Starting phenix.real_space_refine on Tue Mar 3 14:20:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wik_21684/03_2026/6wik_21684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wik_21684/03_2026/6wik_21684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2026/6wik_21684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2026/6wik_21684.map" model { file = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2026/6wik_21684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wik_21684/03_2026/6wik_21684_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 3889 2.51 5 N 1029 2.21 5 O 1127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 8, 'TYR:plan': 4, 'ASP:plan': 6, 'TRP:plan': 2, 'ARG:plan': 3, 'HIS:plan': 2} 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: {'TYR:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 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: 1.44, per 1000 atoms: 0.24 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: 0.49 Conformation dependent library (CDL) restraints added in 363.4 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: 0.21 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: 0.94 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1392 1.33 - 1.45: 1395 1.45 - 1.57: 3348 1.57 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6189 Sorted by residual: bond pdb=" N ILE A 203 " pdb=" CA ILE A 203 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta sigma weight residual 1.459 1.498 -0.040 1.16e-02 7.43e+03 1.17e+01 bond pdb=" N ILE C 126 " pdb=" CA ILE C 126 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 9.99e+00 bond pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.73e+00 bond pdb=" N GLU C 128 " pdb=" CA GLU C 128 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.35e+00 ... (remaining 6184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 7099 1.76 - 3.52: 1207 3.52 - 5.28: 113 5.28 - 7.04: 20 7.04 - 8.80: 3 Bond angle restraints: 8442 Sorted by residual: angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 111.43 -8.18 1.05e+00 9.07e-01 6.07e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 109.48 -6.17 8.90e-01 1.26e+00 4.81e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 110.29 -7.04 1.05e+00 9.07e-01 4.50e+01 angle pdb=" N PRO D 144 " pdb=" CA PRO D 144 " pdb=" CB PRO D 144 " ideal model delta sigma weight residual 102.85 110.34 -7.49 1.13e+00 7.83e-01 4.40e+01 angle pdb=" N PRO D 237 " pdb=" CA PRO D 237 " pdb=" CB PRO D 237 " ideal model delta sigma weight residual 103.25 110.18 -6.93 1.05e+00 9.07e-01 4.35e+01 ... (remaining 8437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 3270 16.56 - 33.12: 247 33.12 - 49.69: 58 49.69 - 66.25: 12 66.25 - 82.81: 7 Dihedral angle restraints: 3594 sinusoidal: 1136 harmonic: 2458 Sorted by residual: dihedral pdb=" CA GLY D 27 " pdb=" C GLY D 27 " pdb=" N ALA D 28 " pdb=" CA ALA D 28 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU D 30 " pdb=" C LEU D 30 " pdb=" N VAL D 31 " pdb=" CA VAL D 31 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA VAL D 161 " pdb=" C VAL D 161 " pdb=" N THR D 162 " pdb=" CA THR D 162 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 596 0.061 - 0.121: 273 0.121 - 0.182: 108 0.182 - 0.242: 30 0.242 - 0.303: 1 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA TYR D 121 " pdb=" N TYR D 121 " pdb=" C TYR D 121 " pdb=" CB TYR D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA THR D 110 " pdb=" N THR D 110 " pdb=" C THR D 110 " pdb=" CB THR D 110 " both_signs ideal model delta sigma weight residual False 2.53 2.77 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL D 112 " pdb=" N VAL D 112 " pdb=" C VAL D 112 " pdb=" CB VAL D 112 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1005 not shown) Planarity restraints: 1070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 165 " 0.015 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C GLU A 165 " -0.055 2.00e-02 2.50e+03 pdb=" O GLU A 165 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 166 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 364 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.97e+00 pdb=" C ARG A 364 " -0.039 2.00e-02 2.50e+03 pdb=" O ARG A 364 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 365 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 63 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO