Starting phenix.real_space_refine on Fri Jul 3 06:10:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.map" model { file = "/net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v1y_31630/07_2026/7v1y_31630.cif" } resolution = 2.82 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= 0.005 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 64 5.16 5 C 8032 2.51 5 N 2104 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3113 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="ALA E 2 " pdbres="B3S E 3 " Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="ALA F 2 " pdbres="B3S F 3 " Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="ALA G 2 " pdbres="B3S G 3 " Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'B3S': 1} Classifications: {'peptide': 2, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 1} Not linked: pdbres="ALA H 2 " pdbres="B3S H 3 " Time building chain proxies: 2.16, per 1000 atoms: 0.17 Number of scatterers: 12524 At special positions: 0 Unit cell: (117.284, 80.7, 153.868, 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 64 16.00 O 2324 8.00 N 2104 7.00 C 8032 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 540.7 milliseconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB B3S E 3 " pdb=" CB B3S F 3 " pdb=" CB B3S G 3 " pdb=" CB B3S H 3 " Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 40.8% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 104 through 123 Processing helix chain 'A' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.716A pdb=" N LEU A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 325 through 340 removed outlier: 3.631A pdb=" N GLY A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.609A pdb=" N GLY A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 removed outlier: 3.675A pdb=" N LEU A 407 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 530 through 545 Processing helix chain 'C' and resid 104 through 123 Processing helix chain 'C' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.717A pdb=" N LEU C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 340 removed outlier: 3.631A pdb=" N GLY C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 403 through 424 removed outlier: 3.674A pdb=" N LEU C 407 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 444 Processing helix chain 'C' and resid 504 through 511 Processing helix chain 'C' and resid 530 through 545 Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 165 through 180 removed outlier: 3.626A pdb=" N LEU B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.717A pdb=" N LEU B 294 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 340 removed outlier: 3.632A pdb=" N GLY B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 403 through 424 removed outlier: 3.676A pdb=" N LEU B 407 " --> pdb=" O THR B 403 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLY B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 504 through 511 Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'D' and resid 165 through 180 removed outlier: 3.627A pdb=" N LEU D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 226 through 235 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.717A pdb=" N LEU D 294 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 325 through 340 removed outlier: 3.631A pdb=" N GLY D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 403 through 424 removed outlier: 3.675A pdb=" N LEU D 407 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU D 422 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 444 Processing helix chain 'D' and resid 504 through 511 Processing helix chain 'D' and resid 530 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 5.211A pdb=" N GLU A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 133 " --> pdb=" O GLU A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AA4, first strand: chain 'C' and resid 152 through 153 removed outlier: 5.212A pdb=" N GLU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 133 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 removed outlier: 5.211A pdb=" N GLU B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL B 133 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 5.212A pdb=" N GLU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 133 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AB3, first strand: chain 'D' and resid 375 through 377 553 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2064 1.31 - 1.43: 3305 1.43 - 1.56: 7311 1.56 - 1.68: 4 1.68 - 1.81: 108 Bond restraints: 12792 Sorted by residual: bond pdb=" C ALA H 1 " pdb=" N ALA H 2 