Starting phenix.real_space_refine on Thu Feb 13 03:32:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukg_26580/02_2025/7ukg_26580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukg_26580/02_2025/7ukg_26580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ukg_26580/02_2025/7ukg_26580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukg_26580/02_2025/7ukg_26580.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukg_26580/02_2025/7ukg_26580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukg_26580/02_2025/7ukg_26580.cif" } resolution = 2.24 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= -0.003 sd= 0.062 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 60 5.16 5 C 5704 2.51 5 N 1424 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8652 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "L" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 163 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.34, per 1000 atoms: 0.85 Number of scatterers: 8652 At special positions: 0 Unit cell: (99.946, 99.946, 79.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 60 16.00 O 1460 8.00 N 1424 7.00 C 5704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 85.5% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 320 Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 4.012A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.011A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 320 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.011A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 424 Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 259 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 4.012A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'I' and resid 96 through 117 Processing helix chain 'J' and resid 96 through 117 Processing helix chain 'K' and resid 96 through 117 Processing helix chain 'L' and resid 96 through 117 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU A 219 " --> pdb=" O CYS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU B 219 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU C 219 " --> pdb=" O CYS C 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 211 removed outlier: 6.111A pdb=" N LEU D 219 " --> pdb=" O CYS D 209 " (cutoff:3.500A) 717 hydrogen bonds defined for protein. 2055 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2616 1.34 - 1.46: 1520 1.46 - 1.57: 4608 1.57 - 1.69: 0 1.69 - 1.80: 92 Bond restraints: 8836 Sorted by residual: bond pdb=" N ARG B 418 " pdb=" CA ARG B 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.81e+00 bond pdb=" N ARG C 418 " pdb=" CA ARG C 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" N ARG A 418 " pdb=" CA ARG A 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.79e+00 bond pdb=" N ARG D 418 " pdb=" CA ARG D 418 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.76e+00 bond pdb=" CB THR B 316 " pdb=" CG2 THR B 316 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 11364 1.05 - 2.09: 493 2.09 - 3.14: 103 3.14 - 4.19: 26 4.19 - 5.24: 26 Bond angle restraints: 12012 Sorted by residual: angle pdb=" CA TYR A 188 " pdb=" CB TYR A 188 " pdb=" CG TYR A 188 " ideal model delta sigma weight residual 113.90 118.83 -4.93 1.80e+00 3.09e-01 7.49e+00 angle pdb=" CA TYR B 188 " pdb=" CB TYR B 188 " pdb=" CG TYR B 188 " ideal model delta sigma weight residual 113.90 118.82 -4.92 1.80e+00 3.09e-01 7.46e+00 angle pdb=" CA TYR D 188 " pdb=" CB TYR D 188 " pdb=" CG TYR D 188 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.36e+00 angle pdb=" CA TYR C 188 " pdb=" CB TYR C 188 " pdb=" CG TYR C 188 " ideal model delta sigma weight residual 113.90 118.77 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CG ARG D 256 " pdb=" CD ARG D 256 " pdb=" NE ARG D 256 " ideal model delta sigma weight residual 112.00 116.92 -4.92 2.20e+00 2.07e-01 4.99e+00 ... (remaining 12007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 4612 15.49 - 30.98: 468 30.98 - 46.47: 84 46.47 - 61.95: 12 61.95 - 77.44: 8 Dihedral angle restraints: 5184 sinusoidal: 1888 harmonic: 3296 Sorted by residual: dihedral pdb=" CG ARG B 411 " pdb=" CD ARG B 411 " pdb=" NE ARG B 411 " pdb=" CZ ARG B 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.87 43.87 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG C 411 " pdb=" CD ARG C 411 " pdb=" NE ARG C 411 " pdb=" CZ ARG C 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.87 43.87 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG D 411 " pdb=" CD ARG D 411 " pdb=" NE ARG D 411 " pdb=" CZ ARG D 411 " ideal model delta sinusoidal sigma weight residual -90.00 -133.86 43.86 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 5181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 714 0.027 - 0.054: 486 0.054 - 0.081: 186 0.081 - 0.108: 50 0.108 - 0.136: 40 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA PHE A 194 " pdb=" N PHE A 194 " pdb=" C PHE A 194 " pdb=" CB PHE A 194 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA PHE B 194 " pdb=" N PHE B 194 " pdb=" C PHE B 194 " pdb=" CB PHE B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1473 not shown) Planarity restraints: 1448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 