C 64 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.031 5.00e-02 4.00e+02 ... (remaining 1067 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 153 2.64 - 3.21: 6067 3.21 - 3.77: 9202 3.77 - 4.34: 11554 4.34 - 4.90: 19877 Nonbonded interactions: 46853 Sorted by model distance: nonbonded pdb=" O ASN A 549 " pdb=" ND2 ASN A 549 " model vdw 2.078 3.120 nonbonded pdb=" O CYS A 387 " pdb=" OG SER A 390 " model vdw 2.254 3.040 nonbonded pdb=" O PHE A 114 " pdb=" OD2 ASP A 118 " model vdw 2.294 3.040 nonbonded pdb=" O ALA A 379 " pdb=" OG SER A 382 " model vdw 2.304 3.040 nonbonded pdb=" O LEU A 322 " pdb=" CD1 LEU A 322 " model vdw 2.315 3.460 ... (remaining 46848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- 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 6191 Z= 0.754 Angle : 1.275 8.804 8446 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.26), 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 ARG 0.015 0.001 ARG D 117 TYR 0.018 0.002 TYR C 111 PHE 0.021 0.002 PHE D 126 TRP 0.026 0.003 TRP D 69 HIS 0.008 0.002 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.01240 ( 6189) covalent geometry : angle 1.27416 ( 8442) SS BOND : bond 0.00814 ( 2) SS BOND : angle 2.11642 ( 4) hydrogen bonds : bond 0.17252 ( 384) hydrogen bonds : angle 8.62498 ( 1092) *********************** 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 : 0.220 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: 0.6496 (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: 0.8703 (tp30) REVERT: A 297 ASP cc_start: 0.9226 (m-30) cc_final: 0.8659 (m-30) REVERT: A 299 TRP cc_start: 0.7513 (t60) cc_final: 0.7298 (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: 0.7947 (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: 0.0789 time to fit residues: 29.9642 Evaluate side-chains 196 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 193 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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 D 76 ASN A 141 ASN A 144 ASN A 494 ASN A 498 ASN A 549 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.090303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.071342 restraints weight = 20348.217| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 5.29 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6191 Z= 0.211 Angle : 0.787 10.427 8446 Z= 0.407 Chirality : 0.044 0.188 1008 Planarity : 0.005 0.039 1070 Dihedral : 4.744 27.783 911 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.24 % Favored : 92.93 % Rotamer: Outliers : 6.92 % Allowed : 27.14 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.28), residues: 849 helix: 0.04 (0.25), residues: 379 sheet: -0.85 (0.37), residues: 189 loop : -2.84 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 117 TYR 0.015 0.002 TYR D 121 PHE 0.025 0.002 PHE A 460 TRP 0.016 0.002 TRP D 69 HIS 0.010 0.003 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 6189) covalent geometry : angle 0.78705 ( 8442) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.91842 ( 4) hydrogen bonds : bond 0.05779 ( 384) hydrogen bonds : angle 5.65268 ( 1092) *********************** 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 254 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.216 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: symmetry clash REVERT: C 26 GLN cc_start: 0.6536 (mt0) cc_final: 0.6247 (mt0) REVERT: C 44 LYS cc_start: 0.9138 (ttmm) cc_final: 0.8762 (tppt) REVERT: C 62 GLN cc_start: 0.7783 (mp10) cc_final: 0.7318 (mp10) REVERT: C 74 ARG cc_start: 0.8445 (ttt180) cc_final: 0.8206 (ttt-90) REVERT: C 101 GLU cc_start: 0.8975 (mp0) cc_final: 0.8541 (pm20) REVERT: C 102 ASP cc_start: 0.8686 (m-30) cc_final: 0.8124 (m-30) REVERT: D 29 GLU cc_start: 0.8478 (mp0) cc_final: 0.7709 (mp0) REVERT: D 32 ARG cc_start: 0.9329 (mmm-85) cc_final: 0.8959 (tpp80) REVERT: D 80 ASP cc_start: 0.9034 (t0) cc_final: 0.8789 (t0) REVERT: D 86 LYS cc_start: 0.8452 (ptmm) cc_final: 0.7874 (ptmt) REVERT: A 112 MET cc_start: 0.8156 (mmm) cc_final: 0.7887 (tmm) REVERT: A 119 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8717 (tp30) REVERT: A 173 MET cc_start: 0.8608 (ttm) cc_final: 0.8261 (ttp) REVERT: A 366 LYS cc_start: 0.8635 (tttt) cc_final: 0.8170 (tptt) REVERT: A 393 MET cc_start: 0.8824 (mtt) cc_final: 0.8556 (mpp) REVERT: A 534 MET cc_start: 0.9058 (mtm) cc_final: 0.8706 (ttt) REVERT: A 538 MET cc_start: 0.8866 (ttp) cc_final: 0.8437 (ttp) outliers start: 38 outliers final: 24 residues processed: 228 average time/residue: 0.0722 time to fit residues: 21.7960 Evaluate side-chains 213 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 90 ASP 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 145 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 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 509 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 536 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 53 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.089493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070819 restraints weight = 20359.933| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 5.27 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.004 0.050 6191 Z= 0.180 Angle : 0.731 8.931 8446 Z= 0.373 Chirality : 0.044 0.179 1008 Planarity : 0.004 0.046 1070 Dihedral : 4.327 20.798 907 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.95 % Favored : 92.23 % Rotamer: Outliers : 7.83 % Allowed : 27.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.29), residues: 849 helix: 1.07 (0.27), residues: 376 sheet: -0.43 (0.38), residues: 190 loop : -2.48 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 119 TYR 0.020 0.002 TYR A 502 PHE 0.011 0.001 PHE A 473 TRP 0.025 0.002 TRP D 69 HIS 0.008 0.002 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6189) covalent geometry : angle 0.73101 ( 8442) SS BOND : bond 0.00868 ( 2) SS BOND : angle 0.99491 ( 4) hydrogen bonds : bond 0.05043 ( 384) hydrogen bonds : angle 5.16952 ( 1092) *********************** 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 253 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 MET cc_start: 0.8551 (mmm) cc_final: 0.8335 (mmt) REVERT: C 44 LYS cc_start: 0.9168 (ttmm) cc_final: 0.8845 (tppt) REVERT: C 62 GLN cc_start: 0.7678 (mp10) cc_final: 0.7382 (mp10) REVERT: C 98 MET cc_start: 0.8481 (tmm) cc_final: 0.8206 (tmm) REVERT: C 101 GLU cc_start: 0.8923 (mp0) cc_final: 0.8519 (pm20) REVERT: C 102 ASP cc_start: 0.8478 (m-30) cc_final: 0.8221 (m-30) REVERT: D 32 ARG cc_start: 0.9340 (mmm-85) cc_final: 0.9015 (tpp80) REVERT: D 71 ASP cc_start: 0.8181 (t0) cc_final: 0.7581 (t0) REVERT: D 80 ASP cc_start: 0.9067 (t0) cc_final: 0.8863 (t0) REVERT: D 83 PHE cc_start: 0.8721 (m-80) cc_final: 0.8394 (m-10) REVERT: D 86 LYS cc_start: 0.8414 (ptmm) cc_final: 0.7787 (ptmt) REVERT: A 85 LYS cc_start: 0.8636 (pttt) cc_final: 0.8373 (mtmt) REVERT: A 173 MET cc_start: 0.8545 (ttm) cc_final: 0.8106 (ttp) REVERT: A 309 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7592 (mm) REVERT: A 366 LYS cc_start: 0.8619 (tttt) cc_final: 0.8109 (tptt) REVERT: A 393 MET cc_start: 0.8764 (mtt) cc_final: 0.8184 (mmt) REVERT: A 506 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8863 (tp) REVERT: A 508 HIS cc_start: 0.8582 (t70) cc_final: 0.8287 (t-90) REVERT: A 511 MET cc_start: 0.8555 (mmm) cc_final: 0.8271 (mmm) REVERT: A 538 MET cc_start: 0.8887 (ttp) cc_final: 0.8553 (ttp) outliers start: 43 outliers final: 28 residues processed: 224 average time/residue: 0.0700 time to fit residues: 20.8213 Evaluate side-chains 216 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 48 ILE 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 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 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 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 358 VAL 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 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN C 99 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS A 144 ASN ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.089889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072057 restraints weight = 20504.740| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 5.15 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6191 Z= 0.160 Angle : 0.694 7.253 8446 Z= 0.358 Chirality : 0.042 0.174 1008 Planarity : 0.004 0.048 1070 Dihedral : 4.250 24.518 907 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.65 % Favored : 93.52 % Rotamer: Outliers : 7.83 % Allowed : 28.96 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.30), residues: 849 helix: 1.34 (0.27), residues: 374 sheet: -0.22 (0.39), residues: 184 loop : -2.20 