Starting phenix.real_space_refine on Fri Jul 25 03:13:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsw_30848/07_2025/7dsw_30848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsw_30848/07_2025/7dsw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsw_30848/07_2025/7dsw_30848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsw_30848/07_2025/7dsw_30848.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsw_30848/07_2025/7dsw_30848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsw_30848/07_2025/7dsw_30848.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6720 Number of models: 1 Model: "" Number of chains: 3 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-2': 6, 'LBN:plan-3': 3, 'LBN:plan-1': 6} 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-2': 6, 'LBN:plan-3': 3, 'LBN:plan-1': 6} Unresolved non-hydrogen planarities: 56 Restraints were copied for chains: B 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: 7.02, per 1000 atoms: 1.04 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: 2.15 Conformation dependent library (CDL) restraints added in 975.9 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: 1.15 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: 2.85 Time building geometry restraints manager: 2.45 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: 0.05 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.910 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:4.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (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 TRP 0.014 0.002 TRP A 386 HIS 0.007 0.001 HIS A 250 PHE 0.020 0.002 PHE A 176 TYR 0.014 0.002 TYR A 274 ARG 0.009 0.001 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.09740 ( 478) hydrogen bonds : angle 5.53892 ( 1404) covalent geometry : bond 0.00771 ( 6892) covalent geometry : angle 0.89576 ( 9350) *********************** 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 : 0.831 Fit side-chains REVERT: B 335 PHE cc_start: 0.8217 (m-80) cc_final: 0.7778 (m-80) REVERT: B 416 SER cc_start: 0.8889 (t) cc_final: 0.8542 (t) REVERT: B 457 LEU cc_start: 0.8142 (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: 0.1968 time to fit residues: 42.8957 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 : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 220 ASN B 250 HIS A 98 HIS A 220 ASN A 250 HIS A 495 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105957 restraints weight = 8495.653| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.82 r_work: 0.3107 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6892 Z= 0.154 Angle : 0.598 6.339 9350 Z= 0.314 Chirality : 0.042 0.207 1120 Planarity : 0.004 0.045 1122 Dihedral : 8.103 65.747 958 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.66 % Allowed : 9.00 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.30), residues: 836 helix: 1.19 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -3.47 (0.36), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.005 0.001 HIS A 325 PHE 0.020 0.001 PHE B 295 TYR 0.017 0.002 TYR B 96 ARG 0.006 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 478) hydrogen bonds : angle 4.67671 ( 1404) covalent geometry : bond 0.00356 ( 6892) covalent geometry : angle 0.59815 ( 9350) *********************** 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 155 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.694 Fit side-chains REVERT: B 234 ILE cc_start: 0.8705 (tt) cc_final: 0.8476 (tt) REVERT: B 247 GLU cc_start: 0.7722 (pm20) cc_final: 0.7466 (pm20) REVERT: B 364 ARG cc_start: 0.7905 (ttt90) cc_final: 0.7661 (tpt-90) REVERT: B 368 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 384 LYS cc_start: 0.8704 (tppt) cc_final: 0.8374 (mmtt) REVERT: B 416 SER cc_start: 0.8983 (t) cc_final: 0.8636 (t) REVERT: B 448 ASP cc_start: 0.8223 (p0) cc_final: 0.7992 (p0) REVERT: B 457 LEU cc_start: 0.8404 (pp) cc_final: 0.8188 (pp) REVERT: B 476 MET cc_start: 0.7651 (mmt) cc_final: 0.7038 (pmm) REVERT: A 234 ILE cc_start: 0.8661 (tt) cc_final: 0.8392 (tt) REVERT: A 247 GLU cc_start: 0.7782 (pm20) cc_final: 0.7520 (pm20) REVERT: A 416 