Starting phenix.real_space_refine on Thu Mar 6 02:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v2a_42903/03_2025/8v2a_42903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v2a_42903/03_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_42903/03_2025/8v2a_42903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v2a_42903/03_2025/8v2a_42903.map" model { file = "/net/cci-nas-00/data/ceres_data/8v2a_42903/03_2025/8v2a_42903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v2a_42903/03_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-5624/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: 5.55, per 1000 atoms: 1.23 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: 1.38 Conformation dependent library (CDL) restraints added in 569.8 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: 0.50 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: 1.18 Time building geometry restraints manager: 1.54 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.990 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:5.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- 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 : 0.551 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: 0.2658 time to fit residues: 27.1804 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 : 0.507 ------------------------------------------------------------------------------- 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 = 0.089543 restraints weight = 11866.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.091630 restraints weight = 7485.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.093042 restraints weight = 5552.028| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 12.967 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 : 0.526 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.6965 (tptm) cc_final: 0.6706 (tptm) REVERT: A 153 MET cc_start: 0.8783 (tpp) cc_final: 0.8508 (tpp) REVERT: A 211 LYS cc_start: 0.7961 (tppp) cc_final: 0.7651 (ttpt) REVERT: C 320 ASP cc_start: 0.7852 (m-30) cc_final: 0.7644 (m-30) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.1938 time to fit residues: 15.3232 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 : 0.522 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.6980 chunk 22 optimal weight: 8.9990 chunk 47 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 0.0980 chunk 33 optimal weight: 0.4980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 ** 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 = 0.3867 r_free = 0.3867 target = 0.105751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.090568 restraints weight = 11900.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.092641 restraints weight = 7436.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.094092 restraints weight = 5490.405| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2011 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= 0.178 Angle : 0.600 7.987 6259 Z= 0.296 Chirality : 0.044 0.180 729 Planarity : 0.004 0.032 793 Dihedral : 10.117 57.314 805 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.03 % Allowed : 15.21 % Favored : 82.76 % 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: -0.22 (0.36), residues: 543 helix: 2.40 (0.46), residues: 127 sheet: -0.32 (0.38), residues: 162 loop : -1.37 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 HIS 0.009 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 TYR 0.009 0.001 TYR A 35 ARG 0.002 0.000 ARG C 381 *********************** 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 64 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8755 (tpp) cc_final: 0.8488 (tpp) REVERT: A 211 LYS cc_start: 0.7940 (tppp) cc_final: 0.7622 (ttpt) REVERT: C 320 ASP cc_start: 0.7909 (m-30) cc_final: 0.7652 (m-30) REVERT: C 349 ILE cc_start: 0.7715 (mt) cc_final: 0.7431 (tt) outliers start: 10 outliers final: 6 residues processed: 60 average time/residue: 0.1930 time to fit residues: 14.6975 Evaluate side-chains 53 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 236 LEU Chi-restraints excluded: chain B residue 299 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3692 r_free = 0.3692 target = 0.098654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.083398 restraints weight = 12282.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.085327 restraints weight = 7810.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086662 restraints weight = 5779.442| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4617 Z= 0.256 Angle : 0.628 6.396 6259 Z= 0.310 Chirality : 0.044 0.155 729 Planarity : 0.004 0.031 793 Dihedral : 7.417 57.590 805 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.23 % Allowed : 17.65 % Favored : 80.12 % 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: -0.13 (0.36), residues: 543 helix: 2.30 (0.46), residues: 127 sheet: -0.26 (0.39), residues: 163 loop : -1.22 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 212 HIS 0.010 0.001 HIS A 108 PHE 0.009 0.001 PHE A 95 TYR 0.012 0.001 TYR C 406 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: 11 poor density : 51 time to evaluate : 0.531 Fit side-chains REVERT: A 153 MET cc_start: 0.8841 (tpp) cc_final: 0.8564 (tpp) REVERT: A 211 LYS cc_start: 0.8094 (tppp) cc_final: 0.7708 (ttpt) REVERT: B 134 CYS cc_start: 0.5390 (m) cc_final: 0.5188 (m) REVERT: C 313 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.9038 (p0) REVERT: C 320 ASP cc_start: 0.7939 (m-30) cc_final: 0.7564 (m-30) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.1930 time to fit residues: 14.4247 Evaluate side-chains 55 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 B residue 318 SER Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 371 LEU 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: 1.9990 chunk 41 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.098945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083746 restraints weight = 12235.