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.40e-02 5.10e+03 7.24e+01 bond pdb=" C ALA G 1 " pdb=" N ALA G 2 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.40e-02 5.10e+03 7.23e+01 bond pdb=" C ALA F 1 " pdb=" N ALA F 2 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.40e-02 5.10e+03 7.19e+01 bond pdb=" C ALA E 1 " pdb=" N ALA E 2 " ideal model delta sigma weight residual 1.329 1.448 -0.119 1.40e-02 5.10e+03 7.17e+01 bond pdb=" C B3S G 3 " pdb=" O B3S G 3 " ideal model delta sigma weight residual 1.231 1.398 -0.167 2.00e-02 2.50e+03 6.97e+01 ... (remaining 12787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16696 1.81 - 3.63: 468 3.63 - 5.44: 52 5.44 - 7.25: 43 7.25 - 9.06: 25 Bond angle restraints: 17284 Sorted by residual: angle pdb=" N ILE D 165 " pdb=" CA ILE D 165 " pdb=" C ILE D 165 " ideal model delta sigma weight residual 113.00 104.01 8.99 1.30e+00 5.92e-01 4.78e+01 angle pdb=" N ILE C 165 " pdb=" CA ILE C 165 " pdb=" C ILE C 165 " ideal model delta sigma weight residual 113.00 104.04 8.96 1.30e+00 5.92e-01 4.75e+01 angle pdb=" N ILE A 165 " pdb=" CA ILE A 165 " pdb=" C ILE A 165 " ideal model delta sigma weight residual 113.00 104.05 8.95 1.30e+00 5.92e-01 4.74e+01 angle pdb=" N ILE B 165 " pdb=" CA ILE B 165 " pdb=" C ILE B 165 " ideal model delta sigma weight residual 113.00 104.07 8.93 1.30e+00 5.92e-01 4.72e+01 angle pdb=" N ILE D 162 " pdb=" CA ILE D 162 " pdb=" C ILE D 162 " ideal model delta sigma weight residual 109.30 101.32 7.98 1.25e+00 6.40e-01 4.07e+01 ... (remaining 17279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 6805 15.55 - 31.10: 681 31.10 - 46.66: 148 46.66 - 62.21: 22 62.21 - 77.76: 12 Dihedral angle restraints: 7668 sinusoidal: 3080 harmonic: 4588 Sorted by residual: dihedral pdb=" C ALA F 2 " pdb=" N ALA F 2 " pdb=" CA ALA F 2 " pdb=" CB ALA F 2 " ideal model delta harmonic sigma weight residual -122.60 -134.67 12.07 0 2.50e+00 1.60e-01 2.33e+01 dihedral pdb=" C ALA G 2 " pdb=" N ALA G 2 " pdb=" CA ALA G 2 " pdb=" CB ALA G 2 " ideal model delta harmonic sigma weight residual -122.60 -134.63 12.03 0 2.50e+00 1.60e-01 2.31e+01 dihedral pdb=" C ALA E 2 " pdb=" N ALA E 2 " pdb=" CA ALA E 2 " pdb=" CB ALA E 2 " ideal model delta harmonic sigma weight residual -122.60 -134.62 12.02 0 2.50e+00 1.60e-01 2.31e+01 ... (remaining 7665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1692 0.100 - 0.200: 169 0.200 - 0.301: 34 0.301 - 0.401: 0 0.401 - 0.501: 5 Chirality restraints: 1900 Sorted by residual: chirality pdb=" CA ALA F 2 " pdb=" N ALA F 2 " pdb=" C ALA F 2 " pdb=" CB ALA F 2 " both_signs ideal model delta sigma weight residual False 2.48 1.98 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA ALA G 2 " pdb=" N ALA G 2 " pdb=" C ALA G 2 " pdb=" CB ALA G 2 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CA ALA E 2 " pdb=" N ALA E 2 " pdb=" C ALA E 2 " pdb=" CB ALA E 2 " both_signs ideal model delta sigma weight residual False 2.48 1.99 0.50 2.00e-01 2.50e+01 6.22e+00 ... (remaining 1897 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 108 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C ILE D 108 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE D 108 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU D 109 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 108 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE A 108 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 108 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 109 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 108 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C ILE C 108 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE C 108 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU C 109 " -0.009 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2684 2.78 - 3.31: 10867 3.31 - 3.84: 19963 3.84 - 4.37: 24569 4.37 - 4.90: 42092 Nonbonded interactions: 100175 Sorted by model distance: nonbonded pdb=" OG1 THR B 358 " pdb=" OD2 ASP B 406 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 358 " pdb=" OD2 ASP A 406 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR C 358 " pdb=" OD2 ASP C 406 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR D 358 " pdb=" OD2 ASP D 406 " model vdw 2.254 3.040 nonbonded pdb=" O VAL C 447 " pdb=" OG1 THR C 450 " model vdw 2.263 3.040 ... (remaining 100170 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.530 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.005 0.167 12800 Z= 0.337 Angle : 0.778 9.065 17284 Z= 0.495 Chirality : 0.065 0.501 1900 Planarity : 0.003 0.033 2196 Dihedral : 12.983 77.760 4732 