Starting phenix.real_space_refine on Mon Jan 13 23:41:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2a_42903/01_2025/8v2a_42903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2a_42903/01_2025/8v2a_42903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v2a_42903/01_2025/8v2a_42903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2a_42903/01_2025/8v2a_42903.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2a_42903/01_2025/8v2a_42903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2a_42903/01_2025/8v2a_42903.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 22 5.16 5 C 2846 2.51 5 N 774 2.21 5 O 880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4522 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1376 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1611 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "C" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1395 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 169} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.99, per 1000 atoms: 0.88 Number of scatterers: 4522 At special positions: 0 Unit cell: (81.7, 108.36, 101.48, 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 22 16.00 O 880 8.00 N 774 7.00 C 2846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 341 " - pdb=" SG CYS C 351 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 701 " - " ASN B 131 " " NAG B 702 " - " ASN B 227 " " NAG B 703 " - " ASN B 157 " " NAG C 901 " - " ASN C 303 " " NAG D 1 " - " ASN A 100 " " NAG E 1 " - " ASN C 407 " " NAG F 1 " - " ASN C 426 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 526.5 milliseconds 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 10 sheets defined 28.5% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 51 through 63 removed outlier: 4.608A pdb=" N ASP A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 93 through 117 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 158 Proline residue: A 141 - end of helix removed outlier: 3.603A pdb=" N ASP A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 212 removed outlier: 4.160A pdb=" N LYS A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 218 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.539A pdb=" N LYS B 250 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.211A pdb=" N ALA B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing sheet with id=AA1, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.805A pdb=" N CYS B 182 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS B 144 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LYS B 221 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL B 136 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.565A pdb=" N SER B 162 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP B 171 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 160 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 201 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 205 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171 removed outlier: 5.565A pdb=" N SER B 162 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP B 171 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 160 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 201 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 194 " --> pdb=" O PHE B 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 226 through 231 removed outlier: 5.494A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR B 245 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 270 through 271 Processing sheet with id=AA6, first strand: chain 'C' and resid 254 through 255 removed outlier: 3.528A pdb=" N ILE C 299 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 262 Processing sheet with id=AA8, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.560A pdb=" N CYS C 287 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA C 280 " --> pdb=" O CYS C 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 337 through 343 removed outlier: 5.613A pdb=" N GLN C 338 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASN C 354 " --> pdb=" O GLN C 338 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 379 through 381 196 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1457 1.34 - 1.46: 727 1.46 - 1.57: 2404 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 4617 Sorted by residual: bond pdb=" N GLU C 386 " pdb=" CA GLU C 386 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.97e+00 bond pdb=" N ASN C 390 " pdb=" CA ASN C 390 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.29e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" N