Starting phenix.real_space_refine on Thu Mar 13 05:14:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukg_26580/03_2025/7ukg_26580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukg_26580/03_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_26580/03_2025/7ukg_26580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukg_26580/03_2025/7ukg_26580.map" model { file = "/net/cci-nas-00/data/ceres_data/7ukg_26580/03_2025/7ukg_26580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukg_26580/03_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-5624/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: 7.16, per 1000 atoms: 0.83 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: 2.63 Conformation dependent library (CDL) restraints added in 1.2 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: 0.88 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: 2.55 Time building geometry restraints manager: 3.05 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: 6.750 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.910 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- 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 : 0.928 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.2113 time to fit residues: 163.8929 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 : 0.930 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103503 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: 0.3000 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- 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 : 1.031 Fit side-chains REVERT: A 170 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6711 (mmt180) outliers start: 4 outliers final: 0 residues processed: 142 average time/residue: 1.2358 time to fit residues: 187.2388 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 : 1.026 ------------------------------------------------------------------------------- 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: 0.7980 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.0470 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: 0.7980 chunk 84 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 = 0.151314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103407 restraints weight = 9061.950| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.61 r_work: 0.3114 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0777 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 : 0.460 5.060 12012 Z= 0.253 Chirality : 0.039 0.124 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.506 11.738 1236 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: 3.70 (0.25), residues: 1112 helix: 2.68 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (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 B 306 PHE 0.018 0.002 PHE A 289 TYR 0.020 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 : 0.950 Fit side-chains REVERT: A 170 ARG cc_start: 0.7053 (mtm180) cc_final: 0.6829 (mmt180) REVERT: A 279 MET cc_start: 0.6508 (mtp) cc_final: 0.6165 (ptt) outliers start: 9 outliers final: 1 residues processed: 148 average time/residue: 0.9977 time to fit residues: 159.1050 Evaluate side-chains 136 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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: 0.2980 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.151623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103480 restraints weight = 8934.719| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.62 r_work: 0.3119 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8836 Z= 0.177 Angle : 0.455 5.006 12012 Z= 0.249 Chirality : 0.039 0.120 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.471 11.851 1236 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.97 % Allowed : 12.45 % Favored : 86.58 % 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: 3.81 (0.25), residues: 1112 helix: 2.75 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.65 (0.48), 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 0.019 0.002 PHE C 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 146 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.950 Fit side-chains REVERT: A 170 ARG cc_start: 0.7007 (mtm180) cc_final: 0.6774 (mmt180) REVERT: A 279 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6221 (ptt) REVERT: B 170 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6760 (mpt90) REVERT: C 170 ARG cc_start: 0.7111 (mtm180) cc_final: 0.6765 (mpt90) REVERT: D 170 ARG cc_start: 0.7125 (mtm180) cc_final: 0.6781 (mpt90) outliers start: 9 outliers final: 1 residues processed: 145 average time/residue: 1.4093 time to fit residues: 217.4709 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 : 1.029 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 96 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.152134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104087 restraints weight = 9046.024| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.62 r_work: 0.3130 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8836 Z= 0.161 Angle : 0.442 5.003 12012 Z= 0.242 Chirality : 0.038 0.117 