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.15 % Allowed : 0.75 % Favored : 99.10 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.48 (0.21), residues: 1560 helix: 2.59 (0.22), residues: 544 sheet: 1.18 (0.50), residues: 116 loop : -0.03 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 221 TYR 0.012 0.001 TYR C 328 PHE 0.009 0.001 PHE B 298 TRP 0.008 0.001 TRP C 454 HIS 0.002 0.001 HIS B 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.33 (12792) covalent geometry : angle 0.77752 / 0.50 (17284) hydrogen bonds : bond 0.18743 / 12.98 ( 553) hydrogen bonds : angle 6.13328 / 4.36 ( 1548) Misc. bond : bond 0.02586 / 1.46 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7459 (tp30) cc_final: 0.7232 (tp30) REVERT: A 440 MET cc_start: 0.8819 (mmm) cc_final: 0.8502 (mmm) REVERT: C 355 ASP cc_start: 0.7517 (t0) cc_final: 0.7238 (t0) REVERT: C 525 MET cc_start: 0.8836 (tpt) cc_final: 0.8416 (tpp) REVERT: B 227 ILE cc_start: 0.8332 (mt) cc_final: 0.8011 (tt) REVERT: D 471 GLN cc_start: 0.8201 (tt0) cc_final: 0.7982 (tt0) REVERT: D 477 ARG cc_start: 0.7666 (ttt90) cc_final: 0.6039 (mpp-170) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.6536 time to fit residues: 156.0069 Evaluate side-chains 121 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN C 289 GLN C 479 GLN B 289 GLN D 289 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093337 restraints weight = 15485.893| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.73 r_work: 0.2844 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12800 Z= 0.159 Angle : 0.581 7.884 17284 Z= 0.316 Chirality : 0.044 0.138 1900 Planarity : 0.004 0.038 2196 Dihedral : 4.625 56.317 1728 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.25 % Allowed : 9.88 % Favored : 87.87 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.60 (0.21), residues: 1560 helix: 2.78 (0.22), residues: 552 sheet: 1.18 (0.48), residues: 116 loop : -0.04 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.019 0.001 TYR C 328 PHE 0.012 0.001 PHE A 374 TRP 0.012 0.002 TRP A 464 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12792) covalent geometry : angle 0.58072 / 0.32 (17284) hydrogen bonds : bond 0.05728 / 4.01 ( 553) hydrogen bonds : angle 4.55782 / 3.26 ( 1548) Misc. bond : bond 0.00079 / 0.05 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.440 Fit side-chains REVERT: A 121 GLU cc_start: 0.8316 (tp30) cc_final: 0.7870 (tp30) REVERT: A 440 MET cc_start: 0.8913 (mmm) cc_final: 0.8611 (mmm) REVERT: A 443 MET cc_start: 0.8598 (mtp) cc_final: 0.8363 (ttm) REVERT: C 355 ASP cc_start: 0.8219 (t0) cc_final: 0.7839 (t0) REVERT: C 525 MET cc_start: 0.9264 (tpt) cc_final: 0.9052 (tpp) REVERT: B 468 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7392 (mm-30) outliers start: 30 outliers final: 11 residues processed: 154 average time/residue: 0.5921 time to fit residues: 97.9667 Evaluate side-chains 133 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 17 optimal weight: 0.0670 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096541 restraints weight = 15551.271| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.71 r_work: 0.2911 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12800 Z= 0.098 Angle : 0.484 5.688 17284 Z= 0.262 Chirality : 0.041 0.155 1900 Planarity : 0.003 0.035 2196 Dihedral : 4.345 56.510 1728 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.87 % Allowed : 11.23 % Favored : 86.90 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.73 (0.21), residues: 1560 helix: 2.88 (0.22), residues: 552 sheet: 1.23 (0.49), residues: 116 loop : 0.04 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.011 0.001 TYR B 328 PHE 0.010 0.001 PHE D 374 TRP 0.008 0.001 TRP D 454 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (12792) covalent geometry : angle 0.48399 / 0.26 (17284) hydrogen bonds : bond 0.04017 / 2.81 ( 553) hydrogen bonds : angle 4.28709 / 3.06 ( 1548) Misc. bond : bond 0.00028 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.387 Fit side-chains REVERT: A 121 GLU cc_start: 0.8223 (tp30) cc_final: 0.7923 (tp30) REVERT: A 440 MET cc_start: 0.8890 (mmm) cc_final: 0.8600 (mmm) REVERT: C 355 ASP cc_start: 0.8147 (t0) cc_final: 0.7793 (t0) REVERT: C 451 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: C 525 MET cc_start: 0.9183 (tpt) cc_final: 0.8914 (tpp) REVERT: B 361 GLN cc_start: 0.8965 (pm20) cc_final: 0.8702 (pm20) REVERT: D 362 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7769 (mm-30) outliers start: 25 outliers final: 9 residues processed: 143 average time/residue: 0.6146 time to fit residues: 94.3540 Evaluate