Starting phenix.real_space_refine on Wed May 14 11:21:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmf_19360/05_2025/8rmf_19360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmf_19360/05_2025/8rmf_19360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmf_19360/05_2025/8rmf_19360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmf_19360/05_2025/8rmf_19360.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmf_19360/05_2025/8rmf_19360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmf_19360/05_2025/8rmf_19360.cif" } resolution = 2.33 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= 0.001 sd= 0.050 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 4 5.49 5 S 69 5.16 5 C 7282 2.51 5 N 2044 2.21 5 O 2483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11886 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3156 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3126 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 400, 3126 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3150 Chain: "B" Number of atoms: 689 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 674 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 939 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Conformer: "D" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} bond proxies already assigned to first conformer: 927 Chain: "I" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "E" Number of atoms: 3082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 3057 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 392, 3057 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3085 Chain: "F" Number of atoms: 689 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 674 Chain: "H" Number of atoms: 939 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Conformer: "D" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} bond proxies already assigned to first conformer: 927 Chain: "G" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2553 SG CYS A 381 32.877 43.211 66.807 1.00 75.60 S ATOM 4899 SG CYS D 95 33.566 40.571 64.304 1.00 64.26 S ATOM 5660 SG CYS I 108 43.003 41.408 75.451 1.00 64.27 S ATOM 5699 SG CYS I 114 42.022 44.922 76.940 1.00 51.67 S ATOM 5718 SG CYS I 117 45.724 43.107 80.963 1.00 49.70 S ATOM 6015 SG CYS I 154 46.513 39.973 79.410 1.00 57.27 S ATOM 8821 SG CYS E 381 72.928 95.827 66.835 1.00 94.77 S ATOM 10522 SG CYS H 95 72.490 98.598 64.314 1.00 79.03 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AASN A 83 " occ=0.77 ... (14 atoms not shown) pdb=" ND2BASN A 83 " occ=0.23 residue: pdb=" N AARG A 321 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG A 321 " occ=0.47 residue: pdb=" N ACYS A 426 " occ=0.39 ... (10 atoms not shown) pdb=" SG BCYS A 426 " occ=0.61 residue: pdb=" N AARG B 14 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG B 14 " occ=0.57 residue: pdb=" N BTYR D 35 " occ=0.56 ... (22 atoms not shown) pdb=" OH DTYR D 35 " occ=0.44 residue: pdb=" N AASN E 83 " occ=0.44 ... (14 atoms not shown) pdb=" ND2BASN E 83 " occ=0.56 residue: pdb=" N AARG E 321 " occ=0.82 ... (20 atoms not shown) pdb=" NH2BARG E 321 " occ=0.18 residue: pdb=" N ACYS E 426 " occ=0.37 ... (10 atoms not shown) pdb=" SG BCYS E 426 " occ=0.63 residue: pdb=" N AARG F 14 " occ=0.31 ... (20 atoms not shown) pdb=" NH2BARG F 14 " occ=0.69 residue: pdb=" N BTYR H 35 " occ=0.42 ... (22 atoms not shown) pdb=" OH DTYR H 35 " occ=0.58 Time building chain proxies: 11.05, per 1000 atoms: 0.93 Number of scatterers: 11886 At special positions: 0 Unit cell: (106.812, 142.416, 108.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 69 16.00 P 4 15.00 O 2483 8.00 N 2044 7.00 C 7282 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES I 201 " pdb="FE1 FES I 201 " - pdb=" SG CYS I 108 " pdb="FE1 FES I 201 " - pdb=" SG CYS I 114 " pdb="FE2 FES I 201 " - pdb=" SG CYS I 154 " pdb="FE2 FES I 201 " - pdb=" SG CYS I 117 " Number of angles added : 6 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2762 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 55.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 126 through 142 Processing helix chain 'A' and resid 156 through 168 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 297 through 337 removed outlier: 5.841A pdb=" N GLU A 316 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 362 through 370 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'B' and resid 6 through 21 Processing helix chain 'B' and resid 25 through 43 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 135 through 157 removed outlier: 4.083A pdb=" N SER D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 100 Processing helix chain 'I' and resid 122 through 127 removed outlier: 4.501A pdb=" N ASP I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 141 Processing helix chain 'I' and resid 154 through 156 No H-bonds generated for 'chain 'I' and resid 154 through 156' Processing helix chain 'I' and resid 159 through 163 removed outlier: 3.811A pdb=" N GLU I 163 " --> pdb=" O PRO I 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 83 Proline residue: E 79 - end of helix Processing helix chain 'E' and resid 93 through 115 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 126 through 142 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 