SER cc_start: 0.8969 (t) cc_final: 0.8629 (t) REVERT: A 448 ASP cc_start: 0.8166 (p0) cc_final: 0.7943 (p0) REVERT: A 476 MET cc_start: 0.7692 (mmt) cc_final: 0.7137 (pmm) outliers start: 12 outliers final: 9 residues processed: 150 average time/residue: 0.1469 time to fit residues: 30.9361 Evaluate side-chains 146 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 481 LEU 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 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 495 GLN A 220 ASN A 250 HIS ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106439 restraints weight = 8632.111| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.78 r_work: 0.3100 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6892 Z= 0.166 Angle : 0.585 6.115 9350 Z= 0.308 Chirality : 0.043 0.223 1120 Planarity : 0.005 0.045 1122 Dihedral : 7.421 67.638 958 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.22 % Allowed : 12.88 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.30), residues: 836 helix: 1.52 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -3.07 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 386 HIS 0.003 0.001 HIS A 325 PHE 0.019 0.001 PHE A 295 TYR 0.013 0.002 TYR B 96 ARG 0.004 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 478) hydrogen bonds : angle 4.57089 ( 1404) covalent geometry : bond 0.00395 ( 6892) covalent geometry : angle 0.58544 ( 9350) *********************** 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 : 0.757 Fit side-chains REVERT: B 208 MET cc_start: 0.8621 (mmm) cc_final: 0.8405 (mmm) REVERT: B 234 ILE cc_start: 0.8769 (tt) cc_final: 0.8554 (tt) REVERT: B 299 PHE cc_start: 0.7931 (m-10) cc_final: 0.7708 (m-80) REVERT: B 335 PHE cc_start: 0.8382 (m-80) cc_final: 0.8074 (m-80) REVERT: B 364 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7644 (tpt-90) REVERT: B 368 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 416 SER cc_start: 0.9003 (t) cc_final: 0.8681 (t) REVERT: B 435 PHE cc_start: 0.8445 (t80) cc_final: 0.8243 (t80) REVERT: B 448 ASP cc_start: 0.8202 (p0) cc_final: 0.7968 (p0) REVERT: B 457 LEU cc_start: 0.8440 (pp) cc_final: 0.8237 (pp) REVERT: B 476 MET cc_start: 0.7640 (mmt) cc_final: 0.7047 (pmm) REVERT: A 234 ILE cc_start: 0.8707 (tt) cc_final: 0.8438 (tt) REVERT: A 247 GLU cc_start: 0.7805 (pm20) cc_final: 0.7518 (pm20) REVERT: A 278 GLU cc_start: 0.8566 (tt0) cc_final: 0.8105 (mt-10) REVERT: A 335 PHE cc_start: 0.8421 (m-80) cc_final: 0.8051 (m-80) REVERT: A 448 ASP cc_start: 0.8265 (p0) cc_final: 0.8011 (p0) REVERT: A 476 MET cc_start: 0.7707 (mmt) cc_final: 0.7125 (pmm) outliers start: 16 outliers final: 13 residues processed: 145 average time/residue: 0.1813 time to fit residues: 37.5368 Evaluate side-chains 139 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 363 MET 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 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS A 250 HIS ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111703 restraints weight = 8597.321| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.73 r_work: 0.3095 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6892 Z= 0.157 Angle : 0.566 6.049 9350 Z= 0.298 Chirality : 0.042 0.239 1120 Planarity : 0.005 0.046 1122 Dihedral : 6.974 68.257 958 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.35 % Allowed : 15.10 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 836 helix: 1.60 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -3.05 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 386 HIS 0.003 0.001 HIS B 250 PHE 0.019 0.001 PHE A 295 TYR 0.013 0.001 TYR A 274 ARG 0.003 0.000 ARG A 364 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 478) hydrogen bonds : angle 4.45635 ( 1404) covalent geometry : bond 0.00369 ( 6892) covalent geometry : angle 0.56577 ( 9350) *********************** 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 145 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.777 Fit side-chains REVERT: B 234 ILE cc_start: 0.8770 (tt) cc_final: 0.8533 (tt) REVERT: B 278 GLU cc_start: 0.8565 (tt0) cc_final: 0.8113 (mt-10) REVERT: B 299 PHE cc_start: 0.7885 (m-10) cc_final: 0.7616 (m-80) REVERT: B 335 PHE cc_start: 0.8407 (m-80) cc_final: 0.8046 (m-80) REVERT: B 435 PHE cc_start: 0.8453 (t80) cc_final: 0.8067 (t80) REVERT: B 448 ASP cc_start: 0.8178 (p0) cc_final: 0.7941 (p0) REVERT: B 476 MET cc_start: 0.7631 (mmt) cc_final: 0.7052 (pmm) REVERT: A 234 ILE cc_start: 0.8764 (tt) cc_final: 0.8504 (tt) REVERT: A 247 GLU cc_start: 0.7850 (pm20) cc_final: 0.7647 (pm20) REVERT: A 278 GLU cc_start: 0.8534 (tt0) cc_final: 0.8094 (mt-10) REVERT: A 335 PHE cc_start: 0.8425 (m-80) cc_final: 0.8061 (m-80) REVERT: A 448 ASP cc_start: 0.8239 (p0) cc_final: 0.7993 (p0) REVERT: A 476 MET cc_start: 0.7655 (mmt) cc_final: 0.7057 (pmm) outliers start: 17 outliers final: 15 residues processed: 140 average time/residue: 0.2000 time to fit residues: 40.1611 Evaluate side-chains 141 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.6980 chunk 45 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113220 restraints weight = 8471.979| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.71 r_work: 0.3104 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1915 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= 0.148 Angle : 0.561 6.589 9350 Z= 0.297 Chirality : 0.042 0.239 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.744 66.132 958 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.16 % Allowed : 15.24 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.30), residues: 836 helix: 1.77 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.95 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 386 HIS 0.004 0.001 HIS A 376 PHE 0.019 0.001 PHE A 295 TYR 0.011 0.001 TYR A 274 ARG 0.007 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 478) hydrogen bonds : angle 4.35986 ( 1404) covalent geometry : bond 0.00341 ( 6892) covalent geometry : angle 0.56117 ( 9350) *********************** 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: 30 poor density : 126 time to evaluate : 0.811 Fit side-chains REVERT: B 192 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7985 (t80) REVERT: B 234 ILE cc_start: 0.8778 (tt) cc_final: 0.8530 (tt) REVERT: B 278 GLU cc_start: 0.8543 (tt0) cc_final: 0.8056 (mt-10) REVERT: B 299 PHE cc_start: 0.7812 (m-10) cc_final: 0.7606 (m-80) REVERT: B 335 PHE cc_start: 0.8344 (m-80) cc_final: 0.8027 (m-80) REVERT: B 448 ASP cc_start: 0.8186 (p0) cc_final: 0.7951 (p0) REVERT: B 476 MET cc_start: 0.7647 (mmt) cc_final: 0.7054 (pmm) REVERT: A 192 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7942 (t80) REVERT: A 234 ILE cc_start: 0.8786 (tt) cc_final: 0.8529 (tt) REVERT: A 247 GLU cc_start: 0.7855 (pm20) cc_final: 0.7635 (pm20) REVERT: A 278 GLU cc_start: 0.8501 (tt0) cc_final: 0.8012 (mt-10) REVERT: A 335 PHE cc_start: 0.8357 (m-80) cc_final: 0.8057 (m-80) REVERT: A 448 ASP cc_start: 0.8228 (p0) cc_final: 0.7983 (p0) REVERT: A 476 MET cc_start: 0.7672 (mmt) cc_final: 0.7061 (pmm) outliers start: 30 outliers final: 20 residues processed: 146 average time/residue: 0.1735 time to fit residues: 36.8209 Evaluate side-chains 148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 243 LEU 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 385 MET Chi-restraints excluded: chain B residue 391 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN A 250 HIS A 266 ASN ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.123182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106667 restraints weight = 8665.315| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.77 r_work: 0.3085 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6892 Z= 0.163 Angle : 0.571 6.010 9350 Z= 0.302 Chirality : 0.042 0.248 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.883 67.133 958 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.29 % Allowed : 15.10 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.30), residues: 836 helix: 1.75 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.93 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.003 0.001 HIS A 250 PHE 0.019 0.001 PHE A 295 TYR 0.012 0.001 TYR B 274 ARG 0.007 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 478) hydrogen bonds : angle 