Starting phenix.real_space_refine on Tue Mar 3 16:17:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsw_30848/03_2026/7dsw_30848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsw_30848/03_2026/7dsw_30848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dsw_30848/03_2026/7dsw_30848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsw_30848/03_2026/7dsw_30848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsw_30848/03_2026/7dsw_30848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsw_30848/03_2026/7dsw_30848.map" } resolution = 3.3 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4584 2.51 5 N 1012 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6720 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain: "A" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3301 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 15, 'TRANS': 404} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-1': 6, 'LBN:plan-2': 6, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 59 Unusual residues: {'LBN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 253 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'LBN:plan-1': 6, 'LBN:plan-2': 6, 'LBN:plan-3': 3} Unresolved non-hydrogen planarities: 56 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C10 LBN B 601 " occ=0.00 ... (7 atoms not shown) pdb=" C7 LBN B 601 " occ=0.00 residue: pdb=" C35 LBN B 602 " occ=0.00 ... (7 atoms not shown) pdb=" C5 LBN B 602 " occ=0.00 residue: pdb=" C11 LBN B 603 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN B 603 " occ=0.00 residue: pdb=" C11 LBN B 604 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN B 604 " occ=0.00 residue: pdb=" C11 LBN B 605 " occ=0.00 ... (4 atoms not shown) pdb=" C23 LBN B 605 " occ=0.00 residue: pdb=" C11 LBN B 606 " occ=0.00 ... (11 atoms not shown) pdb=" C8 LBN B 606 " occ=0.00 residue: pdb=" C11 LBN A 801 " occ=0.00 ... (11 atoms not shown) pdb=" C8 LBN A 801 " occ=0.00 residue: pdb=" C10 LBN A 802 " occ=0.00 ... (7 atoms not shown) pdb=" C7 LBN A 802 " occ=0.00 residue: pdb=" C35 LBN A 803 " occ=0.00 ... (7 atoms not shown) pdb=" C5 LBN A 803 " occ=0.00 residue: pdb=" C11 LBN A 804 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN A 804 " occ=0.00 residue: pdb=" C11 LBN A 805 " occ=0.00 ... (9 atoms not shown) pdb=" C8 LBN A 805 " occ=0.00 residue: pdb=" C11 LBN A 806 " occ=0.00 ... (4 atoms not shown) pdb=" C23 LBN A 806 " occ=0.00 Time building chain proxies: 1.19, per 1000 atoms: 0.18 Number of scatterers: 6720 At special positions: 0 Unit cell: (113.36, 67.6, 68.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1098 8.00 N 1012 7.00 C 4584 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: 0.59 Conformation dependent library (CDL) restraints added in 346.0 milliseconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.752A pdb=" N VAL B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 150 removed outlier: 3.747A pdb=" N LEU B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.921A pdb=" N ILE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 215 Processing helix chain 'B' and resid 224 through 235 removed outlier: 3.728A pdb=" N LEU B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 230 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.868A pdb=" N ALA B 244 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 281 removed outlier: 3.685A pdb=" N HIS B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 321 Processing helix chain 'B' and resid 329 through 348 removed outlier: 3.833A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 Proline residue: B 365 - end of helix Processing helix chain 'B' and resid 372 through 404 Processing helix chain 'B' and resid 410 through 437 Processing helix chain 'B' and resid 445 through 454 Processing helix chain 'B' and resid 461 through 468 Processing helix chain 'B' and resid 476 through 494 Processing helix chain 'B' and resid 499 through 505 removed