185 through 193 Processing helix chain 'E' and resid 214 through 225 Processing helix chain 'E' and resid 297 through 337 removed outlier: 5.704A pdb=" N GLU E 316 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 349 removed outlier: 3.894A pdb=" N HIS E 349 " --> pdb=" O PRO E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 370 Processing helix chain 'E' and resid 379 through 383 Processing helix chain 'E' and resid 389 through 395 Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 415 through 437 Processing helix chain 'E' and resid 437 through 445 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 25 through 43 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 81 through 85 Processing helix chain 'H' and resid 36 through 45 Processing helix chain 'H' and resid 95 through 110 Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 121 through 130 removed outlier: 3.579A pdb=" N ILE H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 135 through 157 removed outlier: 4.037A pdb=" N SER H 139 " --> pdb=" O LYS H 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 36 through 51 Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'G' and resid 65 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.864A pdb=" N LEU A 59 " --> pdb=" O ALA A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.803A pdb=" N SER A 198 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N HIS A 230 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 200 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP A 232 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N HIS A 148 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 200 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A 150 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 149 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 176 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 151 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 340 through 342 removed outlier: 3.619A pdb=" N SER A 376 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 65 removed outlier: 3.558A pdb=" N ASP D 87 " --> pdb=" O GLN D 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 82 through 88 removed outlier: 3.781A pdb=" N ALA I 165 " --> pdb=" O ASN I 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 removed outlier: 6.755A pdb=" N LEU E 59 " --> pdb=" O ALA E 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.787A pdb=" N SER E 198 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS E 230 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 200 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP E 232 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N HIS E 148 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 200 " --> pdb=" O HIS E 148 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE E 150 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 149 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N LEU E 176 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR E 151 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 340 through 342 removed outlier: 3.722A pdb=" N SER E 376 " --> pdb=" O ARG E 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 59 through 65 removed outlier: 3.641A pdb=" N ASP H 87 " --> pdb=" O GLN H 78 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1844 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: 3.19 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 4650 1.40 - 1.60: 7059 1.60 - 1.80: 53 1.80 - 2.00: 57 2.00 - 2.19: 4 Bond restraints: 11823 Sorted by residual: bond pdb=" NZ LLP E 258 " pdb=" C4' LLP E 258 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NZ LLP A 258 " pdb=" C4' LLP A 258 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" OP4 LLP E 258 " pdb=" P LLP E 258 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" OP4 LLP A 258 " pdb=" P LLP A 258 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" CA LYS G 19 " pdb=" C LYS G 19 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 ... (remaining 11818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 15925 3.96 - 7.93: 42 7.93 - 11.89: 4 11.89 - 15.86: 5 15.86 - 19.82: 1 Bond angle restraints: 15977 Sorted by residual: angle pdb=" S1 FES I 201 " pdb="FE2 FES I 201 " pdb=" S2 FES I 201 " ideal model delta sigma weight residual 104.33 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb="FE1 FES I 201 " pdb=" S2 FES I 201 " pdb="FE2 FES I 201 " ideal model delta sigma weight residual 75.66 89.01 -13.35 1.14e+00 7.69e-01 1.37e+02 angle pdb=" S1 FES I 201 " pdb="FE1 FES I 201 " pdb=" S2 FES I 201 " ideal model delta sigma weight residual 104.33 90.95 13.38 1.20e+00 6.94e-01 1.24e+02 angle pdb="FE1 FES I 201 " pdb=" S1 FES I 201 " pdb="FE2 FES I 201 " ideal model delta sigma weight residual 75.66 88.98 -13.32 1.20e+00 6.94e-01 1.23e+02 angle pdb=" NZ LLP A 258 " pdb=" C4' LLP A 258 " pdb=" C4 LLP A 258 " ideal model delta sigma weight residual 120.09 100.27 19.82 3.00e+00 1.11e-01 4.37e+01 ... (remaining 15972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 6933 31.68 - 63.37: 303 63.37 - 95.05: 49 95.05 - 126.73: 1 126.73 - 158.41: 6 Dihedral angle restraints: 7292 sinusoidal: 3001 harmonic: 4291 Sorted by residual: dihedral pdb=" C39 