ALA C 387 " pdb=" CA ALA C 387 " ideal model delta sigma weight residual 1.454 1.482 -0.027 1.44e-02 4.82e+03 3.65e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 ... (remaining 4612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6100 1.64 - 3.29: 142 3.29 - 4.93: 14 4.93 - 6.58: 2 6.58 - 8.22: 1 Bond angle restraints: 6259 Sorted by residual: angle pdb=" N ASN C 313 " pdb=" CA ASN C 313 " pdb=" C ASN C 313 " ideal model delta sigma weight residual 109.15 117.37 -8.22 1.44e+00 4.82e-01 3.26e+01 angle pdb=" CA THR C 389 " pdb=" CB THR C 389 " pdb=" OG1 THR C 389 " ideal model delta sigma weight residual 109.60 104.93 4.67 1.50e+00 4.44e-01 9.70e+00 angle pdb=" C ALA C 385 " pdb=" N GLU C 386 " pdb=" CA GLU C 386 " ideal model delta sigma weight residual 122.99 118.73 4.26 1.41e+00 5.03e-01 9.13e+00 angle pdb=" CA GLU C 391 " pdb=" C GLU C 391 " pdb=" O GLU C 391 " ideal model delta sigma weight residual 121.39 118.38 3.01 1.12e+00 7.97e-01 7.24e+00 angle pdb=" N THR C 389 " pdb=" CA THR C 389 " pdb=" C THR C 389 " ideal model delta sigma weight residual 111.71 108.80 2.91 1.15e+00 7.56e-01 6.42e+00 ... (remaining 6254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.47: 2713 20.47 - 40.94: 158 40.94 - 61.41: 44 61.41 - 81.88: 8 81.88 - 102.34: 17 Dihedral angle restraints: 2940 sinusoidal: 1336 harmonic: 1604 Sorted by residual: dihedral pdb=" CB CYS A 31 " pdb=" SG CYS A 31 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 148.65 -55.65 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CA PRO B 291 " pdb=" C PRO B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" C1 NAG B 702 " pdb=" C2 NAG B 702 " pdb=" C3 NAG B 702 " pdb=" O3 NAG B 702 " ideal model delta sinusoidal sigma weight residual -175.09 -72.75 -102.34 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 2937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 610 0.055 - 0.109: 103 0.109 - 0.164: 15 0.164 - 0.218: 0 0.218 - 0.273: 1 Chirality restraints: 729 Sorted by residual: chirality pdb=" CA ASN C 313 " pdb=" N ASN C 313 " pdb=" C ASN C 313 " pdb=" CB ASN C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE B 272 " pdb=" N ILE B 272 " pdb=" C ILE B 272 " pdb=" CB ILE B 272 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL A 67 " pdb=" N VAL A 67 " pdb=" C VAL A 67 " pdb=" CB VAL A 67 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 726 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 414 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO C 415 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 57 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.56e+00 pdb=" N PRO A 58 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 385 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C ALA C 385 " -0.019 2.00e-02 2.50e+03 pdb=" O ALA C 385 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU C 386 " 0.006 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1061 2.79 - 3.32: 4049 3.32 - 3.85: 6884 3.85 - 4.37: 7539 4.37 - 4.90: 13477 Nonbonded interactions: 33010 Sorted by model distance: nonbonded pdb=" OG SER B 229 " pdb=" OG1 THR B 243 " model vdw 2.267 3.040 nonbonded pdb=" NE ARG A 36 " pdb=" OE2 GLU A 214 " model vdw 2.352 3.120 nonbonded pdb=" OG1 THR C 252 " pdb=" OE1 GLN C 257 " model vdw 2.357 3.040 nonbonded pdb=" NE2 GLN C 420 " pdb=" O6 NAG E 2 " model vdw 2.366 3.120 nonbonded pdb=" O PRO A 82 " pdb=" NH2 ARG A 200 " model vdw 2.385 3.120 ... (remaining 33005 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.003 0.049 4617 Z= 0.234 Angle : 0.584 8.223 6259 Z= 0.327 Chirality : 0.044 0.273 729 Planarity : 0.004 0.044 793 Dihedral : 16.756 102.344 1885 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.20 % Allowed : 5.07 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.33), residues: 543 helix: 0.85 (0.45), residues: 127 sheet: -1.21 (0.36), residues: 171 loop : -2.11 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 212 HIS 0.002 0.000 HIS A 199 PHE 0.005 0.001 PHE C 408 TYR 0.009 0.001 TYR A 35 ARG 0.001 0.000 ARG B 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8728 (tpp) cc_final: 0.8419 (tpp) REVERT: A 211 LYS cc_start: 0.7795 (tppp) cc_final: 0.7379 (ttpt) REVERT: C 402 ASN cc_start: 0.7929 (t0) cc_final: 0.7700 (t0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2418 time to fit residues: 24.8549 Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 0.0980 chunk 49 optimal weight: 30.0000 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 108 HIS ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN B 202 ASN B 258 ASN B 271 GLN C 313 ASN C 321 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.104987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.089544 restraints weight = 11866.