outlier: 3.754A pdb=" N ASP B 504 " --> pdb=" O ARG B 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 121 removed outlier: 3.751A pdb=" N VAL A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.747A pdb=" N LEU A 134 " --> pdb=" O PRO A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.921A pdb=" N ILE A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 215 Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.728A pdb=" N LEU A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.868A pdb=" N ALA A 244 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 281 removed outlier: 3.685A pdb=" N HIS A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 321 Processing helix chain 'A' and resid 329 through 348 removed outlier: 3.834A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 372 through 404 Processing helix chain 'A' and resid 410 through 437 Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.753A pdb=" N ASP A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1404 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: 0.87 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1951 1.34 - 1.46: 1348 1.46 - 1.57: 3551 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 6892 Sorted by residual: bond pdb=" C41 LBN B 606 " pdb=" C42 LBN B 606 " ideal model delta sigma weight residual 1.497 1.568 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C5 LBN B 603 " pdb=" C8 LBN B 603 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C41 LBN A 801 " pdb=" C42 LBN A 801 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C5 LBN A 804 " pdb=" C8 LBN A 804 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C41 LBN A 803 " pdb=" C42 LBN A 803 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 6887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 8885 1.76 - 3.52: 342 3.52 - 5.28: 93 5.28 - 7.03: 24 7.03 - 8.79: 6 Bond angle restraints: 9350 Sorted by residual: angle pdb=" N ILE B 125 " pdb=" CA ILE B 125 " pdb=" C ILE B 125 " ideal model delta sigma weight residual 113.71 108.01 5.70 9.50e-01 1.11e+00 3.60e+01 angle pdb=" N ILE A 125 " pdb=" CA ILE A 125 " pdb=" C ILE A 125 " ideal model delta sigma weight residual 113.71 108.01 5.70 9.50e-01 1.11e+00 3.60e+01 angle pdb=" CA TRP B 386 " pdb=" CB TRP B 386 " pdb=" CG TRP B 386 " ideal model delta sigma weight residual 113.60 119.18 -5.58 1.90e+00 2.77e-01 8.62e+00 angle pdb=" CA TRP A 386 " pdb=" CB TRP A 386 " pdb=" CG TRP A 386 " ideal model delta sigma weight residual 113.60 119.17 -5.57 1.90e+00 2.77e-01 8.61e+00 angle pdb=" CB MET A 208 " pdb=" CG MET A 208 " pdb=" SD MET A 208 " ideal model delta sigma weight residual 112.70 121.49 -8.79 3.00e+00 1.11e-01 8.59e+00 ... (remaining 9345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 3398 14.86 - 29.72: 388 29.72 - 44.59: 106 44.59 - 59.45: 18 59.45 - 74.31: 10 Dihedral angle restraints: 3920 sinusoidal: 1512 harmonic: 2408 Sorted by residual: dihedral pdb=" CA TYR A 366 " pdb=" C TYR A 366 " pdb=" N VAL A 367 " pdb=" CA VAL A 367 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA TYR B 366 " pdb=" C TYR B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASN B 252 " pdb=" C ASN B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 ... (remaining 3917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 650 0.033 - 0.067: 306 0.067 - 0.100: 120 0.100 - 0.134: 36 0.134 - 0.167: 8 Chirality restraints: 1120 Sorted by residual: chirality pdb=" CA PRO B 167 " pdb=" N PRO B 167 " pdb=" C PRO B 167 " pdb=" CB PRO B 167 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA PRO A 167 " pdb=" N PRO A 167 " pdb=" C PRO A 167 " pdb=" CB PRO A 167 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB THR A 124 " pdb=" CA THR A 124 " pdb=" OG1 THR A 124 " pdb=" CG2 THR A 124 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.53e-01 ... (remaining 1117 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 445 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO B 446 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 446 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 446 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 445 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO A 446 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 446 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 446 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 161 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C PHE B 161 " -0.030 2.00e-02 2.50e+03 pdb=" O PHE B 161 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE B 162 " 0.010 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1194 2.76 - 3.29: 6696 3.29 - 3.83: 11443 3.83 - 4.36: 12816 4.36 - 4.90: 23226 Nonbonded interactions: 55375 Sorted by model distance: nonbonded pdb=" O ARG A 440 " pdb=" NZ LYS A 443 " model vdw 2.222 3.120 nonbonded pdb=" O ARG B 440 " pdb=" NZ LYS B 443 " model vdw 2.224 3.120 nonbonded pdb=" O VAL A 494 " pdb=" OG1 THR A 498 " model vdw 2.228 3.040 nonbonded pdb=" O VAL B 494 " pdb=" OG1 THR B 498 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR B 445 " pdb=" OD1 ASP B 448 " model vdw 2.292 3.040 ... (remaining 55370 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 87 through 506 or resid 802 or (resid 803 and (name C40 or \ name C41 or name C42 or name C5 )) or resid 804 or (resid 805 through 806 and ( \ name C11 or name C14 or name C17 or name C20 or name C22 or name C23)))) selection = (chain 'B' and (resid 87 through 506 or resid 602 or (resid 603 and (name C40 or \ name C41 or name C42 or name C5 )) or resid 604 through 605 or (resid 606 and ( \ name C11 or name C14 or name C17 or name C20 or name C22 or name C23)))) } 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=0.00 max=1.00 mean=0.98 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.860 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.008 0.071 6892 Z= 0.346 Angle : 0.896 8.793 9350 Z= 0.457 Chirality : 0.047 0.167 1120 Planarity : 0.005 0.049 1122 Dihedral : 14.346 74.310 2376 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.11 % Allowed : 0.00 % Favored : 98.89 % 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 are not related in a simple way. whole: -0.48 (0.29), residues: 836 helix: 0.58 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -3.35 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 364 TYR 0.014 0.002 TYR A 274 PHE 0.020 0.002 PHE A 176 TRP 0.014 0.002 TRP A 386 HIS 0.007 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00771 ( 6892) covalent geometry : angle 0.89576 ( 9350) hydrogen bonds : bond 0.09740 ( 478) hydrogen bonds : angle 5.53892 ( 1404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.228 Fit side-chains REVERT: B 335 PHE cc_start: 0.8217 (m-80) cc_final: 0.7780 (m-80) REVERT: B 416 SER cc_start: 0.8889 (t) cc_final: 0.8542 (t) REVERT: B 457 LEU cc_start: 0.8141 (pp) cc_final: 0.7920 (pp) REVERT: B 476 MET cc_start: 0.7118 (mmt) cc_final: 0.6904 (pmm) REVERT: A 416 SER cc_start: 0.8891 (t) cc_final: 0.8536 (t) outliers start: 8 outliers final: 0 residues processed: 158 average time/residue: 0.0666 time to fit residues: 14.9221 Evaluate side-chains 128 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 250 HIS A 220 ASN A 250 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106072 restraints weight = 8615.507| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.90 r_work: 0.3119 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6892 Z= 0.147 Angle : 0.591 6.416 9350 Z= 0.310 Chirality : 0.042 0.205 1120 Planarity : 0.004 0.045 1122 Dihedral : 8.022 65.352 958 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.39 % Allowed : 9.00 % Favored : 89.61 % 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 are not related in a simple way. whole: 0.29 (0.30), residues: 836 helix: 1.24 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -3.46 (0.36), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 364 TYR 0.017 0.002 TYR B 96 PHE 0.020 0.001 PHE B 295 TRP 0.007 0.001 TRP A 386 HIS 0.005 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6892) covalent geometry : angle 0.59109 ( 9350) hydrogen bonds : bond 0.04553 ( 478) hydrogen bonds : angle 4.63771 ( 1404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.200 Fit side-chains REVERT: B 234 ILE cc_start: 0.8701 (tt) cc_final: 0.8457 (tt) REVERT: B 247 GLU cc_start: 0.7712 (pm20) cc_final: 0.7464 (pm20) REVERT: B 335 PHE cc_start: 0.8398 (m-80) cc_final: 0.8195 (m-80) REVERT: B 364 ARG cc_start: 0.7965 (ttt90) cc_final: 0.7748 (tpt-90) REVERT: B 368 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7344 (mt-10) REVERT: B 384 LYS cc_start: 0.8737 (tppt) cc_final: 0.8413 (mmtt) REVERT: B 416 SER cc_start: 0.8985 (t) cc_final: 0.8649 (t) REVERT: B 448 ASP cc_start: 0.8215 (p0) cc_final: 0.7982 (p0) REVERT: B 476 MET cc_start: 0.7605 (mmt) cc_final: 0.7003 (pmm) REVERT: A 234 ILE cc_start: 0.8688 (tt) cc_final: 0.8411 (tt) REVERT: A 247 GLU cc_start: 0.7770 (pm20) cc_final: 0.7506 (pm20) REVERT: A 335 PHE cc_start: 0.8320 (m-80) cc_final: 0.8110 (m-80) REVERT: A 448 ASP cc_start: 0.8167 (p0) cc_final: 0.7941 (p0) REVERT: A 476 MET cc_start: 0.7718 (mmt) cc_final: 0.7133 (pmm) outliers start: 10 outliers final: 6 residues processed: 147 average time/residue: 0.0642 time to fit residues: 13.5171 Evaluate side-chains 140 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN B 250 HIS A 220 ASN A 250 HIS A 325 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.122428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.105390 restraints weight = 8652.875| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.85 r_work: 0.3094 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6892 Z= 0.159 Angle : 0.573 6.064 9350 Z= 0.303 Chirality : 0.042 0.230 1120 Planarity : 0.004 0.045 1122 Dihedral : 7.284 66.970 958 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.22 % Allowed : 12.60 % Favored : 85.18 % 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 are not related in a simple way. whole: 0.71 (0.30), residues: 836 helix: 1.57 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -3.05 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.013 0.001 TYR B 96 PHE 0.020 0.001 PHE B 295 TRP 0.007 0.001 TRP B 386 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6892) covalent geometry : angle 0.57326 ( 9350) hydrogen bonds : bond 0.04468 ( 478) hydrogen bonds : angle 4.50226 ( 1404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.249 Fit side-chains REVERT: B 208 MET cc_start: 0.8657 (mmm) cc_final: 0.8442 (mmm) REVERT: B 220 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8762 (m110) REVERT: B 234 ILE cc_start: 0.8762 (tt) cc_final: 0.8528 (tt) REVERT: B 278 GLU cc_start: 0.8566 (tt0) cc_final: 0.8059 (mt-10) REVERT: B 416 SER cc_start: 0.8996 (t) cc_final: 0.8647 (t) REVERT: B 435 PHE cc_start: 0.8402 (t80) cc_final: 0.8198 (t80) REVERT: B 448 ASP cc_start: 0.8189 (p0) cc_final: 0.7954 (p0) REVERT: B 476 MET cc_start: 0.7585 (mmt) cc_final: 0.6970 (pmm) REVERT: A 234 ILE cc_start: 0.8684 (tt) cc_final: 0.8400 (tt) REVERT: A 247 GLU cc_start: 0.7789 (pm20) cc_final: 0.7495 (pm20) REVERT: A 278 GLU cc_start: 0.8478 (tt0) cc_final: 0.8000 (mt-10) REVERT: A 335 PHE cc_start: 0.8363 (m-80) cc_final: 0.8007 (m-80) REVERT: A 448 ASP cc_start: 0.8244 (p0) cc_final: 0.7996 (p0) REVERT: A 476 MET cc_start: 0.7665 (mmt) cc_final: 0.7060 (pmm) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.0580 time to fit residues: 12.3595 Evaluate side-chains 142 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS A 250 HIS A 325 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.113132 restraints weight = 8506.605| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.73 r_work: 0.3113 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6892 Z= 0.156 Angle : 0.562 6.025 9350 Z= 