8Q1 G 101 " pdb=" C42 8Q1 G 101 " pdb=" N41 8Q1 G 101 " pdb=" C43 8Q1 G 101 " ideal model delta sinusoidal sigma weight residual 89.93 -111.66 -158.41 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C LYS G 19 " pdb=" N LYS G 19 " pdb=" CA LYS G 19 " pdb=" CB LYS G 19 " ideal model delta harmonic sigma weight residual -122.60 -133.78 11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C39 8Q1 C 101 " pdb=" C42 8Q1 C 101 " pdb=" N41 8Q1 C 101 " pdb=" C43 8Q1 C 101 " ideal model delta sinusoidal sigma weight residual 89.93 -123.15 -146.92 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 7289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1491 0.057 - 0.115: 273 0.115 - 0.172: 39 0.172 - 0.230: 2 0.230 - 0.287: 2 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA LYS G 19 " pdb=" N LYS G 19 " pdb=" C LYS G 19 " pdb=" CB LYS G 19 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA TRP D 108 " pdb=" N TRP D 108 " pdb=" C TRP D 108 " pdb=" CB TRP D 108 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.47e-01 ... (remaining 1804 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 C 101 " -0.101 2.00e-02 2.50e+03 1.12e-01 1.58e+02 pdb=" C39 8Q1 C 101 " 0.038 2.00e-02 2.50e+03 pdb=" C42 8Q1 C 101 " -0.136 2.00e-02 2.50e+03 pdb=" N41 8Q1 C 101 " 0.180 2.00e-02 2.50e+03 pdb=" O40 8Q1 C 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 8Q1 C 101 " 0.049 2.00e-02 2.50e+03 5.94e-02 4.42e+01 pdb=" C34 8Q1 C 101 " -0.004 2.00e-02 2.50e+03 pdb=" C37 8Q1 C 101 " 0.072 2.00e-02 2.50e+03 pdb=" N36 8Q1 C 101 " -0.099 2.00e-02 2.50e+03 pdb=" O35 8Q1 C 101 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP E 258 " 0.058 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" NZ LLP E 258 " -0.064 2.00e-02 2.50e+03 pdb=" C4 LLP E 258 " 0.057 2.00e-02 2.50e+03 pdb=" C4' LLP E 258 " -0.051 2.00e-02 2.50e+03 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 176 2.63 - 3.20: 10477 3.20 - 3.76: 19995 3.76 - 4.33: 28935 4.33 - 4.90: 45270 Nonbonded interactions: 104853 Sorted by model distance: nonbonded pdb=" OD2 ASP H 71 " pdb="FE FE2 H 201 " model vdw 2.062 3.000 nonbonded pdb=" OD2 ASP D 71 " pdb="FE FE2 D 201 " model vdw 2.097 3.000 nonbonded pdb=" OH TYR B 13 " pdb=" OE2 GLU C 42 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR E 317 " pdb=" OD2 ASP F 38 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASP I 141 " pdb=" NH1 ARG E 277 " model vdw 2.214 3.120 ... (remaining 104848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 367 or resid 369 through 425 or resid 427 through 447)) selection = (chain 'E' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 367 or resid 369 through 425 or resid 427 through 447)) } ncs_group { reference = (chain 'B' and (resid 5 through 13 or resid 15 through 85)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 85)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 36 through 157 or resid 201)) selection = (chain 'H' and (resid 36 through 157 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=0.99 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: 1.710 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.700 Find NCS groups from input model: 0.420 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 0.156 11829 Z= 0.252 Angle : 0.720 19.823 15983 Z= 0.422 Chirality : 0.046 0.287 1807 Planarity : 0.006 0.112 2071 Dihedral : 18.077 158.413 4530 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.87 % Allowed : 15.94 % Favored : 83.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1469 helix: 1.26 (0.18), residues: 799 sheet: 0.12 (0.36), residues: 204 loop : -0.10 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 108 HIS 0.014 0.001 HIS B 71 PHE 0.013 0.002 PHE H 90 TYR 0.013 0.002 TYR A 80 ARG 0.008 0.000 ARG E 273 Details of bonding type rmsd hydrogen bonds : bond 0.10992 ( 633) hydrogen bonds : angle 5.05249 ( 1844) metal coordination : bond 0.01658 ( 4) metal coordination : angle 8.27132 ( 6) covalent geometry : bond 0.00446 (11823) covalent geometry : angle 0.70228 (15977) Misc. bond : bond 0.04645 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7747 (mptt) REVERT: A 273 ARG cc_start: 0.7360 (tpt90) cc_final: 0.7074 (tmt-80) REVERT: A 316 GLU cc_start: 0.7514 (tt0) cc_final: 0.6515 (mp0) REVERT: A 416 GLU cc_start: 0.7626 (tt0) cc_final: 0.6961 (mp0) REVERT: A 417 GLU cc_start: 0.7647 (tt0) cc_final: 0.6905 (mp0) REVERT: B 44 LYS cc_start: 0.8025 (tttm) cc_final: 0.7782 (tttp) REVERT: B 71 HIS cc_start: 0.8142 (t70) cc_final: 0.7941 (t70) REVERT: C 42 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6773 (tt0) REVERT: D 37 LYS cc_start: 0.7266 (pttp) cc_final: 0.6637 (ptmt) REVERT: D 87 ASP cc_start: 0.8056 (t0) cc_final: 0.7692 (t0) REVERT: D 89 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7342 (mtt-85) REVERT: I 166 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7468 (mt-10) REVERT: E 164 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: E 273 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7211 (ttp-110) REVERT: E 316 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6496 (mp0) REVERT: E 327 GLU cc_start: 0.7514 (pt0) cc_final: 0.7249 (pt0) REVERT: E 424 GLU cc_start: 0.7500 (tt0) cc_final: 0.7222 (tt0) REVERT: F 80 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8225 (mtmt) outliers start: 7 outliers final: 3 residues processed: 177 average time/residue: 1.7463 time to fit residues: 327.6040 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 37 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 0.0060 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 194 GLN A 282 GLN B 45 ASN C 25 ASN D 122 ASN I 92 ASN E 64 GLN E 179 GLN E 194 GLN E 207 ASN H 42 HIS G 20 GLN G 25 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.091288 restraints weight = 57427.725| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.89 r_work: 0.2889 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11829 Z= 0.133 Angle : 0.515 7.345 15983 Z= 0.273 Chirality : 0.043 0.151 1807 Planarity : 0.004 0.052 2071 Dihedral : 11.229 160.364 1702 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.43 % Allowed : 15.15 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.55 (0.22), residues: 1469 helix: 1.73 (0.18), residues: 804 sheet: 0.53 (0.39), residues: 199 loop : 0.14 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 440 HIS 0.014 0.001 HIS B 71 PHE 0.011 0.002 PHE D 93 TYR 0.015 0.002 TYR A 80 ARG 0.004 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 633) hydrogen bonds : angle 4.39664 ( 1844) metal coordination : bond 0.00926 ( 4) metal coordination : angle 4.04665 ( 6) covalent geometry : bond 0.00294 (11823) covalent geometry : angle 0.50880 (15977) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8473 (mmtp) cc_final: 0.7879 (mptt) REVERT: A 273 ARG cc_start: 0.7858 (tpt90) cc_final: 0.7433 (tmt-80) REVERT: A 316 GLU cc_start: 0.7933 (tt0) cc_final: 0.6824 (mp0) REVERT: A 364 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: A 416 GLU cc_start: 0.8125 (tt0) cc_final: 0.7123 (mp0) REVERT: A 417 GLU cc_start: 0.7897 (tt0) cc_final: 0.7110 (mp0) REVERT: B 37 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7601 (mtm110) REVERT: D 37 LYS cc_start: 0.7429 (pttp) cc_final: 0.6850 (ptmt) REVERT: D 89 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7516 (mtp85) REVERT: I 81 GLN cc_start: 0.7705 (tt0) cc_final: 0.7487 (tt0) REVERT: I 166 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 273 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7610 (ttp-110) REVERT: E 316 GLU cc_start: 0.8032 (mt-10) cc_final: 0.6930 (mp0) REVERT: E 327 GLU cc_start: 0.7569 (pt0) cc_final: 0.7191 (mt-10) REVERT: E 424 GLU cc_start: 0.7977 (tt0) cc_final: 0.7631 (tt0) REVERT: F 71 HIS cc_start: 0.8158 (t-90) cc_final: 0.7807 (t-90) REVERT: G 21 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6221 (mp0) REVERT: G 61 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6236 (mp0) outliers start: 14 outliers final: 4 residues processed: 163 average time/residue: 1.8976 time to fit residues: 326.9209 Evaluate side-chains 157 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086801 restraints weight = 49180.322| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.70 r_work: 0.2823 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11829 Z= 0.227 Angle : 0.609 9.062 15983 Z= 0.325 Chirality : 0.048 0.174 1807 Planarity : 0.005 0.042 2071 Dihedral : 11.219 175.495 1693 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.38 % Allowed : 13.80 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.46 (0.22), residues: 1469 helix: 1.64 (0.18), residues: 806 sheet: 0.51 (0.38), residues: 198 loop : 0.12 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 440 HIS 0.015 0.002 HIS B 71 PHE 0.010 0.002 PHE E 141 TYR 0.020 0.003 TYR A 80 ARG 0.008 0.001 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.06557 ( 633) hydrogen bonds : angle 4.59730 ( 1844) metal coordination : bond 0.01704 ( 4) metal coordination : angle 4.40588 ( 6) covalent geometry : bond 0.00547 (11823) covalent geometry : angle 0.60309 (15977) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8431 (mmtp) cc_final: 0.7837 (mptt) REVERT: A 273 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7388 (ttt180) REVERT: A 316 GLU cc_start: 0.8033 (tt0) cc_final: 0.6925 (mp0) REVERT: A 327 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7737 (tt0) REVERT: A 364 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: A 416 GLU cc_start: 0.8351 (tt0) cc_final: 0.7083 (mp0) REVERT: A 417 GLU cc_start: 0.8036 (tt0) cc_final: 0.7098 (mp0) REVERT: B 37 ARG cc_start: 0.8302 (mtm110) cc_final: 0.7542 (mtm110) REVERT: D 89 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7588 (mtp85) REVERT: I 81 GLN cc_start: 0.7651 (tt0) cc_final: 0.7418 (tt0) REVERT: I 135 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.6738 (ttp80) REVERT: I 166 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8163 (mt-10) REVERT: E 208 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: E 273 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7621 (ttp-110) REVERT: E 316 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7019 (mp0) REVERT: E 327 GLU cc_start: 0.7680 (pt0) cc_final: 0.7188 (mt-10) REVERT: E 424 GLU cc_start: 0.8029 (tt0) cc_final: 0.7621 (tt0) REVERT: F 42 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7621 (pt0) REVERT: F 71 HIS cc_start: 0.8348 (t-90) cc_final: 0.7945 (t-90) REVERT: G 21 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6173 (mp0) REVERT: G 39 ASP cc_start: 0.7382 (m-30) cc_final: 0.7072 (m-30) REVERT: G 61 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: G 74 ASN cc_start: 0.4678 (OUTLIER) cc_final: 0.4365 (p0) outliers start: 26 outliers final: 5 residues processed: 182 average time/residue: 1.8073 time to fit residues: 348.3938 Evaluate side-chains 169 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085887 restraints weight = 56106.364| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.93 r_work: 0.2822 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11829 Z= 0.169 Angle : 0.549 8.729 15983 Z= 0.292 Chirality : 0.045 0.160 1807 Planarity : 0.004 0.039 2071 Dihedral : 10.928 176.023 1693 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.98 % Allowed : 14.75 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.58 (0.22), residues: 1469 helix: 1.77 (0.18), residues: 806 sheet: 0.46 (0.38), residues: 203 loop : 0.16 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 440 HIS 0.012 0.001 HIS B 71 PHE 0.010 0.002 PHE E 141 TYR 0.017 0.002 TYR E 80 ARG 0.005 0.001 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05786 ( 633) hydrogen bonds : angle 4.44275 ( 1844) metal coordination : bond 0.01461 ( 4) metal coordination : angle 4.00660 ( 6) covalent geometry : bond 0.00396 (11823) covalent geometry : angle 0.54407 (15977) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8429 (mmtp) cc_final: 0.7825 (mptt) REVERT: A 273 ARG cc_start: 0.7894 (tpt90) cc_final: 0.7368 (ttt180) REVERT: A 316 GLU cc_start: 0.7994 (tt0) cc_final: 0.6836 (mp0) REVERT: A 320 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (ttpp) REVERT: A 364 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: A 416 GLU cc_start: 0.8335 (tt0) cc_final: 0.7928 (tt0) REVERT: A 417 GLU cc_start: 0.7984 (tt0) cc_final: 0.7085 (mp0) REVERT: B 37 ARG cc_start: 0.8294 (mtm110) cc_final: 0.7540 (mtm110) REVERT: D 89 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7537 (mtp85) REVERT: I 81 GLN cc_start: 0.7670 (tt0) cc_final: 0.7459 (tt0) REVERT: I 135 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6746 (ttp80) REVERT: I 166 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8181 (mt-10) REVERT: E 208 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: E 273 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7633 (ttp-110) REVERT: E 316 GLU cc_start: 0.8063 (mt-10) cc_final: 0.6964 (mp0) REVERT: E 327 GLU cc_start: 0.7688 (pt0) cc_final: 0.7161 (mt-10) REVERT: E 424 GLU cc_start: 0.8031 (tt0) cc_final: 0.7156 (mp0) REVERT: F 42 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: F 71 HIS cc_start: 0.8347 (t-90) cc_final: 0.7945 (t-90) REVERT: G 5 GLU cc_start: 0.4387 (OUTLIER) cc_final: 0.4027 (tt0) REVERT: G 21 GLU cc_start: 0.6390 (mt-10) cc_final: 0.6123 (mp0) REVERT: G 39 ASP cc_start: 0.7434 (m-30) cc_final: 0.7107 (m-30) REVERT: G 61 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6203 (mp0) outliers start: 21 outliers final: 8 residues processed: 168 average time/residue: 1.9669 time to fit residues: 349.2744 Evaluate side-chains 171 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088341 restraints weight = 57442.677| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.69 r_work: 0.2871 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11829 Z= 0.118 Angle : 0.481 8.505 15983 Z= 0.254 Chirality : 0.042 0.145 1807 Planarity : 0.004 0.038 2071 Dihedral : 10.405 170.070 1693 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.59 % Allowed : 14.99 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.84 (0.23), residues: 1469 helix: 2.02 (0.19), residues: 804 sheet: 0.49 (0.38), residues: 205 loop : 0.25 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 440 HIS 0.009 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.014 0.002 TYR E 80 ARG 0.002 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 633) hydrogen bonds : angle 4.21507 ( 1844) metal coordination : bond 0.01167 ( 4) metal coordination : angle 3.61726 ( 6) covalent geometry : bond 0.00258 (11823) covalent geometry : angle 0.47558 (15977) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8514 (mmtp) cc_final: 0.7898 (mptt) REVERT: A 273 ARG cc_start: 0.7859 (tpt90) cc_final: 0.7341 (ttt180) REVERT: A 316 GLU cc_start: 0.7897 (tt0) cc_final: 0.6756 (mp0) REVERT: A 364 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: A 416 GLU cc_start: 0.8254 (tt0) cc_final: 0.7859 (tt0) REVERT: A 417 GLU cc_start: 0.7926 (tt0) cc_final: 0.7100 (mp0) REVERT: B 37 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7479 (mtm110) REVERT: B 54 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7584 (t) REVERT: D 37 LYS cc_start: 0.7426 (pttp) cc_final: 0.6900 (ptmt) REVERT: D 89 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7545 (mtp85) REVERT: I 81 GLN cc_start: 0.7762 (tt0) cc_final: 0.7515 (tt0) REVERT: I 135 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6660 (ttp80) REVERT: I 166 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8193 (mt-10) REVERT: E 273 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7606 (ttp-110) REVERT: E 291 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8709 (mtm) REVERT: E 316 GLU cc_start: 0.8031 (mt-10) cc_final: 0.6951 (mp0) REVERT: E 327 GLU cc_start: 0.7626 (pt0) cc_final: 0.7120 (mt-10) REVERT: E 424 GLU cc_start: 0.7969 (tt0) cc_final: 0.7132 (mp0) REVERT: F 42 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: F 71 HIS cc_start: 0.8195 (t-90) cc_final: 0.7853 (t-90) REVERT: G 5 GLU cc_start: 0.4457 (OUTLIER) cc_final: 0.4060 (tt0) REVERT: G 21 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6184 (mp0) REVERT: G 39 ASP cc_start: 0.7429 (m-30) cc_final: 0.7033 (m-30) REVERT: G 61 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6223 (mp0) outliers start: 16 outliers final: 5 residues processed: 159 average time/residue: 1.9317 time to fit residues: 324.2899 Evaluate side-chains 161 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.8980 chunk 139 optimal weight: 0.0270 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085538 restraints weight = 49393.276| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.17 r_work: 0.2848 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11829 Z= 0.165 Angle : 0.533 8.131 15983 Z= 0.283 Chirality : 0.044 0.160 1807 Planarity : 0.004 0.038 2071 Dihedral : 10.504 168.755 1692 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.22 % Allowed : 14.51 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.74 (0.22), residues: 1469 helix: 1.92 (0.18), residues: 804 sheet: 0.52 (0.38), residues: 204 loop : 0.19 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 440 HIS 0.010 0.001 HIS B 71 PHE 0.009 0.002 PHE A 408 TYR 0.016 0.002 TYR E 80 ARG 0.004 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05691 ( 633) hydrogen bonds : angle 4.37284 ( 1844) metal coordination : bond 0.01427 ( 4) metal coordination : angle 3.94105 ( 6) covalent geometry : bond 0.00386 (11823) covalent geometry : angle 0.52769 (15977) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 1.391 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8431 (mmtp) cc_final: 0.7828 (mptt) REVERT: A 273 ARG cc_start: 0.7880 (tpt90) cc_final: 0.7379 (ttt180) REVERT: A 316 GLU cc_start: 0.7938 (tt0) cc_final: 0.6816 (mp0) REVERT: A 364 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: A 416 GLU cc_start: 0.8286 (tt0) cc_final: 0.7893 (tt0) REVERT: A 417 GLU cc_start: 0.7978 (tt0) cc_final: 0.7063 (mp0) REVERT: B 37 ARG cc_start: 0.8300 (mtm110) cc_final: 0.7475 (mtm110) REVERT: B 54 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7668 (t) REVERT: D 37 LYS cc_start: 0.7486 (pttp) cc_final: 0.6969 (ptmt) REVERT: D 89 ARG cc_start: 0.7950 (mtt-85) cc_final: 0.7568 (mtp85) REVERT: I 135 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.6722 (ttp80) REVERT: I 166 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8185 (mt-10) REVERT: E 208 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: E 273 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7585 (ttp-110) REVERT: E 291 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8767 (mtm) REVERT: E 316 GLU cc_start: 0.8040 (mt-10) cc_final: 0.6970 (mp0) REVERT: E 327 GLU cc_start: 0.7640 (pt0) cc_final: 0.7158 (mt-10) REVERT: E 424 GLU cc_start: 0.8015 (tt0) cc_final: 0.7162 (mp0) REVERT: F 42 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: F 71 HIS cc_start: 0.8309 (t-90) cc_final: 0.7952 (t-90) REVERT: H 110 LYS cc_start: 0.6665 (OUTLIER) cc_final: 0.5820 (ttmt) REVERT: G 5 GLU cc_start: 0.4376 (OUTLIER) cc_final: 0.4008 (tt0) REVERT: G 21 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6148 (mt-10) REVERT: G 39 ASP cc_start: 0.7367 (m-30) cc_final: 0.6955 (m-30) REVERT: G 61 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6201 (mp0) outliers start: 24 outliers final: 9 residues processed: 167 average time/residue: 1.8488 time to fit residues: 326.6091 Evaluate side-chains 171 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain H residue 110 LYS Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.087976 restraints weight = 45431.922| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.64 r_work: 0.2847 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11829 Z= 0.156 Angle : 0.522 7.850 15983 Z= 0.278 Chirality : 0.044 0.156 1807 Planarity : 0.004 0.037 2071 Dihedral : 10.235 165.287 1692 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.90 % Allowed : 14.75 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1469 helix: 1.94 (0.18), residues: 804 sheet: 0.55 (0.38), residues: 204 loop : 0.18 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 440 HIS 0.010 0.001 HIS B 71 PHE 0.009 0.002 PHE A 408 TYR 0.016 0.002 TYR A 80 ARG 0.004 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 633) hydrogen bonds : angle 4.34613 ( 1844) metal coordination : bond 0.01397 ( 4) metal coordination : angle 3.85588 ( 6) covalent geometry : bond 0.00363 (11823) covalent geometry : angle 0.51694 (15977) Misc. bond : bond 0.00032 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8489 (mmtp) cc_final: 0.7901 (mptt) REVERT: A 273 ARG cc_start: 0.7914 (tpt90) cc_final: 0.7409 (ttt180) REVERT: A 316 GLU cc_start: 0.7968 (tt0) cc_final: 0.6844 (mp0) REVERT: A 364 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: A 416 GLU cc_start: 0.8312 (tt0) cc_final: 0.7918 (tt0) REVERT: A 417 GLU cc_start: 0.7988 (tt0) cc_final: 0.7091 (mp0) REVERT: B 37 ARG cc_start: 0.8361 (mtm110) cc_final: 0.7530 (mtm110) REVERT: B 54 