Starting phenix.real_space_refine on Wed Sep 17 12:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukg_26580/09_2025/7ukg_26580.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukg_26580/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ukg_26580/09_2025/7ukg_26580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukg_26580/09_2025/7ukg_26580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukg_26580/09_2025/7ukg_26580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukg_26580/09_2025/7ukg_26580.map" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 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: 2.41, per 1000 atoms: 0.28 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: 0.89 Conformation dependent library (CDL) restraints added in 331.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.38 Time building geometry restraints manager: 1.14 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: 10.650 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.000 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.010 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:7.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.070 ------------------------------------------------------------------------------- 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= 0.247 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG B 256 TYR 0.021 0.002 TYR B 188 PHE 0.018 0.002 PHE D 194 TRP 0.005 0.001 TRP A 362 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8836) covalent geometry : angle 0.57926 (12012) hydrogen bonds : bond 0.10917 ( 717) hydrogen bonds : angle 4.07936 ( 2055) *********************** 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 : 0.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.6076 time to fit residues: 82.1175 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.151156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102967 restraints weight = 9026.355| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.62 r_work: 0.3110 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0571 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= 0.135 Angle : 0.467 5.039 12012 Z= 0.259 Chirality : 0.039 0.127 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.562 11.791 1236 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 10.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.25), residues: 1112 helix: 2.54 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.45 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.020 0.002 TYR C 188 PHE 0.015 0.002 PHE D 194 TRP 0.006 0.001 TRP C 362 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8836) covalent geometry : angle 0.46659 (12012) hydrogen bonds : bond 0.04745 ( 717) hydrogen bonds : angle 3.47207 ( 2055) *********************** 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 136 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.352 Fit side-chains REVERT: A 170 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6718 (mmt180) outliers start: 5 outliers final: 1 residues processed: 136 average time/residue: 0.5784 time to fit residues: 83.8296 Evaluate side-chains 127 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.8902 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.150704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102412 restraints weight = 8939.047| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.61 r_work: 0.3102 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0697 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= 0.150 Angle : 0.478 5.049 12012 Z= 0.263 Chirality : 0.040 0.127 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.568 11.765 1236 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 12.23 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.57 (0.25), residues: 1112 helix: 2.60 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.52 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.021 0.002 TYR A 188 PHE 0.017 0.002 PHE A 289 TRP 0.007 0.002 TRP A 362 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8836) covalent geometry : angle 0.47801 (12012) hydrogen bonds : bond 0.04853 ( 717) hydrogen bonds : angle 3.46654 ( 2055) *********************** 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 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.326 Fit side-chains REVERT: A 170 ARG cc_start: 0.7027 (mtm180) cc_final: 0.6800 (mmt180) REVERT: A 279 MET cc_start: 0.6517 (mtp) cc_final: 0.6153 (ptt) outliers start: 5 outliers final: 1 residues processed: 142 average time/residue: 0.5419 time to fit residues: 82.2291 Evaluate side-chains 130 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 43 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.151084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102873 restraints weight = 9189.645| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.63 r_work: 0.3110 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0856 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= 0.140 Angle : 0.463 5.053 12012 Z= 0.255 Chirality : 0.039 0.123 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.524 11.836 1236 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.08 % Allowed : 12.01 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.71 (0.25), residues: 1112 helix: 2.69 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.020 0.002 TYR A 188 PHE 0.015 0.002 PHE C 194 TRP 0.006 0.001 TRP D 362 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8836) covalent geometry : angle 0.46331 (12012) hydrogen bonds : bond 0.04676 ( 717) hydrogen bonds : angle 3.38344 ( 2055) *********************** 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 149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.336 Fit side-chains REVERT: A 170 ARG cc_start: 0.7082 (mtm180) cc_final: 0.6813 (mmt180) REVERT: A 279 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.6223 (ptt) REVERT: B 170 ARG cc_start: 0.7100 (mtm180) cc_final: 0.6761 (mpt90) REVERT: C 170 ARG cc_start: 0.7111 (mtm180) cc_final: 0.6763 (mpt90) REVERT: D 170 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6802 (mmt180) outliers start: 10 outliers final: 1 residues processed: 148 average time/residue: 0.5753 time to fit residues: 90.8405 Evaluate side-chains 134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 26 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 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 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 = 0.151677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.103583 restraints weight = 9088.664| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.64 r_work: 0.3122 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0943 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= 0.126 Angle : 0.455 4.996 12012 Z= 0.248 Chirality : 0.039 0.118 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.468 11.813 1236 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.25), residues: 1112 helix: 2.78 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.66 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 256 TYR 0.019 0.002 TYR A 188 PHE 0.014 0.001 PHE D 194 TRP 0.006 0.001 TRP B 362 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8836) covalent geometry : angle 0.45464 (12012) hydrogen bonds : bond 0.04476 ( 717) hydrogen bonds : angle 3.33969 ( 2055) *********************** 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 148 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.328 Fit side-chains REVERT: A 170 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6786 (mmt180) REVERT: B 170 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6764 (mpt90) REVERT: C 170 ARG cc_start: 0.7118 (mtm180) cc_final: 0.6762 (mpt90) REVERT: D 170 ARG cc_start: 0.7124 (mtm180) cc_final: 0.6768 (mpt90) outliers start: 9 outliers final: 0 residues processed: 146 average time/residue: 0.6149 time to fit residues: 95.4623 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 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 = 0.3871 r_free = 0.3871 target = 0.151168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102878 restraints weight = 8994.666| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.63 r_work: 0.3112 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0997 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= 0.139 Angle : 0.471 5.022 12012 Z= 0.257 Chirality : 0.039 0.120 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.501 11.571 1236 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.41 % Allowed : 11.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.25), residues: 1112 helix: 2.74 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.65 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.020 0.002 TYR A 188 PHE 0.015 0.001 PHE A 194 TRP 0.006 0.001 TRP B 362 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8836) covalent geometry : angle 0.47086 (12012) hydrogen bonds : bond 0.04637 ( 717) hydrogen bonds : angle 3.36504 ( 2055) *********************** 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 150 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.312 Fit side-chains REVERT: A 170 ARG cc_start: 0.7045 (mtm180) cc_final: 0.6778 (mmt180) REVERT: B 170 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6752 (mpt90) REVERT: C 170 ARG cc_start: 0.7106 (mtm180) cc_final: 0.6754 (mpt90) REVERT: D 170 ARG cc_start: 0.7122 (mtm180) cc_final: 0.6768 (mpt90) outliers start: 13 outliers final: 1 residues processed: 147 average time/residue: 0.5827 time to fit residues: 91.1582 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.151612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103413 restraints weight = 9154.021| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.65 r_work: 0.3117 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1054 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= 0.128 Angle : 0.463 4.995 12012 Z= 0.251 Chirality : 0.039 0.117 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.464 11.564 1236 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 12.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.86 (0.25), residues: 1112 helix: 2.79 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.67 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 256 TYR 0.019 0.002 TYR A 188 PHE 0.014 0.001 PHE D 194 TRP 0.006 0.001 TRP C 362 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8836) covalent geometry : angle 0.46309 (12012) hydrogen bonds : bond 0.04480 ( 717) hydrogen bonds : angle 3.33398 ( 2055) *********************** 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 141 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.238 Fit side-chains REVERT: A 170 ARG cc_start: 0.7032 (mtm180) cc_final: 0.6773 (mmt180) REVERT: B 170 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6750 (mpt90) REVERT: C 170 ARG cc_start: 0.7099 (mtm180) cc_final: 0.6754 (mpt90) REVERT: D 170 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6756 (mpt90) outliers start: 5 outliers final: 1 residues processed: 141 average time/residue: 0.5822 time to fit residues: 87.2221 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 : 0.386 ------------------------------------------------------------------------------- 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 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 chunk 73 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.153027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105267 restraints weight = 8991.059| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.63 r_work: 0.3153 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1187 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= 0.108 Angle : 0.437 4.973 12012 Z= 0.237 Chirality : 0.038 0.113 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.357 11.072 1236 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.32 % Allowed : 13.