0.297 Chirality : 0.042 0.234 1120 Planarity : 0.005 0.046 1122 Dihedral : 6.943 68.319 958 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.32 % Allowed : 13.02 % Favored : 83.66 % 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 are not related in a simple way. whole: 0.88 (0.30), residues: 836 helix: 1.72 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -3.03 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.012 0.001 TYR A 274 PHE 0.020 0.001 PHE B 295 TRP 0.007 0.001 TRP B 386 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 6892) covalent geometry : angle 0.56176 ( 9350) hydrogen bonds : bond 0.04385 ( 478) hydrogen bonds : angle 4.43135 ( 1404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.247 Fit side-chains REVERT: B 208 MET cc_start: 0.8617 (mmm) cc_final: 0.8376 (mmm) REVERT: B 234 ILE cc_start: 0.8762 (tt) cc_final: 0.8527 (tt) REVERT: B 278 GLU cc_start: 0.8566 (tt0) cc_final: 0.8106 (mt-10) REVERT: B 335 PHE cc_start: 0.8313 (m-80) cc_final: 0.8023 (m-80) REVERT: B 416 SER cc_start: 0.9065 (t) cc_final: 0.8713 (t) REVERT: B 448 ASP cc_start: 0.8167 (p0) cc_final: 0.7930 (p0) REVERT: B 476 MET cc_start: 0.7664 (mmt) cc_final: 0.7066 (pmm) REVERT: A 234 ILE cc_start: 0.8784 (tt) cc_final: 0.8528 (tt) REVERT: A 247 GLU cc_start: 0.7837 (pm20) cc_final: 0.7550 (pm20) REVERT: A 278 GLU cc_start: 0.8475 (tt0) cc_final: 0.8043 (mt-10) REVERT: A 335 PHE cc_start: 0.8470 (m-80) cc_final: 0.8151 (m-80) REVERT: A 448 ASP cc_start: 0.8234 (p0) cc_final: 0.7983 (p0) REVERT: A 476 MET cc_start: 0.7662 (mmt) cc_final: 0.7106 (pmm) outliers start: 24 outliers final: 20 residues processed: 146 average time/residue: 0.0527 time to fit residues: 11.5312 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 63 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS A 495 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.113799 restraints weight = 8469.928| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.72 r_work: 0.3106 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6892 Z= 0.144 Angle : 0.548 5.989 9350 Z= 0.291 Chirality : 0.041 0.237 1120 Planarity : 0.004 0.047 1122 Dihedral : 6.636 66.115 958 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.05 % Allowed : 15.51 % Favored : 81.44 % 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 are not related in a simple way. whole: 1.02 (0.30), residues: 836 helix: 1.81 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.98 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.010 0.001 TYR B 274 PHE 0.019 0.001 PHE B 295 TRP 0.008 0.001 TRP A 386 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6892) covalent geometry : angle 0.54754 ( 9350) hydrogen bonds : bond 0.04275 ( 478) hydrogen bonds : angle 4.33638 ( 1404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.256 Fit side-chains REVERT: B 192 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7951 (t80) REVERT: B 234 ILE cc_start: 0.8786 (tt) cc_final: 0.8538 (tt) REVERT: B 278 GLU cc_start: 0.8554 (tt0) cc_final: 0.8062 (mt-10) REVERT: B 335 PHE cc_start: 0.8334 (m-80) cc_final: 0.8036 (m-80) REVERT: B 448 ASP cc_start: 0.8185 (p0) cc_final: 0.7955 (p0) REVERT: B 476 MET cc_start: 0.7645 (mmt) cc_final: 0.7050 (pmm) REVERT: A 192 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 234 ILE cc_start: 0.8774 (tt) cc_final: 0.8515 (tt) REVERT: A 278 GLU cc_start: 0.8489 (tt0) cc_final: 0.8003 (mt-10) REVERT: A 335 PHE cc_start: 0.8346 (m-80) cc_final: 0.8065 (m-80) REVERT: A 448 ASP cc_start: 0.8224 (p0) cc_final: 0.7981 (p0) REVERT: A 476 MET cc_start: 0.7645 (mmt) cc_final: 0.7050 (pmm) outliers start: 22 outliers final: 16 residues processed: 147 average time/residue: 0.0580 time to fit residues: 12.6923 Evaluate side-chains 149 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS B 266 ASN A 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.115073 restraints weight = 8495.035| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.72 