side-chains 126 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 4.9990 chunk 47 optimal weight: 0.0060 chunk 11 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.093433 restraints weight = 15505.521| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.71 r_work: 0.2858 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12800 Z= 0.150 Angle : 0.539 6.032 17284 Z= 0.292 Chirality : 0.043 0.156 1900 Planarity : 0.004 0.037 2196 Dihedral : 4.524 54.996 1728 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 11.45 % Favored : 86.15 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.62 (0.21), residues: 1560 helix: 2.82 (0.22), residues: 552 sheet: 1.01 (0.47), residues: 116 loop : -0.03 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.015 0.001 TYR C 328 PHE 0.012 0.001 PHE B 374 TRP 0.011 0.001 TRP A 464 HIS 0.006 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (12792) covalent geometry : angle 0.53940 / 0.29 (17284) hydrogen bonds : bond 0.05225 / 3.61 ( 553) hydrogen bonds : angle 4.32250 / 3.09 ( 1548) Misc. bond : bond 0.00074 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8246 (tp30) cc_final: 0.7831 (tp30) REVERT: A 440 MET cc_start: 0.8922 (mmm) cc_final: 0.8659 (mmm) REVERT: C 355 ASP cc_start: 0.8219 (t0) cc_final: 0.7786 (t0) REVERT: C 451 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: C 525 MET cc_start: 0.9300 (tpt) cc_final: 0.9087 (tpp) REVERT: D 121 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: D 362 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7733 (mm-30) outliers start: 32 outliers final: 11 residues processed: 144 average time/residue: 0.5959 time to fit residues: 92.5657 Evaluate side-chains 132 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.123484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094499 restraints weight = 15559.384| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.71 r_work: 0.2879 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12800 Z= 0.113 Angle : 0.501 5.446 17284 Z= 0.271 Chirality : 0.042 0.184 1900 Planarity : 0.003 0.036 2196 Dihedral : 4.425 55.785 1728 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.95 % Allowed : 12.65 % Favored : 85.40 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: 1.63 (0.21), residues: 1560 helix: 2.82 (0.22), residues: 552 sheet: 0.93 (0.46), residues: 116 loop : 0.00 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 112 TYR 0.012 0.001 TYR C 328 PHE 0.010 0.001 PHE D 374 TRP 0.009 0.001 TRP D 454 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (12792) covalent geometry : angle 0.50133 / 0.27 (17284) hydrogen bonds : bond 0.04407 / 3.07 ( 553) hydrogen bonds : angle 4.24108 / 3.03 ( 1548) Misc. bond : bond 0.00035 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8213 (tp30) cc_final: 0.7822 (tp30) REVERT: A 226 ASP cc_start: 0.7027 (t70) cc_final: 0.6693 (m-30) REVERT: A 440 MET cc_start: 0.8901 (mmm) cc_final: 0.8629 (mmm) REVERT: C 355 ASP cc_start: 0.8171 (t0) cc_final: 0.7763 (t0) REVERT: C 451 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 525 MET cc_start: 0.9253 (tpt) cc_final: 0.8999 (tpp) REVERT: B 184 ASP cc_start: 0.8075 (t0) cc_final: 0.7865 (t70) REVERT: B 468 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: D 121 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: D 336 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8217 (tm-30) REVERT: D 362 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7618 (mm-30) outliers start: 26 outliers final: 11 residues processed: 144 average time/residue: 0.5873 time to fit residues: 90.8254 Evaluate side-chains 129 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 20 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 154 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.094757 restraints weight = 15492.462| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.71 r_work: 0.2888 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12800 Z= 0.109 Angle : 0.489 5.675 17284 Z= 0.264 Chirality : 0.041 0.134 1900 Planarity : 0.003 0.036 2196 Dihedral : 4.410 58.150 1728 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.87 % Allowed : 12.87 % Favored : 85.25 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.74 (0.21), residues: 1560 helix: 2.83 (0.22), residues: 552 sheet: 0.67 (0.44), residues: 148 loop : 0.17 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 515 TYR 0.011 0.001 TYR B 328 PHE 0.010 0.001 PHE D 374 TRP 0.009 0.001 TRP D 454 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12792) covalent geometry : angle 0.48922 / 0.26 (17284) hydrogen bonds : bond 