Starting phenix.real_space_refine on Wed Jun 11 06:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v1y_31630/06_2025/7v1y_31630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v1y_31630/06_2025/7v1y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7v1y_31630/06_2025/7v1y_31630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v1y_31630/06_2025/7v1y_31630.map" model { file = "/net/cci-nas-00/data/ceres_data/7v1y_31630/06_2025/7v1y_31630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v1y_31630/06_2025/7v1y_31630.cif" } resolution = 2.82 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= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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': 2} 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': 2} 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': 2} 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': 2} Time building chain proxies: 7.52, per 1000 atoms: 0.60 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.31 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: 3.75 Time building geometry restraints manager: 3.44 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: 7315 1.56 - 1.68: 4 1.68 - 1.81: 108 Bond restraints: 12796 Sorted by residual: bond pdb=" C ALA G 2 " pdb=" N B3S G 3 " ideal model delta sigma weight residual 1.329 1.450 -0.121 1.40e-02 5.10e+03 7.48e+01 bond pdb=" C ALA H 2 " pdb=" N B3S H 3 " ideal model delta sigma weight residual 1.329 1.450 -0.121 1.40e-02 5.10e+03 7.48e+01 bond pdb=" C ALA E 2 " pdb=" N B3S E 3 " ideal model delta sigma weight residual 1.329 1.450 -0.121 1.40e-02 5.10e+03 7.43e+01 bond pdb=" C ALA F 2 " pdb=" N B3S F 3 " ideal model delta sigma weight residual 1.329 1.449 -0.120 1.40e-02 5.10e+03 7.37e+01 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 ... (remaining 12791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16696 1.81 - 3.63: 476 3.63 - 5.44: 56 5.44 - 7.25: 43 7.25 - 9.06: 25 Bond angle restraints: 17296 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 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 6805 15.55 - 31.10: 681 31.10 - 46.66: 152 46.66 - 62.21: 22 62.21 - 77.76: 12 Dihedral angle restraints: 7672 sinusoidal: 3080 harmonic: 4592 Sorted by residual: dihedral pdb=" CA ALA G 2 " pdb=" C ALA G 2 " pdb=" N B3S G 3 " pdb=" CA B3S G 3 " ideal model delta harmonic sigma weight residual 180.00 137.43 42.57 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ALA F 2 " pdb=" C ALA F 2 " pdb=" N B3S F 3 " pdb=" CA B3S F 3 " ideal model delta harmonic sigma weight residual 180.00 137.44 42.56 0 5.00e+00 4.00e-02 7.25e+01 dihedral pdb=" CA ALA H 2 " pdb=" C ALA H 2 " pdb=" N B3S H 3 " pdb=" CA B3S H 3 " ideal model delta harmonic sigma weight residual 180.00 137.44 42.56 0 5.00e+00 4.00e-02 7.24e+01 ... (remaining 7669 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: 2200 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 2197 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: 0.09 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: 1.170 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.540 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 12800 Z= 0.368 Angle : 0.783 9.065 17296 Z= 0.498 Chirality : 0.065 0.501 1900 Planarity : 0.003 0.033 2200 Dihedral : 13.037 77.760 4736 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 (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: 1.48 (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 TRP 0.008 0.001 TRP C 454 HIS 0.002 0.001 HIS B 191 PHE 0.009 0.001 PHE B 298 TYR 0.012 0.001 TYR C 328 ARG 0.004 0.000 ARG B 221 Details of bonding type rmsd hydrogen bonds : bond 0.18743 ( 553) hydrogen bonds : angle 6.13328 ( 1548) covalent geometry : bond 0.00570 (12796) covalent geometry : angle 0.78288 (17296) Misc. bond : bond 0.03077 ( 4) *********************** 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 : 1.381 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: 1.6752 time to fit residues: 399.7152 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 : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3444 r_free = 0.3444 target = 0.126613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097099 restraints weight = 15311.227| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.72 r_work: 0.2915 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12800 Z= 0.114 Angle : 0.528 7.720 17296 Z= 0.287 Chirality : 0.042 0.141 1900 Planarity : 0.004 0.036 2200 Dihedral : 4.248 28.031 1732 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.10 % Allowed : 9.81 % Favored : 88.10 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.81 (0.21), residues: 1560 helix: 2.85 (0.22), residues: 552 sheet: 1.04 (0.46), residues: 148 loop : 0.18 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.004 0.001 HIS A 216 PHE 0.010 0.001 PHE B 374 TYR 0.015 0.001 TYR C 328 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 553) hydrogen bonds : angle 4.52661 ( 1548) covalent geometry : bond 0.00244 (12796) covalent geometry : angle 0.52842 (17296) Misc. bond : bond 0.00034 ( 4) *********************** 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 157 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.479 