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7713 (t) REVERT: D 37 LYS cc_start: 0.7483 (pttp) cc_final: 0.6963 (ptmt) REVERT: D 89 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7642 (mtp85) REVERT: I 135 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6769 (ttp80) REVERT: E 208 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: E 273 ARG cc_start: 0.8109 (ttm-80) cc_final: 0.7597 (ttp-110) REVERT: E 316 GLU cc_start: 0.8058 (mt-10) cc_final: 0.6994 (mp0) REVERT: E 327 GLU cc_start: 0.7690 (pt0) cc_final: 0.7186 (mt-10) REVERT: E 424 GLU cc_start: 0.8068 (tt0) cc_final: 0.7191 (mp0) REVERT: F 42 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7587 (pt0) REVERT: F 71 HIS cc_start: 0.8260 (t-90) cc_final: 0.7921 (t-90) REVERT: G 5 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.4108 (tt0) REVERT: G 21 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5922 (mt-10) REVERT: G 39 ASP cc_start: 0.7427 (m-30) cc_final: 0.7022 (m-30) REVERT: G 61 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.6187 (mp0) outliers start: 20 outliers final: 9 residues processed: 167 average time/residue: 1.9022 time to fit residues: 336.0317 Evaluate side-chains 172 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 106 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.090363 restraints weight = 55714.506| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.73 r_work: 0.2904 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11829 Z= 0.101 Angle : 0.456 9.221 15983 Z= 0.240 Chirality : 0.041 0.138 1807 Planarity : 0.003 0.036 2071 Dihedral : 9.445 153.194 1692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.43 % Allowed : 15.38 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 2.02 (0.23), residues: 1469 helix: 2.15 (0.19), residues: 804 sheet: 0.67 (0.39), residues: 204 loop : 0.30 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 440 HIS 0.007 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.012 0.001 TYR E 80 ARG 0.002 0.000 ARG E 275 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 633) hydrogen bonds : angle 4.09206 ( 1844) metal coordination : bond 0.01139 ( 4) metal coordination : angle 3.43970 ( 6) covalent geometry : bond 0.00212 (11823) covalent geometry : angle 0.45124 (15977) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8534 (mmtp) cc_final: 0.7934 (mptt) REVERT: A 273 ARG cc_start: 0.7866 (tpt90) cc_final: 0.7342 (ttt180) REVERT: A 316 GLU cc_start: 0.7851 (tt0) cc_final: 0.6752 (mp0) REVERT: A 364 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: A 416 GLU cc_start: 0.8250 (tt0) cc_final: 0.7860 (tt0) REVERT: A 417 GLU cc_start: 0.7903 (tt0) cc_final: 0.7114 (mp0) REVERT: B 37 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7480 (mtm110) REVERT: B 54 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7529 (t) REVERT: D 37 LYS cc_start: 0.7488 (pttp) cc_final: 0.6963 (ptmt) REVERT: D 89 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7541 (mtp85) REVERT: I 81 GLN cc_start: 0.7779 (tt0) cc_final: 0.7534 (tt0) REVERT: I 135 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6637 (ttp80) REVERT: E 273 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7539 (ttp-110) REVERT: E 316 GLU cc_start: 0.8024 (mt-10) cc_final: 0.6933 (mp0) REVERT: E 327 GLU cc_start: 0.7595 (pt0) cc_final: 0.7106 (mt-10) REVERT: E 335 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8203 (ttmm) REVERT: E 424 GLU cc_start: 0.7950 (tt0) cc_final: 0.7128 (mp0) REVERT: F 71 HIS cc_start: 0.8134 (t-90) cc_final: 0.7815 (t-90) REVERT: G 21 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5932 (mt-10) REVERT: G 39 ASP cc_start: 0.7350 (m-30) cc_final: 0.6937 (m-30) REVERT: G 61 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6206 (mp0) outliers start: 14 outliers final: 5 residues processed: 159 average time/residue: 1.9157 time to fit residues: 321.6493 Evaluate side-chains 158 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN F 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088405 restraints weight = 58510.940| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.96 r_work: 0.2858 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11829 Z= 0.125 Angle : 0.485 9.049 15983 Z= 0.256 Chirality : 0.042 0.148 1807 Planarity : 0.004 0.037 2071 Dihedral : 9.483 150.085 1692 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.35 % Allowed : 15.46 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.97 (0.23), residues: 1469 helix: 2.11 (0.19), residues: 804 sheet: 0.64 (0.39), residues: 205 loop : 0.28 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 440 HIS 0.008 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.015 0.002 TYR A 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 633) hydrogen bonds : angle 4.19034 ( 1844) metal coordination : bond 0.01168 ( 4) metal coordination : angle 3.70446 ( 6) covalent geometry : bond 0.00278 (11823) covalent geometry : angle 0.47951 (15977) Misc. bond : bond 0.00012 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8551 (mmtp) cc_final: 0.7956 (mptt) REVERT: A 273 ARG cc_start: 0.7916 (tpt90) cc_final: 0.7383 (ttt180) REVERT: A 291 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7250 (mtm) REVERT: A 316 GLU cc_start: 0.7927 (tt0) cc_final: 0.6795 (mp0) REVERT: A 327 