0.04240 / 2.95 ( 553) hydrogen bonds : angle 4.17583 / 2.98 ( 1548) Misc. bond : bond 0.00029 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.450 Fit side-chains REVERT: A 121 GLU cc_start: 0.8215 (tp30) cc_final: 0.7830 (tp30) REVERT: A 226 ASP cc_start: 0.7024 (t70) cc_final: 0.6657 (m-30) REVERT: A 440 MET cc_start: 0.8909 (mmm) cc_final: 0.8628 (mmm) REVERT: C 355 ASP cc_start: 0.8220 (t0) cc_final: 0.7823 (t0) REVERT: C 451 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: C 525 MET cc_start: 0.9253 (tpt) cc_final: 0.8997 (tpp) REVERT: B 361 GLN cc_start: 0.8956 (pm20) cc_final: 0.8686 (pm20) REVERT: D 121 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: D 336 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8225 (tm-30) REVERT: D 362 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7555 (mm-30) outliers start: 25 outliers final: 16 residues processed: 140 average time/residue: 0.6166 time to fit residues: 92.7904 Evaluate side-chains 132 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.088694 restraints weight = 15615.880| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.82 r_work: 0.2775 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12800 Z= 0.305 Angle : 0.708 7.315 17284 Z= 0.381 Chirality : 0.050 0.243 1900 Planarity : 0.005 0.040 2196 Dihedral : 4.961 54.889 1728 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.10 % Allowed : 13.25 % Favored : 84.66 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.09 (0.21), residues: 1560 helix: 2.31 (0.22), residues: 552 sheet: 0.73 (0.43), residues: 116 loop : -0.29 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 480 TYR 0.018 0.002 TYR C 369 PHE 0.015 0.002 PHE B 374 TRP 0.020 0.003 TRP C 464 HIS 0.010 0.002 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.31 (12792) covalent geometry : angle 0.70796 / 0.38 (17284) hydrogen bonds : bond 0.08015 / 5.50 ( 553) hydrogen bonds : angle 4.63367 / 3.29 ( 1548) Misc. bond : bond 0.00123 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.540 Fit side-chains REVERT: A 226 ASP cc_start: 0.7076 (t70) cc_final: 0.6698 (m-30) REVERT: C 355 ASP cc_start: 0.8307 (t0) cc_final: 0.7804 (t0) REVERT: B 229 LYS cc_start: 0.7879 (tppp) cc_final: 0.7226 (tptp) REVERT: D 336 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8139 (tt0) REVERT: D 362 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7705 (mm-30) outliers start: 28 outliers final: 14 residues processed: 143 average time/residue: 0.6309 time to fit residues: 96.5291 Evaluate side-chains 130 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 GLN D 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093452 restraints weight = 15474.055| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.70 r_work: 0.2862 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12800 Z= 0.113 Angle : 0.528 7.382 17284 Z= 0.286 Chirality : 0.042 0.212 1900 Planarity : 0.003 0.037 2196 Dihedral : 4.628 56.013 1728 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.50 % Allowed : 14.82 % Favored : 83.68 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.43 (0.21), residues: 1560 helix: 2.62 (0.22), residues: 552 sheet: 0.79 (0.44), residues: 116 loop : -0.08 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 106 TYR 0.010 0.001 TYR C 328 PHE 0.011 0.001 PHE D 374 TRP 0.009 0.001 TRP B 395 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (12792) covalent geometry : angle 0.52780 / 0.29 (17284) hydrogen bonds : bond 0.04477 / 3.11 ( 553) hydrogen bonds : angle 4.34093 / 3.09 ( 1548) Misc. bond : bond 0.00013 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.6978 (t70) cc_final: 0.6633 (m-30) REVERT: A 440 MET cc_start: 0.8996 (mmm) cc_final: 0.8727 (mmm) REVERT: C 355 ASP cc_start: 0.8262 (t0) cc_final: 0.7883 (t0) REVERT: B 229 LYS cc_start: 0.7857 (tppp) cc_final: 0.7154 (tptp) REVERT: B 424 LYS cc_start: 0.8026 (tptp) cc_final: 0.7728 (mmmt) REVERT: B 469 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7843 (ptp90) REVERT: D 362 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7603 (mm-30) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.6634 time to fit residues: 95.4016 Evaluate side-chains 130 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.089758 restraints weight = 15630.770| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.79 r_work: 0.2794 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12800 Z= 0.248 Angle : 0.651 7.321 17284 Z= 0.351 Chirality : 0.048 0.215 1900 Planarity : 0.005 0.045 2196 Dihedral : 4.888 53.184 1728 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.02 % Allowed : 