4.38627 ( 1404) covalent geometry : bond 0.00383 ( 6892) covalent geometry : angle 0.57140 ( 9350) *********************** 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 156 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.708 Fit side-chains REVERT: B 192 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 234 ILE cc_start: 0.8813 (tt) cc_final: 0.8580 (tt) REVERT: B 278 GLU cc_start: 0.8566 (tt0) cc_final: 0.8141 (mt-10) REVERT: B 299 PHE cc_start: 0.7830 (m-10) cc_final: 0.7592 (m-80) REVERT: B 335 PHE cc_start: 0.8399 (m-80) cc_final: 0.8051 (m-80) REVERT: B 356 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8766 (tt) REVERT: B 448 ASP cc_start: 0.8215 (p0) cc_final: 0.7963 (p0) REVERT: B 476 MET cc_start: 0.7666 (mmt) cc_final: 0.7054 (pmm) REVERT: A 192 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7958 (t80) REVERT: A 234 ILE cc_start: 0.8812 (tt) cc_final: 0.8580 (tt) REVERT: A 247 GLU cc_start: 0.7912 (pm20) cc_final: 0.7519 (pm20) REVERT: A 278 GLU cc_start: 0.8533 (tt0) cc_final: 0.8098 (mt-10) REVERT: A 335 PHE cc_start: 0.8467 (m-80) cc_final: 0.8102 (m-80) REVERT: A 356 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 435 PHE cc_start: 0.8384 (t80) cc_final: 0.8149 (t80) REVERT: A 448 ASP cc_start: 0.8249 (p0) cc_final: 0.7985 (p0) REVERT: A 476 MET cc_start: 0.7695 (mmt) cc_final: 0.7063 (pmm) outliers start: 31 outliers final: 25 residues processed: 144 average time/residue: 0.1451 time to fit residues: 30.4257 Evaluate side-chains 150 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 243 LEU 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 363 MET 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 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 286 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 356 LEU 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 461 ILE Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 80 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.126562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110297 restraints weight = 8481.890| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.73 r_work: 0.3113 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2156 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= 0.135 Angle : 0.556 6.874 9350 Z= 0.294 Chirality : 0.042 0.261 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.625 64.833 958 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.60 % Allowed : 17.31 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.30), residues: 836 helix: 1.90 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.85 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 386 HIS 0.003 0.001 HIS A 376 PHE 0.017 0.001 PHE A 295 TYR 0.010 0.001 TYR A 274 ARG 0.006 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 478) hydrogen bonds : angle 4.26725 ( 1404) covalent geometry : bond 0.00304 ( 6892) covalent geometry : angle 0.55565 ( 9350) *********************** 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 148 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.757 Fit side-chains REVERT: B 192 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7988 (t80) REVERT: B 234 ILE cc_start: 0.8783 (tt) cc_final: 0.8521 (tt) REVERT: B 278 GLU cc_start: 0.8508 (tt0) cc_final: 0.8011 (mt-10) REVERT: B 299 PHE cc_start: 0.7746 (m-10) cc_final: 0.7524 (m-80) REVERT: B 335 PHE cc_start: 0.8323 (m-80) cc_final: 0.8052 (m-80) REVERT: B 448 ASP cc_start: 0.8186 (p0) cc_final: 0.7945 (p0) REVERT: B 476 MET cc_start: 0.7637 (mmt) cc_final: 0.7032 (pmm) REVERT: A 192 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7987 (t80) REVERT: A 234 ILE cc_start: 0.8783 (tt) cc_final: 0.8509 (tt) REVERT: A 278 GLU cc_start: 0.8498 (tt0) cc_final: 0.8007 (mt-10) REVERT: A 299 PHE cc_start: 0.7947 (m-80) cc_final: 0.7646 (m-80) REVERT: A 335 PHE cc_start: 0.8464 (m-80) cc_final: 0.8151 (m-80) REVERT: A 448 ASP cc_start: 0.8202 (p0) cc_final: 0.7945 (p0) REVERT: A 476 MET cc_start: 0.7636 (mmt) cc_final: 0.7030 (pmm) outliers start: 26 outliers final: 16 residues processed: 137 average time/residue: 0.1383 time to fit residues: 27.7410 