r_work: 0.3124 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6892 Z= 0.132 Angle : 0.537 6.293 9350 Z= 0.284 Chirality : 0.041 0.254 1120 Planarity : 0.004 0.049 1122 Dihedral : 6.426 64.804 958 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.46 % Allowed : 16.20 % Favored : 80.33 % 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 are not related in a simple way. whole: 1.16 (0.30), residues: 836 helix: 1.92 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.93 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.010 0.001 TYR A 274 PHE 0.019 0.001 PHE A 295 TRP 0.009 0.001 TRP B 386 HIS 0.004 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6892) covalent geometry : angle 0.53736 ( 9350) hydrogen bonds : bond 0.04161 ( 478) hydrogen bonds : angle 4.24123 ( 1404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.236 Fit side-chains REVERT: B 192 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8028 (t80) REVERT: B 234 ILE cc_start: 0.8776 (tt) cc_final: 0.8508 (tt) REVERT: B 278 GLU cc_start: 0.8458 (tt0) cc_final: 0.7988 (mt-10) REVERT: B 299 PHE cc_start: 0.7957 (m-80) cc_final: 0.7658 (m-80) REVERT: B 335 PHE cc_start: 0.8354 (m-80) cc_final: 0.8028 (m-80) REVERT: B 448 ASP cc_start: 0.8168 (p0) cc_final: 0.7939 (p0) REVERT: B 476 MET cc_start: 0.7620 (mmt) cc_final: 0.7040 (pmm) REVERT: A 192 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8042 (t80) REVERT: A 234 ILE cc_start: 0.8766 (tt) cc_final: 0.8485 (tt) REVERT: A 278 GLU cc_start: 0.8399 (tt0) cc_final: 0.7936 (mt-10) REVERT: A 335 PHE cc_start: 0.8455 (m-80) cc_final: 0.8195 (m-80) REVERT: A 435 PHE cc_start: 0.8332 (t80) cc_final: 0.8117 (t80) REVERT: A 448 ASP cc_start: 0.8210 (p0) cc_final: 0.7961 (p0) REVERT: A 476 MET cc_start: 0.7642 (mmt) cc_final: 0.7023 (pmm) outliers start: 25 outliers final: 14 residues processed: 145 average time/residue: 0.0557 time to fit residues: 12.1492 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 423 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS A 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107084 restraints weight = 8722.680| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.77 r_work: 0.3095 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6892 Z= 0.156 Angle : 0.560 6.440 9350 Z= 0.296 Chirality : 0.042 0.263 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.597 66.153 958 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.43 % Allowed : 16.20 % Favored : 79.36 % 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 are not related in a simple way. whole: 1.11 (0.30), residues: 836 helix: 1.86 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.90 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.011 0.001 TYR A 274 PHE 0.020 0.001 PHE A 295 TRP 0.006 0.001 TRP A 386 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6892) covalent geometry : angle 0.56017 ( 9350) hydrogen bonds : bond 0.04314 ( 478) hydrogen bonds : angle 4.31266 ( 1404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.232 Fit side-chains REVERT: B 192 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 234 ILE cc_start: 0.8794 (tt) cc_final: 0.8552 (tt) REVERT: B 278 GLU cc_start: 0.8558 (tt0) cc_final: 0.8116 (mt-10) REVERT: B 318 PHE cc_start: 0.8068 (t80) cc_final: 0.7486 (t80) REVERT: B 335 PHE cc_start: 0.8403 (m-80) cc_final: 0.8062 (m-80) REVERT: B 356 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 448 ASP cc_start: 0.8200 (p0) cc_final: 0.7961 (p0) REVERT: B 476 MET cc_start: 0.7663 (mmt) cc_final: 0.7043 (pmm) REVERT: A 192 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 234 ILE cc_start: 0.8799 (tt) cc_final: 0.8545 (tt) REVERT: A 278 GLU cc_start: 0.8522 (tt0) cc_final: 0.8080 (mt-10) REVERT: A 335 PHE cc_start: 0.8449 (m-80) cc_final: 0.8189 (m-80) REVERT: A 448 ASP cc_start: 0.8259 (p0) cc_final: 0.8003 (p0) REVERT: A 476 MET cc_start: 0.7680 (mmt) cc_final: 0.7038 (pmm) outliers start: 32 outliers final: 22 residues processed: 146 average time/residue: 0.0556 time to fit residues: 12.1413 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 181 GLN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 45 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.115129 restraints weight = 8535.249| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.72 r_work: 0.3128 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6892 Z= 0.136 Angle : 0.563 7.452 9350 Z= 0.299 Chirality : 0.042 0.264 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.420 64.840 958 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.32 % Allowed : 17.31 % Favored : 79.36 % 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 are not related in a simple way. whole: 1.22 (0.31), residues: 836 helix: 1.96 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.87 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.010 0.001 TYR B 274 PHE 0.017 0.001 PHE B 295 TRP 0.008 0.001 TRP A 386 HIS 0.004 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6892) covalent geometry : angle 0.56260 ( 9350) hydrogen bonds : bond 0.04174 ( 478) hydrogen bonds : angle 4.22897 ( 1404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.239 Fit side-chains REVERT: B 192 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8060 (t80) REVERT: B 234 ILE cc_start: 0.8780 (tt) cc_final: 0.8509 (tt) REVERT: B 278 GLU cc_start: 0.8530 (tt0) cc_final: 0.8043 (mt-10) REVERT: B 448 ASP cc_start: 0.8179 (p0) cc_final: 0.7936 (p0) REVERT: B 476 MET cc_start: 0.7648 (mmt) cc_final: 0.7040 (pmm) REVERT: A 192 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8052 (t80) REVERT: A 234 ILE cc_start: 0.8769 (tt) cc_final: 0.8481 (tt) REVERT: A 278 GLU cc_start: 0.8477 (tt0) cc_final: 0.7980 (mt-10) REVERT: A 335 PHE cc_start: 0.8352 (m-80) cc_final: 0.8126 (m-80) REVERT: A 448 ASP cc_start: 0.8237 (p0) cc_final: 0.7986 (p0) REVERT: A 476 MET cc_start: 0.7676 (mmt) cc_final: 0.7038 (pmm) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.0548 time to fit residues: 11.5086 Evaluate side-chains 140 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 423 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.122913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106546 restraints weight = 8768.293| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.78 r_work: 0.3099 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6892 Z= 0.153 Angle : 0.576 8.255 9350 Z= 0.303 Chirality : 0.043 0.275 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.548 65.957 958 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.05 % Allowed : 17.73 % Favored : 79.22 % 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 are not related in a simple way. whole: 1.14 (0.30), residues: 836 helix: 1.88 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.86 (0.38), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.010 0.001 TYR A 274 PHE 0.018 0.001 PHE A 295 TRP 0.007 0.001 TRP A 386 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6892) covalent geometry : angle 0.57561 ( 9350) hydrogen bonds : bond 0.04260 ( 478) hydrogen bonds : angle 4.28160 ( 1404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.264 Fit side-chains REVERT: B 192 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8079 (t80) REVERT: B 234 ILE cc_start: 0.8806 (tt) cc_final: 0.8590 (tt) REVERT: B 278 GLU cc_start: 0.8549 (tt0) cc_final: 0.8050 (mt-10) REVERT: B 318 PHE cc_start: 0.7980 (t80) cc_final: 0.7545 (t80) REVERT: B 448 ASP cc_start: 0.8187 (p0) cc_final: 0.7940 (p0) REVERT: B 476 MET cc_start: 0.7678 (mmt) cc_final: 0.7022 (pmm) REVERT: A 192 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8105 (t80) REVERT: A 234 ILE cc_start: 0.8797 (tt) cc_final: 0.8540 (tt) REVERT: A 278 GLU cc_start: 0.8524 (tt0) cc_final: 0.8041 (mt-10) REVERT: A 318 PHE cc_start: 0.7991 (t80) cc_final: 0.7484 (t80) REVERT: A 335 PHE cc_start: 