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.091639 restraints weight = 7485.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.093039 restraints weight = 5546.800| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4617 Z= 0.231 Angle : 0.623 6.658 6259 Z= 0.313 Chirality : 0.045 0.187 729 Planarity : 0.004 0.034 793 Dihedral : 12.968 76.152 805 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 13.18 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.35), residues: 543 helix: 1.88 (0.47), residues: 127 sheet: -0.77 (0.37), residues: 161 loop : -1.60 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 212 HIS 0.008 0.001 HIS A 108 PHE 0.009 0.001 PHE C 397 TYR 0.009 0.001 TYR A 35 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6964 (tptm) cc_final: 0.6705 (tptm) REVERT: A 153 MET cc_start: 0.8782 (tpp) cc_final: 0.8507 (tpp) REVERT: A 211 LYS cc_start: 0.7963 (tppp) cc_final: 0.7653 (ttpt) REVERT: C 320 ASP cc_start: 0.7855 (m-30) cc_final: 0.7644 (m-30) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.1925 time to fit residues: 15.1748 Evaluate side-chains 55 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain C residue 313 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 149 ASN C 313 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.088217 restraints weight = 11980.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.090251 restraints weight = 7494.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091654 restraints weight = 5550.124| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4617 Z= 0.245 Angle : 0.626 7.262 6259 Z= 0.311 Chirality : 0.045 0.179 729 Planarity : 0.004 0.031 793 Dihedral : 9.990 57.848 805 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.84 % Allowed : 15.42 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.36), residues: 543 helix: 2.31 (0.47), residues: 126 sheet: -0.47 (0.38), residues: 163 loop : -1.42 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 212 HIS 0.009 0.001 HIS A 108 PHE 0.007 0.001 PHE C 408 TYR 0.010 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.560 Fit side-chains REVERT: A 33 LYS cc_start: 0.6977 (tptm) cc_final: 0.6685 (tptm) REVERT: A 153 MET cc_start: 0.8810 (tpp) cc_final: 0.8536 (tpp) REVERT: A 211 LYS cc_start: 0.8043 (tppp) cc_final: 0.7673 (ttpt) REVERT: B 134 CYS cc_start: 0.5335 (m) cc_final: 0.5129 (m) REVERT: C 320 ASP cc_start: 0.7950 (m-30) cc_final: 0.7645 (m-30) REVERT: C 349 ILE cc_start: 0.7895 (mt) cc_final: 0.7664 (tt) outliers start: 14 outliers final: 8 residues processed: 63 average time/residue: 0.1963 time to fit residues: 15.5763 Evaluate side-chains 57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 371 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 108 HIS A 149 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.083015 restraints weight = 12256.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.084933 restraints weight = 7825.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086243 restraints weight = 5801.888| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4617 Z= 0.242 Angle : 0.612 6.446 6259 Z= 0.304 Chirality : 0.044 0.156 729 Planarity : 0.004 0.035 793 Dihedral : 7.397 58.025 805 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.62 % Allowed : 18.46 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.36), residues: 543 helix: 2.54 (0.47), residues: 126 sheet: -0.30 (0.39), residues: 163 loop : -1.28 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 212 HIS 0.010 0.001 HIS A 108 PHE 0.010 0.001 PHE C 408 TYR 0.010 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.541 Fit side-chains REVERT: A 33 LYS cc_start: 0.7019 (tptm) cc_final: 0.6728 (tptm) REVERT: A 153 MET cc_start: 0.8834 (tpp) cc_final: 0.8519 (tpp) REVERT: A 211 LYS cc_start: 0.8095 (tppp) cc_final: 0.7742 (ttpt) REVERT: C 320 ASP cc_start: 0.7941 (m-30) cc_final: 0.7562 (m-30) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.2131 time to fit residues: 15.5732 Evaluate side-chains 51 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 149 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.083136 restraints weight = 12245.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.085055 restraints weight = 7784.