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.024 0.002 TYR D 99 PHE 0.013 0.001 PHE C 30 TRP 0.018 0.002 TRP A 127 HIS 0.008 0.002 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6189) covalent geometry : angle 0.69335 ( 8442) SS BOND : bond 0.00304 ( 2) SS BOND : angle 1.20647 ( 4) hydrogen bonds : bond 0.04696 ( 384) hydrogen bonds : angle 4.95022 ( 1092) *********************** 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 239 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 MET cc_start: 0.8474 (mmm) cc_final: 0.8171 (mmt) REVERT: C 44 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8908 (tppt) REVERT: C 62 GLN cc_start: 0.7681 (mp10) cc_final: 0.7363 (mp10) REVERT: C 102 ASP cc_start: 0.8451 (m-30) cc_final: 0.7983 (m-30) REVERT: D 59 ARG cc_start: 0.8348 (mtp180) cc_final: 0.8072 (mtt-85) REVERT: D 69 TRP cc_start: 0.7900 (p-90) cc_final: 0.7261 (p-90) REVERT: D 71 ASP cc_start: 0.8071 (t0) cc_final: 0.7631 (t0) REVERT: D 76 ASN cc_start: 0.8223 (m110) cc_final: 0.7477 (m-40) REVERT: D 78 ILE cc_start: 0.8705 (mp) cc_final: 0.8422 (tp) REVERT: D 80 ASP cc_start: 0.9080 (t0) cc_final: 0.8644 (t0) REVERT: D 82 LYS cc_start: 0.9321 (pttt) cc_final: 0.9096 (pttp) REVERT: D 83 PHE cc_start: 0.8500 (m-80) cc_final: 0.8209 (m-10) REVERT: D 86 LYS cc_start: 0.8500 (ptmm) cc_final: 0.8084 (ptmt) REVERT: D 99 TYR cc_start: 0.8780 (m-10) cc_final: 0.8481 (m-10) REVERT: D 108 GLU cc_start: 0.9249 (mp0) cc_final: 0.9012 (mp0) REVERT: A 173 MET cc_start: 0.8520 (ttm) cc_final: 0.8193 (ttm) REVERT: A 309 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7491 (mm) REVERT: A 312 MET cc_start: 0.8229 (mmm) cc_final: 0.7767 (mmm) REVERT: A 366 LYS cc_start: 0.8514 (tttt) cc_final: 0.8011 (tptt) REVERT: A 508 HIS cc_start: 0.8605 (t70) cc_final: 0.8190 (t-90) REVERT: A 511 MET cc_start: 0.8642 (mmm) cc_final: 0.8243 (mmm) REVERT: A 534 MET cc_start: 0.8985 (mtm) cc_final: 0.8558 (ttp) REVERT: A 538 MET cc_start: 0.8885 (ttp) cc_final: 0.8516 (ttp) outliers start: 43 outliers final: 34 residues processed: 216 average time/residue: 0.0724 time to fit residues: 20.6701 Evaluate side-chains 212 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 A residue 30 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 145 LEU 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 326 CYS Chi-restraints excluded: chain A residue 345 LEU 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 504 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 15 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 536 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.089811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.071942 restraints weight = 20754.263| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 5.09 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6191 Z= 0.153 Angle : 0.707 7.905 8446 Z= 0.357 Chirality : 0.042 0.147 1008 Planarity : 0.004 0.050 1070 Dihedral : 4.109 20.454 907 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.18 % Favored : 93.99 % Rotamer: Outliers : 7.65 % Allowed : 33.33 % Favored : 59.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.30), residues: 849 helix: 1.35 (0.27), residues: 378 sheet: 0.08 (0.39), residues: 182 loop : -2.14 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 32 TYR 0.017 0.001 TYR D 99 PHE 0.011 0.001 PHE C 118 TRP 0.013 0.002 TRP A 127 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6189) covalent geometry : angle 0.70662 ( 8442) SS BOND : bond 0.00330 ( 2) SS BOND : angle 0.96028 ( 4) hydrogen bonds : bond 0.04420 ( 384) hydrogen bonds : angle 4.81241 ( 1092) *********************** 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 230 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 MET cc_start: 0.8456 (mmm) cc_final: 0.8243 (mmt) REVERT: C 44 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8875 (tppt) REVERT: C 62 GLN cc_start: 0.7672 (mp10) cc_final: 0.7336 (mp10) REVERT: C 101 GLU cc_start: 0.8764 (pm20) cc_final: 0.8440 (pm20) REVERT: C 102 ASP cc_start: 0.8702 (m-30) cc_final: 0.8363 (m-30) REVERT: D 23 LEU cc_start: 0.8483 (mp) cc_final: 0.8199 (mp) REVERT: D 32 ARG cc_start: 0.9375 (mmm160) cc_final: 0.8719 (mmm-85) REVERT: D 59 ARG cc_start: 0.8321 (mtp180) cc_final: 0.8099 (mtt-85) REVERT: D 69 TRP cc_start: 0.8006 (p-90) cc_final: 0.7524 (p-90) REVERT: D 78 ILE cc_start: 0.8724 (mp) cc_final: 0.8511 (tp) REVERT: D 80 ASP cc_start: 0.9030 (t0) cc_final: 0.8715 (t0) REVERT: D 86 LYS cc_start: 0.8472 (ptmm) cc_final: 0.7811 (ptmt) REVERT: D 131 GLN cc_start: 0.8547 (pm20) cc_final: 0.8285 (pm20) REVERT: A 85 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8270 (mtmm) REVERT: A 173 MET cc_start: 0.8481 (ttm) cc_final: 0.8100 (ttm) REVERT: A 309 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 312 MET cc_start: 0.8325 (mmm) cc_final: 0.7902 (mmm) REVERT: A 366 LYS cc_start: 0.8527 (tttt) cc_final: 0.8012 (tptt) REVERT: A 464 ILE cc_start: 0.8936 (mm) cc_final: 0.8492 (mm) REVERT: A 508 HIS cc_start: 0.8544 (t70) cc_final: 0.8140 (t-90) REVERT: A 511 MET cc_start: 0.8772 (mmm) cc_final: 0.8286 (mmm) REVERT: A 534 MET cc_start: 0.8940 (mtm) cc_final: 0.8541 (ttp) REVERT: A 538 MET cc_start: 0.8921 (ttp) cc_final: 0.8551 (ttp) outliers start: 42 outliers final: 31 residues processed: 205 average time/residue: 0.0594 time to fit residues: 16.5840 Evaluate side-chains 209 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 147 SER 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 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 326 CYS Chi-restraints excluded: chain A residue 345 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.091316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073243 restraints weight = 20133.984| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 5.12 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6191 Z= 0.134 Angle : 0.696 9.024 8446 Z= 0.348 Chirality : 0.041 0.163 1008 Planarity : 0.004 0.050 1070 Dihedral : 4.068 21.193 907 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.30 % Favored : 93.99 % Rotamer: Outliers : 7.47 % Allowed : 34.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.30), residues: 849 helix: 1.54 (0.27), residues: 380 sheet: 0.08 (0.39), residues: 177 loop : -1.99 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.013 0.001 TYR D 99 PHE 0.008 0.001 PHE A 324 TRP 0.022 0.002 TRP A 127 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6189) covalent geometry : angle 0.69623 ( 8442) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.06940 ( 4) hydrogen bonds : bond 0.04125 ( 384) hydrogen bonds : angle 4.68417 ( 1092) *********************** 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 229 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8815 (tppt) REVERT: C 62 GLN cc_start: 0.7589 (mp10) cc_final: 0.7302 (mp10) REVERT: C 102 ASP cc_start: 0.8796 (m-30) cc_final: 0.8339 (m-30) REVERT: D 23 LEU cc_start: 0.8452 (mp) cc_final: 0.8157 (mp) REVERT: D 32 ARG cc_start: 0.9343 (mmm160) cc_final: 0.8757 (mmm-85) REVERT: D 65 GLU cc_start: 0.8847 (tp30) cc_final: 0.8403 (tt0) REVERT: D 71 ASP cc_start: 0.7901 (t0) cc_final: 0.7619 (t0) REVERT: D 76 ASN cc_start: 0.8119 (m110) cc_final: 0.7700 (m-40) REVERT: D 86 LYS cc_start: 0.8572 (ptmm) cc_final: 0.7904 (ptmt) REVERT: D 99 TYR cc_start: 0.8719 (m-10) cc_final: 0.8353 (m-10) REVERT: D 131 GLN cc_start: 0.8636 (pm20) cc_final: 0.8352 (pm20) REVERT: A 82 TRP cc_start: 0.9187 (t60) cc_final: 0.8742 (t60) REVERT: A 85 LYS cc_start: 0.8429 (mtmt) cc_final: 0.8129 (mtmm) REVERT: A 173 MET cc_start: 0.8456 (ttm) cc_final: 0.8214 (ttp) REVERT: A 217 CYS cc_start: 0.9205 (t) cc_final: 0.8885 (m) REVERT: A 309 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7501 (mm) REVERT: A 312 MET cc_start: 0.8335 (mmm) cc_final: 0.7905 (mmm) REVERT: A 366 LYS cc_start: 0.8428 (tttt) cc_final: 0.7908 (tptt) REVERT: A 464 ILE cc_start: 0.8938 (mm) cc_final: 0.8416 (mm) REVERT: A 467 ARG cc_start: 0.9053 (mmm-85) cc_final: 0.8793 (mmm-85) REVERT: A 508 HIS cc_start: 0.8521 (t70) cc_final: 0.8129 (t-90) REVERT: A 511 MET cc_start: 0.8821 (mmm) cc_final: 0.8277 (mmm) REVERT: A 534 MET cc_start: 0.8917 (mtm) cc_final: 0.8497 (ttp) REVERT: A 538 MET cc_start: 0.8928 (ttp) cc_final: 0.8674 (ttp) outliers start: 41 outliers final: 31 residues processed: 208 average time/residue: 0.0668 time to fit residues: 18.5328 Evaluate side-chains 211 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 137 VAL 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 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 509 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 526 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 39 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.090801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072550 restraints weight = 20635.838| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 5.19 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6191 Z= 0.141 Angle : 0.703 9.381 8446 Z= 0.353 Chirality : 0.041 0.170 1008 Planarity : 0.004 0.050 1070 Dihedral : 3.997 20.890 907 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.71 % Allowed : 5.18 % Favored : 94.11 % Rotamer: Outliers : 8.01 % Allowed : 35.34 % Favored : 56.