0.8458 (m-80) cc_final: 0.8185 (m-80) REVERT: A 382 PHE cc_start: 0.7478 (t80) cc_final: 0.7221 (t80) REVERT: A 448 ASP cc_start: 0.8245 (p0) cc_final: 0.7989 (p0) REVERT: A 476 MET cc_start: 0.7693 (mmt) cc_final: 0.7027 (pmm) outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 0.0562 time to fit residues: 11.2841 Evaluate side-chains 142 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS A 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.124866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.108685 restraints weight = 8662.655| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.75 r_work: 0.3123 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6892 Z= 0.142 Angle : 0.567 8.996 9350 Z= 0.298 Chirality : 0.043 0.277 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.502 65.556 958 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.19 % Allowed : 17.59 % Favored : 79.22 % 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 are not related in a simple way. whole: 1.20 (0.31), residues: 836 helix: 1.91 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.77 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.009 0.001 TYR B 274 PHE 0.017 0.001 PHE A 295 TRP 0.009 0.001 TRP A 386 HIS 0.003 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6892) covalent geometry : angle 0.56730 ( 9350) hydrogen bonds : bond 0.04186 ( 478) hydrogen bonds : angle 4.25804 ( 1404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.176 Fit side-chains REVERT: B 192 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.8066 (t80) REVERT: B 234 ILE cc_start: 0.8785 (tt) cc_final: 0.8541 (tt) REVERT: B 278 GLU cc_start: 0.8542 (tt0) cc_final: 0.8046 (mt-10) REVERT: B 318 PHE cc_start: 0.7972 (t80) cc_final: 0.7491 (t80) REVERT: B 335 PHE cc_start: 0.8272 (m-80) cc_final: 0.8066 (m-80) REVERT: B 448 ASP cc_start: 0.8174 (p0) cc_final: 0.7933 (p0) REVERT: B 476 MET cc_start: 0.7672 (mmt) cc_final: 0.7028 (pmm) REVERT: A 192 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 234 ILE cc_start: 0.8786 (tt) cc_final: 0.8529 (tt) REVERT: A 278 GLU cc_start: 0.8499 (tt0) cc_final: 0.7999 (mt-10) REVERT: A 318 PHE cc_start: 0.7968 (t80) cc_final: 0.7474 (t80) REVERT: A 335 PHE cc_start: 0.8452 (m-80) cc_final: 0.8165 (m-80) REVERT: A 382 PHE cc_start: 0.7505 (t80) cc_final: 0.7247 (t80) REVERT: A 435 PHE cc_start: 0.8310 (t80) cc_final: 0.8014 (t80) REVERT: A 448 ASP cc_start: 0.8214 (p0) cc_final: 0.7962 (p0) REVERT: A 476 MET cc_start: 0.7703 (mmt) cc_final: 0.7029 (pmm) outliers start: 23 outliers final: 20 residues processed: 134 average time/residue: 0.0558 time to fit residues: 11.2069 Evaluate side-chains 141 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ASP Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 181 GLN Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 45 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.108133 restraints weight = 8683.707| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.77 r_work: 0.3098 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6892 Z= 0.141 Angle : 0.575 9.047 9350 Z= 0.299 Chirality : 0.043 0.278 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.484 65.477 958 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.05 % Allowed : 18.01 % Favored : 78.95 % 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 are not related in a simple way. whole: 1.23 (0.31), residues: 836 helix: 1.92 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.73 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.010 0.001 TYR B 283 PHE 0.017 0.001 PHE A 295 TRP 0.008 0.001 TRP A 386 HIS 0.003 0.001 HIS B 376 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6892) covalent geometry : angle 0.57539 ( 9350) hydrogen bonds : bond 0.04182 ( 478) hydrogen bonds : angle 4.25747 ( 1404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1430.14 seconds wall clock time: 25 minutes 14.09 seconds (1514.09 seconds total)