14.97 % Favored : 83.01 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.27 % 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: 1.13 (0.21), residues: 1560 helix: 2.36 (0.22), residues: 552 sheet: 0.73 (0.43), residues: 116 loop : -0.28 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 545 TYR 0.015 0.002 TYR D 328 PHE 0.014 0.002 PHE B 374 TRP 0.017 0.002 TRP C 464 HIS 0.008 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.25 (12792) covalent geometry : angle 0.65141 / 0.35 (17284) hydrogen bonds : bond 0.07046 / 4.84 ( 553) hydrogen bonds : angle 4.56070 / 3.25 ( 1548) Misc. bond : bond 0.00075 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7157 (t70) cc_final: 0.6783 (m-30) REVERT: A 440 MET cc_start: 0.8983 (mmm) cc_final: 0.8756 (mmm) REVERT: C 355 ASP cc_start: 0.8327 (t0) cc_final: 0.7849 (t0) REVERT: B 229 LYS cc_start: 0.7860 (tppp) cc_final: 0.7352 (tptp) REVERT: B 424 LYS cc_start: 0.8075 (tptp) cc_final: 0.7701 (mmmt) REVERT: B 469 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7897 (ptp90) REVERT: D 362 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: D 543 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8040 (mtmm) outliers start: 27 outliers final: 18 residues processed: 142 average time/residue: 0.6270 time to fit residues: 95.4022 Evaluate side-chains 142 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain C residue 479 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 191 HIS Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 289 GLN C 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092519 restraints weight = 15561.285| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.76 r_work: 0.2849 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12800 Z= 0.134 Angle : 0.562 7.793 17284 Z= 0.304 Chirality : 0.043 0.204 1900 Planarity : 0.004 0.040 2196 Dihedral : 4.750 54.499 1728 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.50 % Allowed : 15.64 % Favored : 82.86 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.27 % 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: 1.30 (0.21), residues: 1560 helix: 2.49 (0.22), residues: 552 sheet: 0.75 (0.44), residues: 116 loop : -0.15 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 480 TYR 0.012 0.001 TYR C 328 PHE 0.011 0.001 PHE D 374 TRP 0.011 0.001 TRP D 454 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (12792) covalent geometry : angle 0.56180 / 0.30 (17284) hydrogen bonds : bond 0.05083 / 3.50 ( 553) hydrogen bonds : angle 4.43727 / 3.16 ( 1548) Misc. bond : bond 0.00021 / 0.01 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.6988 (t70) cc_final: 0.6623 (m-30) REVERT: A 440 MET cc_start: 0.8996 (mmm) cc_final: 0.8721 (mmm) REVERT: C 355 ASP cc_start: 0.8249 (t0) cc_final: 0.7839 (t0) REVERT: B 229 LYS cc_start: 0.7891 (tppp) cc_final: 0.7121 (tptp) REVERT: B 424 LYS cc_start: 0.8024 (tptp) cc_final: 0.7698 (mmmt) REVERT: B 469 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7845 (ptp90) REVERT: D 362 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: D 543 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8016 (mtmm) outliers start: 20 outliers final: 15 residues processed: 131 average time/residue: 0.6344 time to fit residues: 88.9125 Evaluate side-chains 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 469 ARG Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 53 optimal weight: 0.0470 chunk 108 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 479 GLN C 509 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.094334 restraints weight = 15619.080| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.70 r_work: 0.2876 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12800 Z= 0.109 Angle : 0.518 7.769 17284 Z= 0.279 Chirality : 0.042 0.208 1900 Planarity : 0.003 0.037 2196 Dihedral : 4.570 56.301 1728 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.27 % Allowed : 16.32 % Favored : 82.41 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.50 (0.22), residues: 1560 helix: 2.65 (0.22), residues: 552 sheet: -0.03 (0.37), residues: 188 loop : 0.15 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.010 0.001 TYR B 328 PHE 0.012 0.001 PHE D 374 TRP 0.012 0.001 TRP B 395 HIS 0.003 0.001 HIS B 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12792) covalent geometry : angle 0.51826 / 0.28 (17284) hydrogen bonds : bond 0.04184 / 2.89 ( 553) hydrogen bonds : angle 4.26322 / 3.04 ( 1548) Misc. bond : bond 0.00017 / 0.01 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.43 seconds wall clock time: 62 minutes 3.80 seconds (3723.80 seconds total)