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.086373 restraints weight = 5745.965| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4617 Z= 0.213 Angle : 0.599 8.811 6259 Z= 0.297 Chirality : 0.043 0.159 729 Planarity : 0.004 0.036 793 Dihedral : 6.600 57.587 805 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.85 % Allowed : 18.46 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.36), residues: 543 helix: 2.71 (0.46), residues: 126 sheet: -0.14 (0.40), residues: 163 loop : -1.20 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 212 HIS 0.010 0.001 HIS A 108 PHE 0.008 0.001 PHE C 408 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.602 Fit side-chains REVERT: A 33 LYS cc_start: 0.7027 (tptm) cc_final: 0.6717 (tptm) REVERT: A 86 THR cc_start: 0.6639 (OUTLIER) cc_final: 0.6146 (t) REVERT: A 153 MET cc_start: 0.8810 (tpp) cc_final: 0.8518 (tpp) REVERT: A 211 LYS cc_start: 0.8063 (tppp) cc_final: 0.7741 (ttpt) REVERT: C 320 ASP cc_start: 0.7866 (m-30) cc_final: 0.7443 (m-30) REVERT: C 347 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6928 (mmtt) outliers start: 19 outliers final: 9 residues processed: 66 average time/residue: 0.2194 time to fit residues: 17.8514 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 420 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.0570 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 40.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.098451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.083432 restraints weight = 12127.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085392 restraints weight = 7688.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086705 restraints weight = 5668.864| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4617 Z= 0.202 Angle : 0.598 6.837 6259 Z= 0.298 Chirality : 0.043 0.158 729 Planarity : 0.004 0.038 793 Dihedral : 6.273 56.979 805 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.45 % Allowed : 19.07 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.37), residues: 543 helix: 2.69 (0.46), residues: 128 sheet: -0.25 (0.39), residues: 166 loop : -1.05 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.011 0.001 HIS A 108 PHE 0.008 0.001 PHE C 397 TYR 0.008 0.001 TYR A 35 ARG 0.006 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6116 (t) REVERT: A 153 MET cc_start: 0.8799 (tpp) cc_final: 0.8504 (tpp) REVERT: A 211 LYS cc_start: 0.8064 (tppp) cc_final: 0.7699 (ttpt) REVERT: B 293 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7036 (p) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.1870 time to fit residues: 15.3384 Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 420 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.098518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.083052 restraints weight = 12106.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.085070 restraints weight = 7563.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.086451 restraints weight = 5547.613| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4617 Z= 0.203 Angle : 0.603 5.802 6259 Z= 0.301 Chirality : 0.043 0.160 729 Planarity : 0.004 0.037 793 Dihedral : 6.091 56.742 805 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.45 % Allowed : 20.08 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.37), residues: 543 helix: 2.67 (0.46), residues: 128 sheet: -0.09 (0.40), residues: 161 loop : -1.05 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.011 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 TYR 0.008 0.001 TYR A 35 ARG 0.001 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6124 (t) REVERT: A 153 MET cc_start: 0.8802 (tpp) cc_final: 0.8483 (tpp) REVERT: A 211 LYS cc_start: 0.8088 (tppp) cc_final: 0.7698 (ttpt) REVERT: B 293 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6961 (p) outliers start: 17 outliers final: 12 residues processed: 62 average time/residue: 0.2066 time to fit residues: 15.9664 Evaluate side-chains 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 420 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.098170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.082741 restraints weight = 12110.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.084771 restraints weight = 7552.