Fit side-chains REVERT: A 121 GLU cc_start: 0.8292 (tp30) cc_final: 0.7906 (tp30) REVERT: A 136 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7595 (tttm) REVERT: A 440 MET cc_start: 0.8860 (mmm) cc_final: 0.8658 (mmm) REVERT: C 136 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7823 (tptm) REVERT: C 355 ASP cc_start: 0.8196 (t0) cc_final: 0.7849 (t0) REVERT: C 525 MET cc_start: 0.9119 (tpt) cc_final: 0.8867 (tpp) REVERT: C 540 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: B 361 GLN cc_start: 0.8883 (pm20) cc_final: 0.8660 (pm20) REVERT: B 468 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: D 543 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7924 (mtmm) outliers start: 28 outliers final: 11 residues processed: 150 average time/residue: 1.5615 time to fit residues: 251.7005 Evaluate side-chains 136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 136 LYS Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 540 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 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 Chi-restraints excluded: chain D residue 543 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 0.0370 chunk 69 optimal weight: 0.0070 chunk 126 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 148 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN B 352 HIS D 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.098736 restraints weight = 15526.015| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.73 r_work: 0.2939 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12800 Z= 0.093 Angle : 0.473 5.567 17296 Z= 0.256 Chirality : 0.041 0.152 1900 Planarity : 0.003 0.033 2200 Dihedral : 4.012 35.915 1732 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.72 % Allowed : 10.93 % Favored : 87.35 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.92 (0.22), residues: 1560 helix: 2.95 (0.22), residues: 552 sheet: 1.03 (0.47), residues: 148 loop : 0.24 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.004 0.001 HIS B 352 PHE 0.009 0.001 PHE B 374 TYR 0.011 0.001 TYR C 328 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 553) hydrogen bonds : angle 4.25086 ( 1548) covalent geometry : bond 0.00196 (12796) covalent geometry : angle 0.47255 (17296) Misc. bond : bond 0.00018 ( 4) *********************** 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 152 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 1.621 Fit side-chains REVERT: A 121 GLU cc_start: 0.8201 (tp30) cc_final: 0.7901 (tp30) REVERT: A 136 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7523 (tttm) REVERT: A 440 MET cc_start: 0.8834 (mmm) cc_final: 0.8526 (mmm) REVERT: C 355 ASP cc_start: 0.8084 (t0) cc_final: 0.7751 (t0) REVERT: C 422 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 525 MET cc_start: 0.9067 (tpt) cc_final: 0.8716 (tpp) REVERT: B 361 GLN cc_start: 0.8891 (pm20) cc_final: 0.8668 (pm20) REVERT: D 187 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7472 (tp) outliers start: 23 outliers final: 5 residues processed: 146 average time/residue: 2.2731 time to fit residues: 357.7042 Evaluate side-chains 127 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 187 ILE 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 116 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 83 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.090237 restraints weight = 15436.775| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.70 r_work: 0.2798 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12800 Z= 0.216 Angle : 0.619 6.743 17296 Z= 0.334 Chirality : 0.046 0.151 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.494 40.324 1732 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.54 % Allowed : 11.15 % Favored : 86.30 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.48 (0.21), residues: 1560 helix: 2.70 (0.22), residues: 552 sheet: 0.89 (0.46), residues: 116 loop : -0.10 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 464 HIS 0.008 0.002 HIS B 216 PHE 0.013 0.002 PHE B 374 TYR 0.017 0.002 TYR C 328 ARG 0.004 0.001 ARG A 112 Details of bonding type rmsd hydrogen bonds : bond 0.06738 ( 553) hydrogen bonds : angle 4.51581 ( 1548) covalent geometry : bond 0.00534 (12796) covalent geometry : angle 0.61936 (17296) Misc. bond : bond 0.00051 ( 4) *********************** 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 163 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.503 Fit side-chains REVERT: A 440 MET cc_start: 0.8955 (mmm) cc_final: 0.8736 (mmm) REVERT: C 355 ASP cc_start: 0.8267 (t0) cc_final: 0.7807 (t0) REVERT: C 451 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 379 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8398 (mmtt) REVERT: B 468 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: D 121 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: D 380 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8705 (mttp) outliers start: 34 outliers final: 12 residues processed: 154 average time/residue: 1.4838 time to fit residues: 246.2233 Evaluate side-chains 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 C residue 479 GLN Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 217 