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.30), residues: 849 helix: 1.63 (0.27), residues: 380 sheet: 0.17 (0.39), residues: 176 loop : -1.79 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 119 TYR 0.011 0.001 TYR C 69 PHE 0.033 0.001 PHE A 460 TRP 0.034 0.002 TRP A 127 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6189) covalent geometry : angle 0.70325 ( 8442) SS BOND : bond 0.00463 ( 2) SS BOND : angle 0.96310 ( 4) hydrogen bonds : bond 0.03995 ( 384) hydrogen bonds : angle 4.62877 ( 1092) *********************** 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 233 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 LYS cc_start: 0.9026 (ttmm) cc_final: 0.8782 (tppt) REVERT: C 62 GLN cc_start: 0.7776 (mp10) cc_final: 0.7483 (mp10) REVERT: C 102 ASP cc_start: 0.8928 (m-30) cc_final: 0.8471 (m-30) REVERT: C 107 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8371 (p90) REVERT: D 23 LEU cc_start: 0.8473 (mp) cc_final: 0.8204 (mp) REVERT: D 59 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7896 (mtt-85) REVERT: D 65 GLU cc_start: 0.8875 (tp30) cc_final: 0.8504 (tt0) REVERT: D 71 ASP cc_start: 0.7873 (t0) cc_final: 0.7549 (t0) REVERT: D 76 ASN cc_start: 0.8216 (m110) cc_final: 0.7582 (m-40) REVERT: D 79 TYR cc_start: 0.8645 (m-80) cc_final: 0.8283 (m-80) REVERT: D 86 LYS cc_start: 0.8603 (ptmm) cc_final: 0.7958 (ptmt) REVERT: D 99 TYR cc_start: 0.8582 (m-10) cc_final: 0.8347 (m-10) REVERT: A 85 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8191 (mtmm) REVERT: A 173 MET cc_start: 0.8379 (ttm) cc_final: 0.8099 (ttp) REVERT: A 196 MET cc_start: 0.8624 (ptt) cc_final: 0.8387 (ppp) REVERT: A 309 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7486 (mm) REVERT: A 312 MET cc_start: 0.8382 (mmm) cc_final: 0.8022 (mmm) REVERT: A 319 MET cc_start: 0.8490 (tmm) cc_final: 0.8240 (tmm) REVERT: A 366 LYS cc_start: 0.8394 (tttt) cc_final: 0.7866 (tptt) REVERT: A 464 ILE cc_start: 0.8910 (mm) cc_final: 0.8445 (mm) REVERT: A 467 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8744 (mmm-85) REVERT: A 508 HIS cc_start: 0.8509 (t70) cc_final: 0.8046 (t-90) REVERT: A 511 MET cc_start: 0.8921 (mmm) cc_final: 0.8403 (mmm) REVERT: A 534 MET cc_start: 0.8967 (mtm) cc_final: 0.8520 (ttp) REVERT: A 538 MET cc_start: 0.8961 (ttp) cc_final: 0.8704 (ttp) outliers start: 44 outliers final: 32 residues processed: 213 average time/residue: 0.0692 time to fit residues: 19.5423 Evaluate side-chains 214 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 137 VAL 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 105 LEU Chi-restraints excluded: chain A residue 145 LEU 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 321 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 349 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 74 optimal weight: 0.1980 chunk 35 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.090212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.071589 restraints weight = 20854.557| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 5.25 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6191 Z= 0.154 Angle : 0.725 8.788 8446 Z= 0.365 Chirality : 0.042 0.182 1008 Planarity : 0.004 0.052 1070 Dihedral : 3.996 21.171 907 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.77 % Favored : 93.76 % Rotamer: Outliers : 6.38 % Allowed : 37.70 % Favored : 55.