417 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN C 417 " 0.062 2.00e-02 2.50e+03 pdb=" O GLN C 417 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG C 418 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 417 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN A 417 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN A 417 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 418 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 417 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C GLN B 417 " -0.062 2.00e-02 2.50e+03 pdb=" O GLN B 417 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 418 " 0.021 2.00e-02 2.50e+03 ... (remaining 1445 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 2177 2.79 - 3.38: 10535 3.38 - 3.97: 16944 3.97 - 4.55: 24020 4.55 - 5.14: 33707 Nonbonded interactions: 87383 Sorted by model distance: nonbonded pdb=" OG1 THR D 166 " pdb=" NE2 GLN D 169 " model vdw 2.208 3.120 nonbonded pdb=" OG1 THR C 166 " pdb=" NE2 GLN C 169 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR B 166 " pdb=" OE1 GLN B 169 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR A 166 " pdb=" OE1 GLN A 169 " model vdw 2.328 3.040 nonbonded pdb=" O THR A 369 " pdb=" OG1 THR A 370 " model vdw 2.393 3.040 ... (remaining 87378 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 'A' and resid 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.200 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.060 Find NCS groups from input model: 0.410 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 : 0.006 0.049 8836 Z= 0.376 Angle : 0.579 5.237 12012 Z= 0.331 Chirality : 0.043 0.136 1476 Planarity : 0.004 0.036 1448 Dihedral : 13.160 77.443 3056 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.25), residues: 1112 helix: 2.16 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.32 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.002 0.000 HIS C 306 PHE 0.018 0.002 PHE D 194 TYR 0.021 0.002 TYR B 188 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.938 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.2071 time to fit residues: 163.4946 Evaluate side-chains 124 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 179 HIS B 169 GLN B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103504 restraints weight = 8957.329| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.60 r_work: 0.3118 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8836 Z= 0.171 Angle : 0.458 5.024 12012 Z= 0.254 Chirality : 0.039 0.123 1476 Planarity : 0.004 0.032 1448 Dihedral : 3.537 11.773 1236 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.43 % Allowed : 10.28 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.25), residues: 1112 helix: 2.59 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.46 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 362 HIS 0.002 0.001 HIS C 306 PHE 0.015 0.002 PHE D 194 TYR 0.019 0.002 TYR B 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.841 Fit side-chains REVERT: A 170 ARG cc_start: 0.7019 (mtm180) cc_final: 0.6705 (mmt180) outliers start: 4 outliers final: 0 residues processed: 142 average time/residue: 1.1833 time to fit residues: 179.1095 Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103036 restraints weight = 9044.547| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.61 r_work: 0.3111 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8836 Z= 0.193 Angle : 0.466 5.034 12012 Z= 0.256 Chirality : 0.039 0.124 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.523 11.747 1236 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.97 % Allowed : 11.58 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.25), residues: 1112 helix: 2.66 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.56 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS B 306 PHE 0.017 0.002 PHE A 289 TYR 0.021 0.002 TYR D 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.923 Fit side-chains REVERT: A 170 ARG cc_start: 0.7062 (mtm180) cc_final: 0.6825 (mmt180) REVERT: A 279 MET cc_start: 0.6509 (mtp) cc_final: 0.6157 (ptt) outliers start: 9 outliers final: 1 residues processed: 148 average time/residue: 1.0953 time to fit residues: 173.7520 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 77 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 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.151381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103199 restraints weight = 8936.791| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.62 r_work: 0.3113 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8836 Z= 0.189 Angle : 0.465 4.989 12012 Z= 0.254 Chirality : 0.039 0.121 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.501 11.854 1236 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.76 % Allowed : 12.99 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.25), residues: 1112 helix: 2.72 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.64 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS A 306 PHE 0.018 0.002 PHE D 289 TYR 0.020 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.920 Fit side-chains REVERT: A 170 ARG cc_start: 0.7027 (mtm180) cc_final: 0.6796 (mmt180) REVERT: A 279 