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085683 restraints weight = 7778.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.086979 restraints weight = 5760.952| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4617 Z= 0.233 Angle : 0.609 8.672 6259 Z= 0.300 Chirality : 0.043 0.155 729 Planarity : 0.004 0.034 793 Dihedral : 6.766 57.713 805 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % 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: 0.01 (0.36), residues: 543 helix: 2.44 (0.46), residues: 128 sheet: -0.18 (0.39), residues: 163 loop : -1.17 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 212 HIS 0.010 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 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 68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.500 Fit side-chains REVERT: A 33 LYS cc_start: 0.7165 (mmmm) cc_final: 0.6907 (tptm) REVERT: A 153 MET cc_start: 0.8824 (tpp) cc_final: 0.8539 (tpp) REVERT: A 211 LYS cc_start: 0.8073 (tppp) cc_final: 0.7736 (ttpt) REVERT: C 320 ASP cc_start: 0.7878 (m-30) cc_final: 0.7479 (m-30) outliers start: 16 outliers final: 8 residues processed: 63 average time/residue: 0.2101 time to fit residues: 16.4269 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 : 0.529 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 26 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 40 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.098662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083652 restraints weight = 12103.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085624 restraints weight = 7633.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.086903 restraints weight = 5614.101| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2752 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= 0.198 Angle : 0.593 7.158 6259 Z= 0.294 Chirality : 0.043 0.156 729 Planarity : 0.004 0.036 793 Dihedral : 6.348 57.133 805 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.04 % Allowed : 18.26 % Favored : 78.70 % 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: 0.19 (0.37), residues: 543 helix: 2.61 (0.46), residues: 128 sheet: -0.11 (0.39), residues: 166 loop : -1.04 (0.39), residues: 249 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 0.007 0.001 PHE B 297 TYR 0.008 0.001 TYR A 35 ARG 0.002 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 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: 15 poor density : 51 time to evaluate : 0.532 Fit side-chains REVERT: A 33 LYS cc_start: 0.7128 (mmmm) cc_final: 0.6891 (tptm) REVERT: A 86 THR cc_start: 0.6652 (OUTLIER) cc_final: 0.6170 (t) REVERT: A 153 MET cc_start: 0.8827 (tpp) cc_final: 0.8541 (tpp) REVERT: A 211 LYS cc_start: 0.8055 (tppp) cc_final: 0.7728 (ttpt) REVERT: B 293 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7120 (p) REVERT: C 320 ASP cc_start: 0.7854 (m-30) cc_final: 0.7431 (m-30) outliers start: 15 outliers final: 7 residues processed: 61 average time/residue: 0.1890 time to fit residues: 14.5894 Evaluate side-chains 57 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.099005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.083853 restraints weight = 12075.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085763 restraints weight = 7706.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.087087 restraints weight = 5747.633| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2839 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= 0.201 Angle : 0.614 7.581 6259 Z= 0.305 Chirality : 0.043 0.157 729 Planarity : 0.004 0.036 793 Dihedral : 6.121 56.788 805 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.64 % Allowed : 19.68 % 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: 0.20 (0.37), residues: 543 helix: 2.64 (0.46), residues: 128 sheet: -0.07 (0.40), residues: 161 loop : -1.06 (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 0.007 0.001 PHE B 292 TYR 0.008 0.001 TYR A 35 ARG 0.003 0.000 ARG B 143 *********************** 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 62 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7173 (mmmm) cc_final: 0.6941 (tptm) REVERT: A 86 THR cc_start: 0.6583 (OUTLIER) cc_final: 0.6122 (t) REVERT: A 153 MET cc_start: 0.8825 (tpp) cc_final: 0.8518 (tpp) REVERT: A 211 LYS cc_start: 0.8053 (tppp) cc_final: 0.7684 (ttpt) REVERT: B 293 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.6987 (p) outliers start: 13 outliers final: 9 residues processed: 58 average time/residue: 0.1892 time to fit residues: 14.0431 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.544 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.099634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.084501 restraints weight = 11973.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.086469 restraints weight = 7628.