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.30), residues: 849 helix: 1.60 (0.27), residues: 380 sheet: 0.22 (0.39), residues: 176 loop : -1.80 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 119 TYR 0.011 0.001 TYR C 69 PHE 0.009 0.001 PHE C 118 TRP 0.045 0.003 TRP D 69 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6189) covalent geometry : angle 0.72444 ( 8442) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.93529 ( 4) hydrogen bonds : bond 0.03988 ( 384) hydrogen bonds : angle 4.62221 ( 1092) *********************** 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 219 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.225 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 62 GLN cc_start: 0.7826 (mp10) cc_final: 0.7529 (mp10) REVERT: C 102 ASP cc_start: 0.8928 (m-30) cc_final: 0.8481 (m-30) REVERT: C 107 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8393 (p90) REVERT: D 59 ARG cc_start: 0.8134 (mtt-85) cc_final: 0.7780 (mtt-85) REVERT: D 65 GLU cc_start: 0.8890 (tp30) cc_final: 0.8571 (tt0) REVERT: D 71 ASP cc_start: 0.7912 (t0) cc_final: 0.7295 (t0) REVERT: D 76 ASN cc_start: 0.8194 (m110) cc_final: 0.7582 (m-40) REVERT: D 79 TYR cc_start: 0.8694 (m-80) cc_final: 0.8365 (m-80) REVERT: D 86 LYS cc_start: 0.8634 (ptmm) cc_final: 0.7824 (ptmt) REVERT: D 99 TYR cc_start: 0.8587 (m-10) cc_final: 0.8310 (m-10) REVERT: A 173 MET cc_start: 0.8374 (ttm) cc_final: 0.8114 (ttp) REVERT: A 196 MET cc_start: 0.8583 (ptt) cc_final: 0.8360 (ppp) REVERT: A 309 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7627 (mm) REVERT: A 312 MET cc_start: 0.8424 (mmm) cc_final: 0.8078 (mmm) REVERT: A 366 LYS cc_start: 0.8393 (tttt) cc_final: 0.7849 (tptt) REVERT: A 467 ARG cc_start: 0.8991 (mmm-85) cc_final: 0.8775 (mmm-85) REVERT: A 508 HIS cc_start: 0.8495 (t70) cc_final: 0.8013 (t-90) REVERT: A 511 MET cc_start: 0.8952 (mmm) cc_final: 0.8412 (mmm) REVERT: A 534 MET cc_start: 0.8967 (mtm) cc_final: 0.8534 (ttp) REVERT: A 538 MET cc_start: 0.8947 (ttp) cc_final: 0.8734 (ttp) outliers start: 35 outliers final: 30 residues processed: 202 average time/residue: 0.0726 time to fit residues: 19.5343 Evaluate side-chains 209 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 137 VAL 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 105 LEU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN A 182 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.088540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.070400 restraints weight = 21087.091| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 5.12 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6191 Z= 0.183 Angle : 0.770 8.859 8446 Z= 0.388 Chirality : 0.044 0.226 1008 Planarity : 0.005 0.093 1070 Dihedral : 4.212 21.394 907 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 7.10 % Allowed : 37.70 % Favored : 55.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.30), residues: 849 helix: 1.55 (0.26), residues: 380 sheet: 0.24 (0.39), residues: 174 loop : -1.83 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 32 TYR 0.015 0.002 TYR D 121 PHE 0.010 0.001 PHE C 118 TRP 0.054 0.003 TRP D 69 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6189) covalent geometry : angle 0.76984 ( 8442) SS BOND : bond 0.00729 ( 2) SS BOND : angle 1.51867 ( 4) hydrogen bonds : bond 0.04150 ( 384) hydrogen bonds : angle 4.73251 ( 1092) *********************** 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 215 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.7886 (mp10) cc_final: 0.7580 (mp10) REVERT: C 102 ASP cc_start: 0.9045 (m-30) cc_final: 0.8611 (m-30) REVERT: C 107 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8359 (p90) REVERT: D 59 ARG cc_start: 0.8108 (mtt-85) cc_final: 0.7662 (mtt-85) REVERT: D 65 GLU cc_start: 0.8898 (tp30) cc_final: 0.8522 (tt0) REVERT: D 76 ASN cc_start: 0.8350 (m110) cc_final: 0.7983 (m-40) REVERT: D 79 TYR cc_start: 0.8687 (m-80) cc_final: 0.8214 (m-80) REVERT: D 86 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8017 (ptmt) REVERT: D 99 TYR cc_start: 0.8676 (m-10) cc_final: 0.8330 (m-10) REVERT: D 108 GLU cc_start: 0.9373 (pm20) cc_final: 0.9010 (pm20) REVERT: A 112 MET cc_start: 0.7574 (tmm) cc_final: 0.7356 (tmm) REVERT: A 145 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8314 (tt) REVERT: A 173 MET cc_start: 0.8506 (ttm) cc_final: 0.8269 (ttp) REVERT: A 196 MET cc_start: 0.8620 (ptt) cc_final: 0.8360 (ppp) REVERT: A 309 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7568 (mm) REVERT: A 312 MET cc_start: 0.8410 (mmm) cc_final: 0.8054 (mmm) REVERT: A 366 LYS cc_start: 0.8428 (tttt) cc_final: 0.7886 (tptt) REVERT: A 464 ILE cc_start: 0.9020 (mm) cc_final: 0.8600 (mm) REVERT: A 467 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8765 (mmm-85) REVERT: A 508 HIS cc_start: 0.8421 (t70) cc_final: 