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.418 11.720 1236 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.08 % Allowed : 12.12 % Favored : 86.80 % 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: 3.95 (0.25), residues: 1112 helix: 2.84 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.72 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 362 HIS 0.003 0.001 HIS A 306 PHE 0.013 0.001 PHE B 289 TYR 0.018 0.002 TYR A 188 ARG 0.005 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 147 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.104 Fit side-chains REVERT: A 170 ARG cc_start: 0.7006 (mtm180) cc_final: 0.6750 (mmt180) REVERT: B 170 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6762 (mpt90) REVERT: C 170 ARG cc_start: 0.7106 (mtm180) cc_final: 0.6755 (mpt90) REVERT: D 170 ARG cc_start: 0.7116 (mtm180) cc_final: 0.6763 (mpt90) outliers start: 10 outliers final: 1 residues processed: 146 average time/residue: 1.4628 time to fit residues: 227.6034 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.150041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101515 restraints weight = 8945.282| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.63 r_work: 0.3082 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8836 Z= 0.264 Angle : 0.507 5.079 12012 Z= 0.276 Chirality : 0.041 0.128 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.579 11.806 1236 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.40 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: 3.68 (0.25), residues: 1112 helix: 2.65 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.66 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 362 HIS 0.002 0.001 HIS A 306 PHE 0.016 0.002 PHE B 194 TYR 0.022 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 151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.001 Fit side-chains REVERT: A 170 ARG cc_start: 0.7045 (mtm180) cc_final: 0.6782 (mmt180) REVERT: B 170 ARG cc_start: 0.7129 (mtm180) cc_final: 0.6789 (mpt90) REVERT: B 183 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.6382 (mpp) REVERT: C 170 ARG cc_start: 0.7124 (mtm180) cc_final: 0.6778 (mpt90) REVERT: C 183 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6381 (mpp) REVERT: D 170 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6785 (mpt90) REVERT: D 183 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6381 (mpp) outliers start: 9 outliers final: 1 residues processed: 148 average time/residue: 1.1858 time to fit residues: 187.0910 Evaluate side-chains 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain D residue 183 MET 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: 0.7980 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 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 = 0.3874 r_free = 0.3874 target = 0.151333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103173 restraints weight = 9074.147| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.63 r_work: 0.3110 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8836 Z= 0.182 Angle : 0.464 5.005 12012 Z= 0.253 Chirality : 0.039 0.118 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.492 11.988 1236 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.54 % Allowed : 13.31 % Favored : 86.15 % 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: 3.80 (0.25), residues: 1112 helix: 2.74 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.67 (0.48), 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 0.014 0.002 PHE A 194 TYR 0.019 0.002 TYR A 188 ARG 0.005 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: 5 poor density : 140 time to evaluate : 0.968 Fit side-chains REVERT: A 170 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6767 (mmt180) REVERT: B 170 ARG cc_start: 0.7112 (mtm180) cc_final: 0.6757 (mpt90) REVERT: C 170 ARG cc_start: 0.7116 (mtm180) cc_final: 0.6766 (mpt90) REVERT: D 170 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6756 (mpt90) outliers start: 5 outliers final: 1 residues processed: 145 average time/residue: 1.2919 time to fit residues: 200.1944 Evaluate side-chains 135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 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 = 0.151404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103226 restraints weight = 9078.415| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.64 r_work: 0.3111 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8836 Z= 0.182 Angle : 0.464 4.990 12012 Z= 0.253 Chirality : 0.039 0.117 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.469 11.513 1236 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 13.42 % 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: 3.85 (0.25), residues: 1112 helix: 2.78 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.68 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 362 HIS 0.002 0.001 HIS A 306 PHE 0.014 0.001 PHE B 194 TYR 0.020 0.002 TYR A 188 ARG 0.006 0.000 ARG C 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 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 1.039 Fit side-chains REVERT: A 170 ARG cc_start: 