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.086114 restraints weight = 5526.945| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4617 Z= 0.216 Angle : 0.622 9.123 6259 Z= 0.311 Chirality : 0.043 0.163 729 Planarity : 0.004 0.038 793 Dihedral : 5.952 57.071 805 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.45 % Allowed : 20.28 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.37), residues: 543 helix: 2.66 (0.46), residues: 128 sheet: -0.03 (0.40), residues: 161 loop : -1.01 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.013 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 TYR 0.008 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6591 (OUTLIER) cc_final: 0.6164 (t) REVERT: A 153 MET cc_start: 0.8801 (tpp) cc_final: 0.8479 (tpp) REVERT: A 211 LYS cc_start: 0.8088 (tppp) cc_final: 0.7690 (ttpt) REVERT: B 293 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.6956 (p) REVERT: B 302 MET cc_start: 0.6476 (ptm) cc_final: 0.6256 (ptt) outliers start: 17 outliers final: 12 residues processed: 61 average time/residue: 0.1832 time to fit residues: 14.4877 Evaluate side-chains 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 420 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.0010 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.098477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.083403 restraints weight = 12136.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085329 restraints weight = 7747.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086635 restraints weight = 5741.109| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4617 Z= 0.203 Angle : 0.629 8.504 6259 Z= 0.316 Chirality : 0.043 0.162 729 Planarity : 0.004 0.038 793 Dihedral : 5.819 56.792 805 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 20.69 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.37), residues: 543 helix: 2.68 (0.46), residues: 128 sheet: -0.01 (0.41), residues: 161 loop : -0.95 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 212 HIS 0.013 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 TYR 0.008 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6608 (OUTLIER) cc_final: 0.6202 (t) REVERT: A 153 MET cc_start: 0.8805 (tpp) cc_final: 0.8504 (tpp) REVERT: A 211 LYS cc_start: 0.8043 (tppp) cc_final: 0.7709 (ttpt) REVERT: B 293 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.7023 (p) REVERT: C 379 TYR cc_start: 0.8136 (p90) cc_final: 0.7733 (p90) outliers start: 16 outliers final: 12 residues processed: 58 average time/residue: 0.1771 time to fit residues: 13.2006 Evaluate side-chains 59 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 372 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.097650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082655 restraints weight = 11993.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084543 restraints weight = 7700.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085836 restraints weight = 5718.292| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4617 Z= 0.225 Angle : 0.649 8.471 6259 Z= 0.324 Chirality : 0.043 0.171 729 Planarity : 0.004 0.038 793 Dihedral : 5.782 57.243 805 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 20.49 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.37), residues: 543 helix: 2.59 (0.46), residues: 128 sheet: 0.15 (0.41), residues: 157 loop : -1.01 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 310 HIS 0.008 0.001 HIS A 108 PHE 0.008 0.001 PHE B 297 TYR 0.008 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1086 Ramachandran restraints generated. 543 Oldfield, 0 Emsley, 543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6645 (OUTLIER) cc_final: 0.6260 (t) REVERT: A 153 MET cc_start: 0.8886 (tpp) cc_final: 0.8581 (tpp) REVERT: A 211 LYS cc_start: 0.8037 (tppp) cc_final: 0.7676 (ttpt) REVERT: B 293 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7083 (p) REVERT: C 379 TYR cc_start: 0.8148 (p90) cc_final: 0.7876 (p90) outliers start: 16 outliers final: 13 residues processed: 58 average time/residue: 0.1722 time to fit residues: 12.9788 Evaluate side-chains 60 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 420 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** C 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.098566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.083572 restraints weight = 12049.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085485 restraints weight = 7698.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086814 restraints weight = 5702.964| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4617 Z= 0.190 Angle : 0.637 8.595 6259 Z= 0.312 Chirality : 0.043 0.163 729 Planarity : 0.004 0.038 793 Dihedral : 5.610 56.655 805 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.25 % Allowed : 20.69 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.37), residues: 543 helix: 2.71 (0.46), residues: 128 sheet: 0.22 (0.41), residues: 157 loop : -0.89 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.008 0.001 HIS A 108 PHE 0.007 0.001 PHE B 292 TYR 0.008 0.001 TYR A 35 ARG 0.001 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1853.45 seconds wall clock time: 34 minutes 17.65 seconds (2057.65 seconds total)