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6205 (ptt) REVERT: B 170 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6761 (mpt90) REVERT: C 170 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6756 (mpt90) REVERT: D 170 ARG cc_start: 0.7126 (mtm180) cc_final: 0.6820 (mmt180) outliers start: 7 outliers final: 1 residues processed: 143 average time/residue: 1.2019 time to fit residues: 183.3298 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.100804 restraints weight = 9050.214| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.63 r_work: 0.3070 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8836 Z= 0.323 Angle : 0.540 5.102 12012 Z= 0.294 Chirality : 0.043 0.138 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.691 11.972 1236 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.84 % Allowed : 11.47 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.25), residues: 1112 helix: 2.48 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.59 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 362 HIS 0.002 0.001 HIS B 306 PHE 0.019 0.002 PHE C 194 TYR 0.022 0.003 TYR A 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.921 Fit side-chains REVERT: A 170 ARG cc_start: 0.6996 (mtm180) cc_final: 0.6714 (mmt180) REVERT: A 183 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6455 (mpp) REVERT: C 170 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6790 (mmt180) REVERT: D 170 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6796 (mmt180) outliers start: 17 outliers final: 1 residues processed: 151 average time/residue: 1.1960 time to fit residues: 192.7984 Evaluate side-chains 136 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102491 restraints weight = 8953.686| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.64 r_work: 0.3105 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8836 Z= 0.204 Angle : 0.480 5.071 12012 Z= 0.261 Chirality : 0.040 0.125 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.565 12.068 1236 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.97 % Allowed : 12.55 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.25), residues: 1112 helix: 2.61 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 362 HIS 0.003 0.001 HIS D 306 PHE 0.016 0.002 PHE B 194 TYR 0.020 0.002 TYR A 188 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.949 Fit side-chains REVERT: A 170 ARG cc_start: 0.7029 (mtm180) cc_final: 0.6773 (mmt180) REVERT: A 181 SER cc_start: 0.6315 (OUTLIER) cc_final: 0.5973 (t) REVERT: B 170 ARG cc_start: 0.7102 (mtm180) cc_final: 0.6762 (mpt90) REVERT: B 181 SER cc_start: 0.6341 (OUTLIER) cc_final: 0.5996 (t) REVERT: C 170 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6762 (mpt90) REVERT: C 181 SER cc_start: 0.6341 (OUTLIER) cc_final: 0.5995 (t) REVERT: D 170 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6768 (mpt90) REVERT: D 181 SER cc_start: 0.6351 (OUTLIER) cc_final: 0.6005 (t) outliers start: 9 outliers final: 1 residues processed: 146 average time/residue: 1.1935 time to fit residues: 185.8891 Evaluate side-chains 138 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 181 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.151805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103526 restraints weight = 9067.980| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.65 r_work: 0.3126 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8836 Z= 0.166 Angle : 0.454 5.002 12012 Z= 0.247 Chirality : 0.039 0.116 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.461 11.822 1236 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.87 % Allowed : 13.10 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.25), residues: 1112 helix: 2.76 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.69 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 PHE 0.014 0.001 PHE A 194 TYR 0.018 0.002 TYR A 188 ARG 0.006 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 1.032 Fit side-chains REVERT: A 170 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6772 (mmt180) REVERT: A 181 SER cc_start: 0.6250 (OUTLIER) cc_final: 0.5913 (t) REVERT: B 170 ARG cc_start: 0.7118 (mtm180) cc_final: 0.6757 (mpt90) REVERT: B 181 SER cc_start: 0.6240 (OUTLIER) cc_final: 0.5914 (t) REVERT: C 170 ARG cc_start: 0.7120 (mtm180) cc_final: 0.6760 (mpt90) REVERT: C 181 SER cc_start: 0.6294 (OUTLIER) cc_final: 0.5962 (t) REVERT: D 170 ARG cc_start: 0.7124 (mtm180) cc_final: 0.6761 (mpt90) REVERT: D 181 SER cc_start: 0.6285 (OUTLIER) cc_final: 0.5954 (t) outliers start: 8 outliers final: 1 residues processed: 145 average time/residue: 1.2167 time to fit residues: 188.5166 Evaluate side-chains 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.151038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102926 restraints weight = 9083.879| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.63 r_work: 0.3107 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8836 Z= 0.200 Angle : 0.476 5.017 12012 Z= 0.259 Chirality : 0.039 0.119 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.504 11.618 1236 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.87 % Allowed : 13.85 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.25), residues: 