0.7026 (mtm180) cc_final: 0.6772 (mmt180) REVERT: B 170 ARG cc_start: 0.7084 (mtm180) cc_final: 0.6731 (mmt180) REVERT: B 181 SER cc_start: 0.6285 (OUTLIER) cc_final: 0.5979 (t) REVERT: C 170 ARG cc_start: 0.7106 (mtm180) cc_final: 0.6756 (mpt90) REVERT: C 181 SER cc_start: 0.6287 (OUTLIER) cc_final: 0.5973 (t) REVERT: D 170 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6761 (mpt90) REVERT: D 181 SER cc_start: 0.6322 (OUTLIER) cc_final: 0.5976 (t) outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 1.2343 time to fit residues: 182.9188 Evaluate side-chains 137 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.150536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102308 restraints weight = 9027.948| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.64 r_work: 0.3094 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8836 Z= 0.222 Angle : 0.489 5.050 12012 Z= 0.266 Chirality : 0.040 0.122 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.538 11.885 1236 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.97 % Allowed : 13.10 % Favored : 85.93 % 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: 2.67 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.61 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 362 HIS 0.002 0.001 HIS A 306 PHE 0.015 0.002 PHE B 194 TYR 0.021 0.002 TYR A 188 ARG 0.006 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 150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.832 Fit side-chains REVERT: A 170 ARG cc_start: 0.7013 (mtm180) cc_final: 0.6771 (mmt180) REVERT: A 181 SER cc_start: 0.6324 (OUTLIER) cc_final: 0.5981 (t) REVERT: B 170 ARG cc_start: 0.7128 (mtm180) cc_final: 0.6788 (mpt90) REVERT: B 181 SER cc_start: 0.6335 (OUTLIER) cc_final: 0.5986 (t) REVERT: C 170 ARG cc_start: 0.7134 (mtm180) cc_final: 0.6792 (mpt90) REVERT: C 181 SER cc_start: 0.6302 (OUTLIER) cc_final: 0.5979 (t) REVERT: D 170 ARG cc_start: 0.7143 (mtm180) cc_final: 0.6800 (mpt90) REVERT: D 181 SER cc_start: 0.6342 (OUTLIER) cc_final: 0.5991 (t) outliers start: 9 outliers final: 1 residues processed: 149 average time/residue: 1.2789 time to fit residues: 203.7865 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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: 2.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.151020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102868 restraints weight = 9050.490| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.65 r_work: 0.3104 rms_B_bonded: 2.17 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: 0.8749 moved from start: 0.1110 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= 0.197 Angle : 0.483 5.802 12012 Z= 0.261 Chirality : 0.039 0.120 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.506 11.957 1236 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.76 % Allowed : 13.31 % Favored : 85.93 % 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: 3.73 (0.25), residues: 1112 helix: 2.70 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.56 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 362 HIS 0.002 0.001 HIS B 306 PHE 0.014 0.002 PHE A 194 TYR 0.020 0.002 TYR A 188 ARG 0.006 0.000 ARG D 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 145 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.971 Fit side-chains REVERT: A 170 ARG cc_start: 0.7010 (mtm180) cc_final: 0.6751 (mmt180) REVERT: A 181 SER cc_start: 0.6299 (OUTLIER) cc_final: 0.5959 (t) REVERT: B 170 ARG cc_start: 0.7092 (mtm180) cc_final: 0.6750 (mpt90) REVERT: B 181 SER cc_start: 0.6284 (OUTLIER) cc_final: 0.5950 (t) REVERT: C 170 ARG cc_start: 0.7091 (mtm180) cc_final: 0.6748 (mpt90) REVERT: C 181 SER cc_start: 0.6352 (OUTLIER) cc_final: 0.5998 (t) REVERT: D 170 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6751 (mpt90) REVERT: D 181 SER cc_start: 0.6289 (OUTLIER) cc_final: 0.5952 (t) outliers start: 7 outliers final: 1 residues processed: 145 average time/residue: 1.1527 time to fit residues: 178.4229 Evaluate side-chains 140 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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: 4.9990 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 0.0010 chunk 87 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 = 0.151253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.103178 restraints weight = 9072.987| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.64 r_work: 0.3108 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1150 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= 0.189 Angle : 0.473 5.412 12012 Z= 0.256 Chirality : 0.039 0.119 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.486 12.269 1236 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 13.53 % Favored : 85.93 % 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: 2.74 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (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 A 306 PHE 0.013 0.001 PHE C 194 TYR 0.020 0.002 TYR A 188 ARG 0.005 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9024.04 seconds wall clock time: 156 minutes 47.77 seconds (9407.77 seconds total)