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.08 (0.25), residues: 1112 helix: 2.94 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.74 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.016 0.002 TYR A 188 PHE 0.011 0.001 PHE D 194 TRP 0.005 0.001 TRP C 172 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8836) covalent geometry : angle 0.43704 (12012) hydrogen bonds : bond 0.04071 ( 717) hydrogen bonds : angle 3.24717 ( 2055) *********************** 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 144 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.332 Fit side-chains REVERT: A 170 ARG cc_start: 0.6984 (mtm180) cc_final: 0.6755 (mmt180) REVERT: B 170 ARG cc_start: 0.7061 (mtm180) cc_final: 0.6707 (mmt180) REVERT: B 181 SER cc_start: 0.6272 (OUTLIER) cc_final: 0.5975 (t) REVERT: C 170 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6706 (mmt180) REVERT: D 170 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6712 (mmt180) REVERT: D 181 SER cc_start: 0.6263 (OUTLIER) cc_final: 0.5966 (t) outliers start: 3 outliers final: 0 residues processed: 144 average time/residue: 0.5824 time to fit residues: 89.1563 Evaluate side-chains 133 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B 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 39 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103948 restraints weight = 9036.795| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.65 r_work: 0.3132 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: 0.8728 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8836 Z= 0.117 Angle : 0.452 5.008 12012 Z= 0.244 Chirality : 0.038 0.112 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.368 11.102 1236 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 13.96 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.07 (0.25), residues: 1112 helix: 2.94 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.71 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 256 TYR 0.019 0.002 TYR D 188 PHE 0.012 0.001 PHE D 194 TRP 0.005 0.001 TRP D 362 HIS 0.002 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8836) covalent geometry : angle 0.45210 (12012) hydrogen bonds : bond 0.04255 ( 717) hydrogen bonds : angle 3.25507 ( 2055) *********************** 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 142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.348 Fit side-chains REVERT: A 170 ARG cc_start: 0.6986 (mtm180) cc_final: 0.6737 (mmt180) REVERT: A 181 SER cc_start: 0.6288 (OUTLIER) cc_final: 0.5949 (t) REVERT: B 170 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6656 (mmt180) REVERT: B 181 SER cc_start: 0.6217 (OUTLIER) cc_final: 0.5918 (t) REVERT: C 170 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6648 (mmt180) REVERT: C 181 SER cc_start: 0.6303 (OUTLIER) cc_final: 0.5971 (t) REVERT: D 170 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6639 (mmt180) REVERT: D 181 SER cc_start: 0.6219 (OUTLIER) cc_final: 0.5919 (t) outliers start: 5 outliers final: 0 residues processed: 142 average time/residue: 0.5905 time to fit residues: 89.0852 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 : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER 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 48 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 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 = 0.3880 r_free = 0.3880 target = 0.151779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103797 restraints weight = 9020.478| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.64 r_work: 0.3121 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1199 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= 0.122 Angle : 0.465 5.894 12012 Z= 0.250 Chirality : 0.038 0.114 1476 Planarity : 0.004 0.030 1448 Dihedral : 3.378 11.471 1236 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 13.96 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.00 (0.25), residues: 1112 helix: 2.89 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.65 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.019 0.002 TYR A 188 PHE 0.012 0.001 PHE D 194 TRP 0.006 0.001 TRP B 362 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8836) covalent geometry : angle 0.46458 (12012) hydrogen bonds : bond 0.04325 ( 717) hydrogen bonds : angle 3.27274 ( 2055) ********************** 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 139 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.344 Fit side-chains REVERT: A 170 ARG cc_start: 0.6982 (mtm180) cc_final: 0.6736 (mmt180) REVERT: A 181 SER cc_start: 0.6276 (OUTLIER) cc_final: 0.5956 (t) REVERT: B 170 ARG cc_start: 0.7089 (mtm180) cc_final: 0.6657 (mmt180) REVERT: B 181 SER cc_start: 0.6223 (OUTLIER) cc_final: 0.5923 (t) REVERT: C 170 ARG cc_start: 0.7085 (mtm180) cc_final: 0.6652 (mmt180) REVERT: C 181 SER cc_start: 0.6316 (OUTLIER) cc_final: 0.5982 (t) REVERT: D 170 ARG cc_start: 0.7091 (mtm180) cc_final: 0.6658 (mmt180) REVERT: D 181 SER cc_start: 0.6274 (OUTLIER) cc_final: 0.5961 (t) outliers start: 5 outliers final: 0 residues processed: 139 average time/residue: 0.5758 time to fit residues: 85.0990 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 : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER 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 56 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.150468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102406 restraints weight = 8962.058| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.62 r_work: 0.3089 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1129 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= 0.154 Angle : 0.497 5.447 12012 Z= 0.268 Chirality : 0.040 0.122 1476 Planarity : 0.004 0.031 1448 Dihedral : 3.494 12.118 1236 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.87 % Allowed : 13.64 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.78 (0.25), residues: 1112 helix: 2.74 (0.17), residues: 892 sheet: None (None), residues: 0 loop : 1.58 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.021 0.002 TYR A 188 PHE 0.014 0.002 PHE A 194 TRP 0.007 0.001 TRP B 362 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8836) covalent geometry : angle 0.49657 (12012) hydrogen bonds : bond 0.04789 ( 717) hydrogen bonds : angle 3.37616 ( 2055) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4417.42 seconds wall clock time: 75 minutes 55.97 seconds (4555.97 seconds total)