1112 helix: 2.72 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.67 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 362 HIS 0.002 0.001 HIS C 306 PHE 0.014 0.002 PHE C 194 TYR 0.020 0.002 TYR A 188 ARG 0.005 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.914 Fit side-chains REVERT: A 170 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6780 (mmt180) REVERT: A 181 SER cc_start: 0.6310 (OUTLIER) cc_final: 0.5970 (t) REVERT: B 170 ARG cc_start: 0.7124 (mtm180) cc_final: 0.6760 (mmt180) REVERT: B 181 SER cc_start: 0.6336 (OUTLIER) cc_final: 0.5992 (t) REVERT: C 170 ARG cc_start: 0.7123 (mtm180) cc_final: 0.6771 (mpt90) REVERT: C 181 SER cc_start: 0.6337 (OUTLIER) cc_final: 0.5992 (t) REVERT: D 170 ARG cc_start: 0.7132 (mtm180) cc_final: 0.6773 (mpt90) REVERT: D 181 SER cc_start: 0.6330 (OUTLIER) cc_final: 0.5981 (t) outliers start: 8 outliers final: 1 residues processed: 152 average time/residue: 1.1617 time to fit residues: 188.7257 Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 181 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.150593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102407 restraints weight = 9033.876| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.64 r_work: 0.3097 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8836 Z= 0.217 Angle : 0.490 5.032 12012 Z= 0.266 Chirality : 0.040 0.121 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.549 12.174 1236 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.65 % Allowed : 14.29 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.25), residues: 1112 helix: 2.66 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.61 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.002 0.001 HIS D 306 PHE 0.015 0.002 PHE C 194 TYR 0.020 0.002 TYR B 188 ARG 0.005 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.994 Fit side-chains REVERT: A 170 ARG cc_start: 0.7000 (mtm180) cc_final: 0.6752 (mmt180) REVERT: A 181 SER cc_start: 0.6290 (OUTLIER) cc_final: 0.5948 (t) REVERT: B 170 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6763 (mpt90) REVERT: B 181 SER cc_start: 0.6307 (OUTLIER) cc_final: 0.5950 (t) REVERT: C 170 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6750 (mpt90) REVERT: C 181 SER cc_start: 0.6317 (OUTLIER) cc_final: 0.5957 (t) REVERT: D 170 ARG cc_start: 0.7109 (mtm180) cc_final: 0.6751 (mpt90) REVERT: D 181 SER cc_start: 0.6316 (OUTLIER) cc_final: 0.5957 (t) outliers start: 6 outliers final: 1 residues processed: 148 average time/residue: 1.1776 time to fit residues: 185.9726 Evaluate side-chains 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 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 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.151391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103364 restraints weight = 9074.959| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.64 r_work: 0.3112 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8836 Z= 0.181 Angle : 0.471 5.664 12012 Z= 0.256 Chirality : 0.039 0.117 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.492 12.241 1236 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.54 % Allowed : 14.29 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.25), residues: 1112 helix: 2.73 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.62 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 362 HIS 0.003 0.001 HIS A 306 PHE 0.013 0.001 PHE D 194 TYR 0.019 0.002 TYR A 188 ARG 0.005 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.931 Fit side-chains REVERT: A 170 ARG cc_start: 0.7016 (mtm180) cc_final: 0.6761 (mmt180) REVERT: A 181 SER cc_start: 0.6268 (OUTLIER) cc_final: 0.5928 (t) REVERT: B 170 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6762 (mmt180) REVERT: B 181 SER cc_start: 0.6274 (OUTLIER) cc_final: 0.5939 (t) REVERT: C 170 ARG cc_start: 0.7078 (mtm180) cc_final: 0.6712 (mmt180) REVERT: C 181 SER cc_start: 0.6338 (OUTLIER) cc_final: 0.5992 (t) REVERT: D 170 ARG cc_start: 0.7086 (mtm180) cc_final: 0.6716 (mmt180) REVERT: D 181 SER cc_start: 0.6327 (OUTLIER) cc_final: 0.5978 (t) outliers start: 5 outliers final: 1 residues processed: 142 average time/residue: 1.2297 time to fit residues: 186.1123 Evaluate side-chains 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain D residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.151294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103385 restraints weight = 9075.919| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.63 r_work: 0.3111 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8836 Z= 0.186 Angle : 0.478 5.753 12012 Z= 0.259 Chirality : 0.039 0.117 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.493 12.199 1236 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.65 % Allowed : 14.07 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.25), residues: 1112 helix: 2.72 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.57 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 362 HIS 0.002 0.001 HIS A 306 PHE 0.013 0.001 PHE A 194 TYR 0.019 0.002 TYR B 188 ARG 0.003 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8335.17 seconds wall clock time: 147 minutes 39.80 seconds (8859.80 seconds total)