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7723 (tt0) REVERT: A 364 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: A 416 GLU cc_start: 0.8276 (tt0) cc_final: 0.7887 (tt0) REVERT: A 417 GLU cc_start: 0.7974 (tt0) cc_final: 0.7137 (mp0) REVERT: B 54 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7614 (t) REVERT: D 37 LYS cc_start: 0.7533 (pttp) cc_final: 0.7007 (ptmt) REVERT: D 89 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7656 (mtp85) REVERT: I 135 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6685 (ttp80) REVERT: I 161 GLU cc_start: 0.8118 (pm20) cc_final: 0.7327 (mp0) REVERT: E 273 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7592 (ttp-110) REVERT: E 316 GLU cc_start: 0.8041 (mt-10) cc_final: 0.6957 (mp0) REVERT: E 327 GLU cc_start: 0.7641 (pt0) cc_final: 0.7138 (mt-10) REVERT: E 335 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8263 (ttmm) REVERT: E 424 GLU cc_start: 0.7997 (tt0) cc_final: 0.7147 (mp0) REVERT: F 71 HIS cc_start: 0.8210 (t-90) cc_final: 0.7873 (t-90) REVERT: G 21 GLU cc_start: 0.6236 (mt-10) cc_final: 0.5935 (mt-10) REVERT: G 39 ASP cc_start: 0.7392 (m-30) cc_final: 0.6992 (m-30) REVERT: G 61 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6170 (mp0) outliers start: 13 outliers final: 6 residues processed: 159 average time/residue: 1.8531 time to fit residues: 311.1745 Evaluate side-chains 159 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087437 restraints weight = 56397.467| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.88 r_work: 0.2850 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11829 Z= 0.135 Angle : 0.498 9.013 15983 Z= 0.264 Chirality : 0.043 0.152 1807 Planarity : 0.004 0.036 2071 Dihedral : 9.506 149.047 1692 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.35 % Allowed : 15.78 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 (0.23), residues: 1469 helix: 2.08 (0.19), residues: 804 sheet: 0.60 (0.39), residues: 205 loop : 0.25 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 440 HIS 0.008 0.001 HIS B 71 PHE 0.008 0.001 PHE D 93 TYR 0.016 0.002 TYR A 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 633) hydrogen bonds : angle 4.24306 ( 1844) metal coordination : bond 0.01231 ( 4) metal coordination : angle 3.71217 ( 6) covalent geometry : bond 0.00305 (11823) covalent geometry : angle 0.49238 (15977) Misc. bond : bond 0.00010 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8552 (mmtp) cc_final: 0.7964 (mptt) REVERT: A 273 ARG cc_start: 0.7929 (tpt90) cc_final: 0.7404 (ttt180) REVERT: A 291 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7244 (mtm) REVERT: A 316 GLU cc_start: 0.7951 (tt0) cc_final: 0.6814 (mp0) REVERT: A 327 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7746 (tt0) REVERT: A 364 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: A 416 GLU cc_start: 0.8312 (tt0) cc_final: 0.7914 (tt0) REVERT: A 417 GLU cc_start: 0.7996 (tt0) cc_final: 0.7140 (mp0) REVERT: B 37 ARG cc_start: 0.8198 (mtp-110) cc_final: 0.7502 (mtm110) REVERT: B 54 THR cc_start: 0.7878 (OUTLIER) cc_final: 0.7604 (t) REVERT: D 37 LYS cc_start: 0.7478 (pttp) cc_final: 0.6948 (ptmt) REVERT: D 89 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7713 (mtp85) REVERT: I 135 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: I 161 GLU cc_start: 0.8113 (pm20) cc_final: 0.7366 (mp0) REVERT: E 273 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7615 (ttp-110) REVERT: E 316 GLU cc_start: 0.8062 (mt-10) cc_final: 0.6983 (mp0) REVERT: E 327 GLU cc_start: 0.7661 (pt0) cc_final: 0.7150 (mt-10) REVERT: E 335 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8282 (ttmm) REVERT: E 424 GLU cc_start: 0.8033 (tt0) cc_final: 0.7178 (mp0) REVERT: F 71 HIS cc_start: 0.8235 (t-90) cc_final: 0.7898 (t-90) REVERT: G 39 ASP cc_start: 0.7449 (m-30) cc_final: 0.7049 (m-30) REVERT: G 61 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6168 (mp0) outliers start: 13 outliers final: 6 residues processed: 161 average time/residue: 1.9343 time to fit residues: 329.5399 Evaluate side-chains 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 chunk 79 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.087507 restraints weight = 56372.662| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.91 r_work: 0.2851 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11829 Z= 0.134 Angle : 0.496 8.956 15983 Z= 0.263 Chirality : 0.043 0.151 1807 Planarity : 0.004 0.037 2071 Dihedral : 9.433 148.467 1692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.27 % Allowed : 15.70 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.91 (0.23), residues: 1469 helix: 2.07 (0.19), residues: 804 sheet: 0.57 (0.39), residues: 205 loop : 0.26 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 440 HIS 0.008 0.001 HIS B 71 PHE 0.008 0.001 PHE D 93 TYR 0.015 0.002 TYR A 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 633) hydrogen bonds : angle 4.23810 ( 1844) metal coordination : bond 0.01211 ( 4) metal coordination : angle 3.67192 ( 6) covalent geometry : bond 0.00303 (11823) covalent geometry : angle 0.49084 (15977) Misc. bond : bond 0.00014 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11533.23 seconds wall clock time: 198 minutes 48.50 seconds (11928.50 seconds total)