LEU 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 222 HIS Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 380 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 25 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.092294 restraints weight = 15518.779| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.69 r_work: 0.2841 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12800 Z= 0.143 Angle : 0.544 5.824 17296 Z= 0.295 Chirality : 0.043 0.211 1900 Planarity : 0.004 0.037 2200 Dihedral : 4.378 41.714 1732 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.72 % Allowed : 12.95 % Favored : 85.33 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.49 (0.21), residues: 1560 helix: 2.71 (0.22), residues: 552 sheet: 0.85 (0.45), residues: 116 loop : -0.08 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 454 HIS 0.005 0.001 HIS B 216 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR C 328 ARG 0.003 0.000 ARG C 477 Details of bonding type rmsd hydrogen bonds : bond 0.05321 ( 553) hydrogen bonds : angle 4.39656 ( 1548) covalent geometry : bond 0.00340 (12796) covalent geometry : angle 0.54420 (17296) Misc. bond : bond 0.00039 ( 4) *********************** 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 143 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8227 (tp30) cc_final: 0.7979 (tp30) REVERT: A 440 MET cc_start: 0.8948 (mmm) cc_final: 0.8697 (mmm) REVERT: C 355 ASP cc_start: 0.8227 (t0) cc_final: 0.7775 (t0) REVERT: C 451 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: C 540 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: B 379 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8411 (mmtt) REVERT: D 336 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8211 (tm-30) REVERT: D 362 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7607 (mm-30) outliers start: 23 outliers final: 12 residues processed: 137 average time/residue: 1.5728 time to fit residues: 231.4962 Evaluate side-chains 133 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 540 GLU 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 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 94 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 0.0020 chunk 89 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.094395 restraints weight = 15588.287| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.69 r_work: 0.2880 rms_B_bonded: 2.10 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: 0.8602 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12800 Z= 0.104 Angle : 0.498 6.780 17296 Z= 0.267 Chirality : 0.042 0.143 1900 Planarity : 0.003 0.037 2200 Dihedral : 4.198 41.036 1732 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.50 % Allowed : 13.47 % Favored : 85.03 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.63 (0.21), residues: 1560 helix: 2.82 (0.22), residues: 552 sheet: 0.88 (0.46), residues: 116 loop : 0.02 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.003 0.001 HIS B 216 PHE 0.010 0.001 PHE D 374 TYR 0.012 0.001 TYR B 328 ARG 0.001 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 553) hydrogen bonds : angle 4.25864 ( 1548) covalent geometry : bond 0.00235 (12796) covalent geometry : angle 0.49768 (17296) Misc. bond : bond 0.00041 ( 4) *********************** 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 142 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.550 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.7048 (t70) cc_final: 0.6655 (m-30) REVERT: A 440 MET cc_start: 0.8935 (mmm) cc_final: 0.8654 (mmm) REVERT: C 355 ASP cc_start: 0.8258 (t0) cc_final: 0.7783 (t0) REVERT: C 451 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 336 GLU cc_start: 0.8085 (tt0) cc_final: 0.7606 (tm-30) REVERT: B 361 GLN cc_start: 0.8968 (pm20) cc_final: 0.8747 (pm20) REVERT: B 379 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8416 (mmtt) REVERT: D 121 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: D 336 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8209 (tm-30) REVERT: D 362 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7573 (mm-30) outliers start: 20 outliers final: 11 residues processed: 137 average time/residue: 1.5270 time to fit residues: 225.0258 Evaluate side-chains 128 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 232 GLU 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 187 ILE 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 35 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 70 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 147 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN C 510 ASN ** B 191 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 = 0.3406 r_free = 0.3406 target = 0.123611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.094948 restraints weight = 15482.118| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.68 r_work: 0.2887 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12800 Z= 0.106 Angle : 0.499 6.416 17296 Z= 0.269 Chirality : 0.041 0.134 1900 Planarity : 0.003 0.038 2200 Dihedral : 4.122 40.161 1732 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.50 % Allowed : 14.07 % Favored : 84.43 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.72 (0.21), residues: 1560 helix: 2.82 (0.22), residues: 552 sheet: 0.61 (0.43), residues: 148 loop : 0.17 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.003 0.001 HIS B 216 PHE 0.010 0.001 PHE D 374 TYR 0.012 0.001 TYR B 328 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 553) hydrogen bonds : angle 4.20524 ( 1548) covalent geometry : bond 0.00243 (12796) covalent geometry : angle 0.49919 (17296) Misc. bond : bond 0.00034 ( 4) *********************** 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 143 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.6995 (t70) cc_final: 0.6631 (m-30) REVERT: A 440 MET cc_start: 0.8914 (mmm) cc_final: 0.8610 (mmm) REVERT: A 462 MET cc_start: 0.8790 (mtt) cc_final: 0.8585 (mtt) REVERT: C 355 ASP cc_start: 0.8244 (t0) cc_final: 0.7786 (t0) REVERT: C 451 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: B 336 GLU cc_start: 0.8088 (tt0) cc_final: 0.7629 (tm-30) REVERT: B 361 GLN cc_start: 0.8954 (pm20) cc_final: 0.8729 (pm20) REVERT: B 379 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8411 (mmtt) REVERT: B 459 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8473 (ttmm) REVERT: D 121 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: D 336 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8200 (tm-30) REVERT: D 362 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7575 (mm-30) REVERT: D 543 LYS cc_start: 0.8355 (mtmm) cc_final: 0.7935 (mtmm) outliers start: 20 outliers final: 13 residues processed: 139 average time/residue: 1.5791 time to fit residues: 236.2012 Evaluate side-chains 133 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 451 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 31 optimal weight: 0.0170 chunk 113 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 138 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096965 restraints weight = 15664.461| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.69 r_work: 0.2922 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12800 Z= 0.092 Angle : 0.483 6.457 17296 Z= 0.260 Chirality : 0.041 0.225 1900 Planarity : 0.003 0.038 2200 Dihedral : 4.008 40.099 1732 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.57 % Allowed : 14.52 % Favored : 83.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.75 (0.22), residues: 1560 helix: 2.88 (0.22), residues: 552 sheet: 0.06 (0.38), residues: 188 loop : 0.30 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 395 HIS 0.002 0.001 HIS D 191 PHE 0.010 0.001 PHE D 374 TYR 0.009 0.001 TYR A 328 ARG 0.002 0.000 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 553) hydrogen bonds : angle 4.11409 ( 1548) covalent geometry : bond 0.00200 (12796) covalent geometry : angle 0.48297 (17296) Misc. bond : bond 0.00031 ( 4) *********************** 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 136 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.403 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8184 (tp30) cc_final: 0.7863 (tp30) REVERT: A 226 ASP cc_start: 0.6931 (t70) cc_final: 0.6576 (m-30) REVERT: A 440 MET cc_start: 0.8938 (mmm) cc_final: 0.8609 (mmm) REVERT: C 355 ASP cc_start: 0.8202 (t0) cc_final: 0.7781 (t0) REVERT: C 451 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: C 540 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: B 229 LYS cc_start: 0.7855 (tptm) cc_final: 0.7372 (tptp) REVERT: B 336 GLU cc_start: 0.8183 (tt0) cc_final: 0.7716 (tm-30) REVERT: B 361 GLN cc_start: 0.8935 (pm20) cc_final: 0.8682 (pm20) REVERT: B 459 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8388 (ttmm) REVERT: D 121 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: D 336 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8176 (tm-30) REVERT: D 362 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: D 543 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7899 (mtmm) outliers start: 21 outliers final: 10 residues processed: 131 average time/residue: 1.5256 time to fit residues: 214.7923 Evaluate side-chains 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL 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 C residue 540 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 136 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.090234 restraints weight = 15538.968| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.68 r_work: 0.2808 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12800 Z= 0.205 Angle : 0.608 8.015 17296 Z= 0.326 Chirality : 0.046 0.227 1900 Planarity : 0.004 0.038 2200 Dihedral : 4.420 41.917 1732 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.80 % Allowed : 14.15 % Favored : 84.06 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.45 (0.21), residues: 1560 helix: 2.62 (0.22), residues: 552 sheet: 0.86 (0.44), residues: 116 loop : -0.07 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 464 HIS 0.007 0.001 HIS B 216 PHE 0.014 0.002 PHE A 374 TYR 0.015 0.002 TYR C 328 ARG 0.003 0.000 ARG C 545 Details of bonding type rmsd hydrogen bonds : bond 0.06250 ( 553) hydrogen bonds : angle 4.41016 ( 1548) covalent geometry : bond 0.00506 (12796) covalent geometry : angle 0.60765 (17296) Misc. bond : bond 0.00046 ( 4) *********************** 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 