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 : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 385 MET Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 423 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105898 restraints weight = 8629.876| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.76 r_work: 0.3092 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6892 Z= 0.167 Angle : 0.594 7.372 9350 Z= 0.315 Chirality : 0.043 0.267 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.893 66.897 958 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.02 % Allowed : 17.45 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 836 helix: 1.80 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 386 HIS 0.003 0.001 HIS A 376 PHE 0.018 0.001 PHE A 295 TYR 0.012 0.001 TYR B 274 ARG 0.006 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 478) hydrogen bonds : angle 4.35010 ( 1404) covalent geometry : bond 0.00395 ( 6892) covalent geometry : angle 0.59383 ( 9350) *********************** 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 149 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.746 Fit side-chains REVERT: B 192 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8021 (t80) REVERT: B 234 ILE cc_start: 0.8773 (tt) cc_final: 0.8563 (tt) REVERT: B 278 GLU cc_start: 0.8551 (tt0) cc_final: 0.8119 (mt-10) REVERT: B 299 PHE cc_start: 0.7783 (m-10) cc_final: 0.7563 (m-80) REVERT: B 356 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8747 (tt) REVERT: B 448 ASP cc_start: 0.8211 (p0) cc_final: 0.7959 (p0) REVERT: B 476 MET cc_start: 0.7752 (mmt) cc_final: 0.7137 (pmm) REVERT: A 192 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 234 ILE cc_start: 0.8815 (tt) cc_final: 0.8574 (tt) REVERT: A 278 GLU cc_start: 0.8548 (tt0) cc_final: 0.8093 (mt-10) REVERT: A 335 PHE cc_start: 0.8385 (m-80) cc_final: 0.8049 (m-80) REVERT: A 448 ASP cc_start: 0.8246 (p0) cc_final: 0.7990 (p0) REVERT: A 471 LYS cc_start: 0.8232 (tppp) cc_final: 0.7811 (tptp) REVERT: A 476 MET cc_start: 0.7679 (mmt) cc_final: 0.7042 (pmm) outliers start: 29 outliers final: 22 residues processed: 137 average time/residue: 0.1388 time to fit residues: 27.6673 Evaluate side-chains 145 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 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 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 457 LEU Chi-restraints excluded: chain A residue 481 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104721 restraints weight = 8678.596| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.78 r_work: 0.3076 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6892 Z= 0.174 Angle : 0.599 8.329 9350 Z= 0.316 Chirality : 0.043 0.271 1120 Planarity : 0.005 0.050 1122 Dihedral : 7.000 67.440 958 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.74 % Allowed : 18.28 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.30), residues: 836 helix: 1.76 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.93 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.003 0.001 HIS A 376 PHE 0.018 0.001 PHE A 295 TYR 0.012 0.002 TYR B 283 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 478) hydrogen bonds : angle 4.39818 ( 1404) covalent geometry : bond 0.00414 ( 6892) covalent geometry : angle 0.59950 ( 9350) *********************** 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 153 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.662 Fit side-chains REVERT: B 192 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 234 ILE cc_start: 0.8779 (tt) cc_final: 0.8576 (tt) REVERT: B 278 GLU cc_start: 0.8583 (tt0) cc_final: 0.8128 (mt-10) REVERT: B 299 PHE cc_start: 0.7815 (m-10) cc_final: 0.7600 (m-80) REVERT: B 335 PHE cc_start: 0.8421 (m-80) cc_final: 0.8120 (m-80) REVERT: B 356 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8754 (tt) REVERT: B 448 ASP cc_start: 0.8214 (p0) cc_final: 0.7948 (p0) REVERT: B 476 MET cc_start: 0.7762 (mmt) cc_final: 0.7143 (pmm) REVERT: A 192 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7986 (t80) REVERT: A 234 ILE cc_start: 0.8836 (tt) cc_final: 0.8623 (tt) REVERT: A 278 GLU