0.7977 (t-90) REVERT: A 511 MET cc_start: 0.9070 (mmm) cc_final: 0.8412 (mmm) REVERT: A 534 MET cc_start: 0.8998 (mtm) cc_final: 0.8542 (ttp) REVERT: A 538 MET cc_start: 0.8925 (ttp) cc_final: 0.8705 (ttp) outliers start: 39 outliers final: 32 residues processed: 196 average time/residue: 0.0631 time to fit residues: 16.8311 Evaluate side-chains 207 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 107 PHE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 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 166 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065836 restraints weight = 21310.098| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.02 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 6191 Z= 0.304 Angle : 0.844 9.952 8446 Z= 0.436 Chirality : 0.046 0.199 1008 Planarity : 0.005 0.068 1070 Dihedral : 4.633 21.852 907 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.95 % Favored : 92.70 % Rotamer: Outliers : 7.10 % Allowed : 37.89 % Favored : 55.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.29), residues: 849 helix: 1.22 (0.26), residues: 380 sheet: 0.13 (0.39), residues: 179 loop : -1.99 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 117 TYR 0.017 0.002 TYR C 111 PHE 0.014 0.002 PHE A 460 TRP 0.090 0.004 TRP D 69 HIS 0.005 0.002 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 6189) covalent geometry : angle 0.84385 ( 8442) SS BOND : bond 0.00567 ( 2) SS BOND : angle 1.10048 ( 4) hydrogen bonds : bond 0.04642 ( 384) hydrogen bonds : angle 5.08913 ( 1092) ********************** 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 211 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.7967 (mp10) cc_final: 0.7576 (mp10) REVERT: C 102 ASP cc_start: 0.9099 (m-30) cc_final: 0.8619 (m-30) REVERT: C 107 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8572 (p90) REVERT: D 65 GLU cc_start: 0.8904 (tp30) cc_final: 0.8418 (tt0) REVERT: D 76 ASN cc_start: 0.8497 (m110) cc_final: 0.8196 (m-40) REVERT: D 86 LYS cc_start: 0.8553 (ptmm) cc_final: 0.7918 (ptmt) REVERT: A 112 MET cc_start: 0.7568 (tmm) cc_final: 0.7351 (tmm) REVERT: A 145 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 196 MET cc_start: 0.8640 (ptt) cc_final: 0.8381 (ppp) REVERT: A 309 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7607 (mm) REVERT: A 366 LYS cc_start: 0.8411 (tttt) cc_final: 0.7873 (tptt) REVERT: A 464 ILE cc_start: 0.8993 (mm) cc_final: 0.8553 (mm) REVERT: A 508 HIS cc_start: 0.8487 (t70) cc_final: 0.8035 (t-90) REVERT: A 511 MET cc_start: 0.9144 (mmm) cc_final: 0.8294 (mmp) REVERT: A 534 MET cc_start: 0.9117 (mtm) cc_final: 0.8654 (ttp) REVERT: A 538 MET cc_start: 0.8968 (ttp) cc_final: 0.8598 (ttp) outliers start: 39 outliers final: 30 residues processed: 195 average time/residue: 0.0626 time to fit residues: 16.7140 Evaluate side-chains 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 107 PHE Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 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 183 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 383 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 50.0000 chunk 76 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 HIS A 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.085528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067571 restraints weight = 20949.889| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 5.00 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6191 Z= 0.208 Angle : 0.830 11.508 8446 Z= 0.416 Chirality : 0.045 0.212 1008 Planarity : 0.004 0.052 1070 Dihedral : 4.581 25.518 907 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.36 % Favored : 93.29 % Rotamer: Outliers : 6.56 % Allowed : 38.43 % Favored : 55.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.29), residues: 849 helix: 1.31 (0.26), residues: 379 sheet: 0.07 (0.40), residues: 169 loop : -1.93 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 32 TYR 0.022 0.002 TYR D 99 PHE 0.011 0.001 PHE C 118 TRP 0.092 0.003 TRP D 69 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6189) covalent geometry : angle 0.82953 ( 8442) SS BOND : bond 0.00537 ( 2) SS BOND : angle 1.11860 ( 4) hydrogen bonds : bond 0.04480 ( 384) hydrogen bonds : angle 4.90178 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.91 seconds wall clock time: 26 minutes 21.75 seconds (1581.75 seconds total)