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087788 restraints weight = 5640.178| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2903 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= 0.180 Angle : 0.596 7.201 6259 Z= 0.297 Chirality : 0.042 0.152 729 Planarity : 0.004 0.038 793 Dihedral : 5.849 56.337 805 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 19.47 % Favored : 77.28 % 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: 2.76 (0.46), residues: 128 sheet: 0.04 (0.41), residues: 160 loop : -1.00 (0.39), residues: 255 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 0.007 0.001 TYR A 35 ARG 0.001 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 68 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7092 (mmmm) cc_final: 0.6859 (tptm) REVERT: A 86 THR cc_start: 0.6585 (OUTLIER) cc_final: 0.6146 (t) REVERT: A 153 MET cc_start: 0.8808 (tpp) cc_final: 0.8523 (tpp) REVERT: A 211 LYS cc_start: 0.8000 (tppp) cc_final: 0.7673 (ttpt) REVERT: B 293 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.6941 (p) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 0.1997 time to fit residues: 15.6927 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 : 0.554 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.098969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.083758 restraints weight = 12112.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.085712 restraints weight = 7731.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.087017 restraints weight = 5743.228| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3013 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= 0.209 Angle : 0.629 9.676 6259 Z= 0.312 Chirality : 0.043 0.159 729 Planarity : 0.004 0.037 793 Dihedral : 5.805 56.777 805 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.25 % Allowed : 20.28 % 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: 0.37 (0.37), residues: 543 helix: 2.64 (0.46), residues: 128 sheet: 0.08 (0.41), residues: 161 loop : -0.90 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.012 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 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 : 0.487 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6906 (tptm) REVERT: A 86 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.6175 (t) REVERT: A 153 MET cc_start: 0.8823 (tpp) cc_final: 0.8526 (tpp) REVERT: A 211 LYS cc_start: 0.8028 (tppp) cc_final: 0.7712 (ttpt) REVERT: B 293 THR cc_start: 0.7257 (OUTLIER) cc_final: 0.6982 (p) outliers start: 16 outliers final: 12 residues processed: 58 average time/residue: 0.1857 time to fit residues: 13.7060 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 : 0.536 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.099041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083853 restraints weight = 11969.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.085782 restraints weight = 7662.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087087 restraints weight = 5707.484| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3109 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= 0.202 Angle : 0.638 9.014 6259 Z= 0.313 Chirality : 0.043 0.159 729 Planarity : 0.004 0.038 793 Dihedral : 5.704 56.664 805 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.46 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: 0.40 (0.37), residues: 543 helix: 2.68 (0.46), residues: 128 sheet: 0.08 (0.41), residues: 161 loop : -0.88 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 212 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 0.001 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 63 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7124 (mmmm) cc_final: 0.6910 (tptm) REVERT: A 86 THR cc_start: 0.6597 (OUTLIER) cc_final: 0.6190 (t) REVERT: A 153 MET cc_start: 0.8821 (tpp) cc_final: 0.8532 (tpp) REVERT: A 211 LYS cc_start: 0.8043 (tppp) cc_final: 0.7717 (ttpt) REVERT: B 293 THR cc_start: 0.7247 (OUTLIER) cc_final: 0.6962 (p) REVERT: C 379 TYR cc_start: 0.8135 (p90) cc_final: 0.7819 (p90) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.1948 time to fit residues: 14.5805 Evaluate side-chains 58 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.0770 chunk 36 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.2756 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.100694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.085528 restraints weight = 11980.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.087445 restraints weight = 7668.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.088803 restraints weight = 5704.165| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3135 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= 0.175 Angle : 0.646 8.997 6259 Z= 0.314 Chirality : 0.042 0.175 729 Planarity : 0.004 0.039 793 Dihedral : 5.464 55.655 805 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.84 % Allowed : 21.30 % 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: 0.55 (0.37), residues: 543 helix: 2.82 (0.46), residues: 128 sheet: 0.23 (0.41), residues: 160 loop : -0.83 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 353 HIS 0.008 0.001 HIS A 108 PHE 0.007 0.001 PHE B 297 TYR 0.009 0.001 TYR C 331 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: 1917.77 seconds wall clock time: 34 minutes 38.39 seconds (2078.39 seconds total)