cc_start: 0.8590 (tt0) cc_final: 0.8130 (mt-10) REVERT: A 335 PHE cc_start: 0.8526 (m-80) cc_final: 0.8230 (m-80) REVERT: A 382 PHE cc_start: 0.7490 (t80) cc_final: 0.7227 (t80) REVERT: A 448 ASP cc_start: 0.8233 (p0) cc_final: 0.7969 (p0) REVERT: A 476 MET cc_start: 0.7681 (mmt) cc_final: 0.7053 (pmm) outliers start: 27 outliers final: 22 residues processed: 143 average time/residue: 0.1367 time to fit residues: 28.3795 Evaluate side-chains 146 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 461 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 28 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.128109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112150 restraints weight = 8565.187| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.72 r_work: 0.3094 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2217 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= 0.157 Angle : 0.598 9.293 9350 Z= 0.312 Chirality : 0.043 0.272 1120 Planarity : 0.005 0.049 1122 Dihedral : 6.859 66.749 958 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.46 % Allowed : 18.70 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 836 helix: 1.65 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.75 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 386 HIS 0.003 0.001 HIS A 376 PHE 0.017 0.001 PHE A 295 TYR 0.011 0.001 TYR B 274 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 478) hydrogen bonds : angle 4.38013 ( 1404) covalent geometry : bond 0.00366 ( 6892) covalent geometry : angle 0.59764 ( 9350) ********************** 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 147 residues out of total 722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.761 Fit side-chains REVERT: B 192 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 234 ILE cc_start: 0.8801 (tt) cc_final: 0.8573 (tt) REVERT: B 278 GLU cc_start: 0.8528 (tt0) cc_final: 0.8087 (mt-10) REVERT: B 299 PHE cc_start: 0.7795 (m-10) cc_final: 0.7583 (m-80) REVERT: B 335 PHE cc_start: 0.8434 (m-80) cc_final: 0.8119 (m-80) REVERT: B 356 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8752 (tt) REVERT: B 476 MET cc_start: 0.7743 (mmt) cc_final: 0.7158 (pmm) REVERT: A 192 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7980 (t80) REVERT: A 234 ILE cc_start: 0.8813 (tt) cc_final: 0.8570 (tt) REVERT: A 278 GLU cc_start: 0.8523 (tt0) cc_final: 0.8012 (mt-10) REVERT: A 335 PHE cc_start: 0.8505 (m-80) cc_final: 0.8209 (m-80) REVERT: A 382 PHE cc_start: 0.7477 (t80) cc_final: 0.7234 (t80) REVERT: A 448 ASP cc_start: 0.8217 (p0) cc_final: 0.7959 (p0) REVERT: A 476 MET cc_start: 0.7669 (mmt) cc_final: 0.7062 (pmm) outliers start: 25 outliers final: 20 residues processed: 137 average time/residue: 0.1426 time to fit residues: 28.6504 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 : 0.738 ------------------------------------------------------------------------------- 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 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 461 ILE 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 286 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 0.0770 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.104027 restraints weight = 8753.372| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.79 r_work: 0.3071 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6892 Z= 0.170 Angle : 0.607 8.602 9350 Z= 0.317 Chirality : 0.044 0.273 1120 Planarity : 0.005 0.050 1122 Dihedral : 6.916 67.291 958 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.02 % Allowed : 18.42 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 836 helix: 1.61 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.75 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 386 HIS 0.003 0.001 HIS A 376 PHE 0.018 0.001 PHE A 295 TYR 0.012 0.001 TYR A 283 ARG 0.005 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 478) hydrogen bonds : angle 4.41128 ( 1404) covalent geometry : bond 0.00403 ( 6892) covalent geometry : angle 0.60737 ( 9350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.84 seconds wall clock time: 62 minutes 26.84 seconds (3746.84 seconds total)