 5.65 % Allowed : 37.16 % 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: 0.12 (0.30), residues: 849 helix: 1.49 (0.26), residues: 374 sheet: 0.08 (0.39), residues: 182 loop : -1.80 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 69 HIS 0.003 0.001 HIS A 32 PHE 0.014 0.002 PHE A 207 TYR 0.018 0.002 TYR D 52 ARG 0.006 0.001 ARG C 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.73 seconds wall clock time: 57 minutes 56.21 seconds (3476.21 seconds total)