142 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.575 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8298 (tp30) cc_final: 0.7809 (tp30) REVERT: A 226 ASP cc_start: 0.7034 (t70) cc_final: 0.6661 (m-30) REVERT: A 440 MET cc_start: 0.8987 (mmm) cc_final: 0.8726 (mmm) REVERT: C 355 ASP cc_start: 0.8313 (t0) cc_final: 0.7830 (t0) REVERT: C 451 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: B 229 LYS cc_start: 0.7808 (tptm) cc_final: 0.7436 (tptp) REVERT: B 459 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8554 (ttmm) REVERT: B 468 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: D 121 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: D 336 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8197 (tm-30) REVERT: D 362 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: D 380 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8683 (mttp) REVERT: D 543 LYS cc_start: 0.8503 (mtmm) cc_final: 0.7993 (mtmm) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 1.6350 time to fit residues: 238.7578 Evaluate side-chains 131 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 451 GLU Chi-restraints excluded: chain C residue 479 GLN 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 468 GLU Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 362 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 148 optimal weight: 0.0870 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 110 optimal weight: 0.4980 chunk 129 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS D 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.096368 restraints weight = 15441.770| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.71 r_work: 0.2905 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12800 Z= 0.097 Angle : 0.508 8.445 17296 Z= 0.273 Chirality : 0.042 0.211 1900 Planarity : 0.003 0.038 2200 Dihedral : 4.194 43.561 1732 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.05 % Allowed : 15.04 % Favored : 83.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.67 (0.21), residues: 1560 helix: 2.75 (0.22), residues: 552 sheet: 0.69 (0.43), residues: 152 loop : 0.12 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 395 HIS 0.004 0.001 HIS C 481 PHE 0.010 0.001 PHE D 374 TYR 0.010 0.001 TYR A 328 ARG 0.014 0.000 ARG C 480 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 553) hydrogen bonds : angle 4.26300 ( 1548) covalent geometry : bond 0.00212 (12796) covalent geometry : angle 0.50848 (17296) Misc. bond : bond 0.00046 ( 4) ********************** 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 130 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8180 (tp30) cc_final: 0.7770 (tp30) REVERT: A 226 ASP cc_start: 0.6939 (t70) cc_final: 0.6598 (m-30) REVERT: A 440 MET cc_start: 0.8943 (mmm) cc_final: 0.8640 (mmm) REVERT: C 355 ASP cc_start: 0.8172 (t0) cc_final: 0.7777 (t0) REVERT: C 451 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: B 229 LYS cc_start: 0.7797 (tptm) cc_final: 0.7422 (tptp) REVERT: B 336 GLU cc_start: 0.8135 (tt0) cc_final: 0.7707 (tm-30) REVERT: B 361 GLN cc_start: 0.8952 (pm20) cc_final: 0.8732 (pm20) REVERT: B 459 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (ttmm) REVERT: D 121 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7118 (tt0) REVERT: D 336 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 543 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7890 (mtmm) outliers start: 14 outliers final: 9 residues processed: 127 average time/residue: 1.5643 time to fit residues: 213.5163 Evaluate side-chains 128 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 451 GLU 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 D residue 121 GLU Chi-restraints excluded: chain D residue 379 LYS Chi-restraints excluded: chain D residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 36 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 87 optimal weight: 0.0170 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS C 479 GLN ** B 191 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 = 0.3387 r_free = 0.3387 target = 0.122231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.093308 restraints weight = 15570.143| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.69 r_work: 0.2863 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12800 Z= 0.120 Angle : 0.523 8.935 17296 Z= 0.280 Chirality : 0.042 0.210 1900 Planarity : 0.003 0.038 2200 Dihedral : 4.198 44.693 1732 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.27 % Allowed : 14.82 % Favored : 83.91 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.21), residues: 1560 helix: 2.75 (0.22), residues: 552 sheet: 0.92 (0.45), residues: 116 loop : 0.04 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 454 HIS 0.004 0.001 HIS B 216 PHE 0.012 0.001 PHE D 374 TYR 0.012 0.001 TYR C 328 ARG 0.001 0.000 ARG B 112 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 553) hydrogen bonds : angle 4.24031 ( 1548) covalent geometry : bond 0.00279 (12796) covalent geometry : angle 0.52252 (17296) Misc. bond : bond 0.00036 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9186.01 seconds wall clock time: 159 minutes 25.88 seconds (9565.88 seconds total)