Starting phenix.real_space_refine on Fri Dec 27 11:51:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2a_42903/12_2024/8v2a_42903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2a_42903/12_2024/8v2a_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_42903/12_2024/8v2a_42903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2a_42903/12_2024/8v2a_42903.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2a_42903/12_2024/8v2a_42903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2a_42903/12_2024/8v2a_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.38, per 1000 atoms: 0.97 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: 1.23 Conformation dependent library (CDL) restraints added in 534.2 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: 0.63 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: 1.22 Time building geometry restraints manager: 1.41 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: 7.260 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 15.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.990 ------------------------------------------------------------------------------- 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 : 0.557 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: 0.2500 time to fit residues: 26.1201 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 : 0.552 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.547 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7019 (tptm) cc_final: 0.6769 (tptm) REVERT: A 153 MET cc_start: 0.8778 (tpp) cc_final: 0.8475 (tpp) REVERT: A 211 LYS cc_start: 0.7982 (tppp) cc_final: 0.7612 (ttpt) REVERT: C 320 ASP cc_start: 0.7846 (m-30) cc_final: 0.7630 (m-30) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.2170 time to fit residues: 17.2309 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 : 0.700 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4617 Z= 0.282 Angle : 0.644 7.347 6259 Z= 0.320 Chirality : 0.045 0.175 729 Planarity : 0.004 0.031 793 Dihedral : 9.886 58.190 805 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.84 % Allowed : 16.02 % Favored : 81.14 % 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: -0.40 (0.35), residues: 543 helix: 2.27 (0.47), residues: 126 sheet: -0.50 (0.38), residues: 163 loop : -1.43 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 212 HIS 0.009 0.001 HIS A 108 PHE 0.008 0.001 PHE A 95 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 65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.548 Fit side-chains REVERT: A 33 LYS cc_start: 0.7039 (tptm) cc_final: 0.6764 (tptm) REVERT: A 153 MET cc_start: 0.8828 (tpp) cc_final: 0.8521 (tpp) REVERT: A 211 LYS cc_start: 0.8094 (tppp) cc_final: 0.7640 (ttpt) REVERT: B 134 CYS cc_start: 0.5422 (m) cc_final: 0.5191 (m) REVERT: C 320 ASP cc_start: 0.7909 (m-30) cc_final: 0.7583 (m-30) REVERT: C 349 ILE cc_start: 0.7959 (mt) cc_final: 0.7650 (tt) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.1987 time to fit residues: 15.4377 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 : 0.521 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2548 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= 0.228 Angle : 0.606 6.445 6259 Z= 0.301 Chirality : 0.043 0.154 729 Planarity : 0.004 0.035 793 Dihedral : 7.389 58.109 805 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.62 % Allowed : 18.66 % Favored : 79.72 % 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: -0.10 (0.36), residues: 543 helix: 2.53 (0.47), residues: 126 sheet: -0.25 (0.39), residues: 163 loop : -1.30 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 212 HIS 0.010 0.001 HIS A 108 PHE 0.009 0.001 PHE C 408 TYR 0.010 0.001 TYR A 35 ARG 0.003 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 : 0.517 Fit side-chains REVERT: A 33 LYS cc_start: 0.7069 (tptm) cc_final: 0.6783 (tptm) REVERT: A 153 MET cc_start: 0.8835 (tpp) cc_final: 0.8495 (tpp) REVERT: A 211 LYS cc_start: 0.8139 (tppp) cc_final: 0.7686 (ttpt) REVERT: C 320 ASP cc_start: 0.7939 (m-30) cc_final: 0.7559 (m-30) REVERT: C 349 ILE cc_start: 0.8065 (mt) cc_final: 0.7803 (tt) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 0.1945 time to fit residues: 14.2581 Evaluate side-chains 50 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 29 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2680 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= 0.211 Angle : 0.597 8.958 6259 Z= 0.296 Chirality : 0.043 0.160 729 Planarity : 0.004 0.036 793 Dihedral : 6.575 57.443 805 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.45 % Allowed : 18.66 % Favored : 77.89 % 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: 0.07 (0.36), residues: 543 helix: 2.65 (0.46), residues: 126 sheet: -0.13 (0.39), residues: 163 loop : -1.20 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.011 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 69 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.491 Fit side-chains REVERT: A 33 LYS cc_start: 0.7106 (tptm) cc_final: 0.6796 (tptm) REVERT: A 86 THR cc_start: 0.6615 (OUTLIER) cc_final: 0.6121 (t) REVERT: A 153 MET cc_start: 0.8814 (tpp) cc_final: 0.8498 (tpp) REVERT: A 211 LYS cc_start: 0.8108 (tppp) cc_final: 0.7679 (ttpt) REVERT: C 320 ASP cc_start: 0.7845 (m-30) cc_final: 0.7421 (m-30) outliers start: 17 outliers final: 9 residues processed: 65 average time/residue: 0.2127 time to fit residues: 17.0339 Evaluate side-chains 56 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2849 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= 0.217 Angle : 0.605 6.856 6259 Z= 0.302 Chirality : 0.043 0.163 729 Planarity : 0.004 0.038 793 Dihedral : 6.367 57.332 805 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.25 % Allowed : 18.66 % Favored : 78.09 % 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: 0.16 (0.37), residues: 543 helix: 2.61 (0.46), residues: 128 sheet: -0.11 (0.40), residues: 161 loop : -1.08 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.003 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 66 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6560 (OUTLIER) cc_final: 0.6106 (t) REVERT: A 153 MET cc_start: 0.8840 (tpp) cc_final: 0.8517 (tpp) REVERT: A 211 LYS cc_start: 0.8107 (tppp) cc_final: 0.7647 (ttpt) REVERT: B 293 THR cc_start: 0.7288 (OUTLIER) cc_final: 0.7052 (p) outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.1855 time to fit residues: 14.6192 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 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 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 29 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 24 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4617 Z= 0.171 Angle : 0.596 7.063 6259 Z= 0.296 Chirality : 0.042 0.152 729 Planarity : 0.004 0.038 793 Dihedral : 5.988 56.204 805 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.64 % Allowed : 21.30 % 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: 0.30 (0.37), residues: 543 helix: 2.77 (0.46), residues: 128 sheet: -0.13 (0.39), residues: 165 loop : -0.95 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 310 HIS 0.011 0.001 HIS A 108 PHE 0.007 0.001 PHE C 408 TYR 0.008 0.001 TYR C 379 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: 13 poor density : 55 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6564 (OUTLIER) cc_final: 0.6115 (t) REVERT: A 153 MET cc_start: 0.8780 (tpp) cc_final: 0.8469 (tpp) REVERT: A 211 LYS cc_start: 0.8035 (tppp) cc_final: 0.7625 (ttpt) REVERT: B 293 THR cc_start: 0.7166 (OUTLIER) cc_final: 0.6883 (p) outliers start: 13 outliers final: 8 residues processed: 63 average time/residue: 0.2063 time to fit residues: 16.2912 Evaluate side-chains 57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3022 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= 0.215 Angle : 0.620 7.392 6259 Z= 0.307 Chirality : 0.043 0.163 729 Planarity : 0.004 0.038 793 Dihedral : 5.999 56.878 805 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.25 % Allowed : 20.89 % Favored : 75.86 % 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: 0.26 (0.37), residues: 543 helix: 2.62 (0.46), residues: 128 sheet: -0.05 (0.41), residues: 161 loop : -0.96 (0.39), 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 0.002 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: 16 poor density : 50 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6584 (OUTLIER) cc_final: 0.6160 (t) REVERT: A 153 MET cc_start: 0.8846 (tpp) cc_final: 0.8513 (tpp) REVERT: A 211 LYS cc_start: 0.8089 (tppp) cc_final: 0.7650 (ttpt) REVERT: B 293 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6938 (p) REVERT: C 379 TYR cc_start: 0.8201 (p90) cc_final: 0.7842 (p90) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 0.2129 time to fit residues: 16.7016 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 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 420 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4617 Z= 0.210 Angle : 0.641 9.363 6259 Z= 0.318 Chirality : 0.043 0.162 729 Planarity : 0.004 0.038 793 Dihedral : 5.857 56.994 805 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.04 % Allowed : 20.89 % 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: 0.34 (0.37), residues: 543 helix: 2.65 (0.46), residues: 128 sheet: -0.02 (0.41), residues: 161 loop : -0.87 (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 0.008 0.001 PHE B 297 TYR 0.009 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 65 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.6166 (t) REVERT: A 153 MET cc_start: 0.8804 (tpp) cc_final: 0.8480 (tpp) REVERT: A 211 LYS cc_start: 0.8084 (tppp) cc_final: 0.7638 (ttpt) REVERT: B 293 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6909 (p) REVERT: C 379 TYR cc_start: 0.8175 (p90) cc_final: 0.7816 (p90) outliers start: 15 outliers final: 12 residues processed: 62 average time/residue: 0.1984 time to fit residues: 15.6043 Evaluate side-chains 61 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3168 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= 0.196 Angle : 0.656 8.929 6259 Z= 0.322 Chirality : 0.043 0.160 729 Planarity : 0.004 0.039 793 Dihedral : 5.724 56.620 805 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.25 % Allowed : 20.89 % Favored : 75.86 % 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: 0.39 (0.37), residues: 543 helix: 2.70 (0.46), residues: 128 sheet: 0.02 (0.41), residues: 161 loop : -0.86 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 212 HIS 0.008 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 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 66 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 86 THR cc_start: 0.6595 (OUTLIER) cc_final: 0.6182 (t) REVERT: A 153 MET cc_start: 0.8799 (tpp) cc_final: 0.8481 (tpp) REVERT: A 157 LEU cc_start: 0.7547 (tt) cc_final: 0.7176 (tp) REVERT: A 211 LYS cc_start: 0.8065 (tppp) cc_final: 0.7630 (ttpt) REVERT: B 293 THR cc_start: 0.7149 (OUTLIER) cc_final: 0.6862 (p) REVERT: C 379 TYR cc_start: 0.8140 (p90) cc_final: 0.7843 (p90) outliers start: 16 outliers final: 12 residues processed: 63 average time/residue: 0.2022 time to fit residues: 15.9944 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 : 0.540 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 0.0000 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.099345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.084308 restraints weight = 11941.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.086214 restraints weight = 7658.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.087530 restraints weight = 5686.998| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3167 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= 0.192 Angle : 0.657 8.783 6259 Z= 0.323 Chirality : 0.043 0.175 729 Planarity : 0.004 0.039 793 Dihedral : 5.618 56.469 805 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.04 % Allowed : 21.30 % Favored : 75.66 % 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: 0.50 (0.37), residues: 543 helix: 2.77 (0.46), residues: 128 sheet: 0.13 (0.41), residues: 159 loop : -0.81 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 212 HIS 0.008 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 TYR 0.007 0.001 TYR A 35 ARG 0.001 0.000 ARG A 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.06 seconds wall clock time: 28 minutes 28.78 seconds (1708.78 seconds total)