Starting phenix.real_space_refine on Fri Jul 3 02:52:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmf_19360/07_2026/8rmf_19360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmf_19360/07_2026/8rmf_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_19360/07_2026/8rmf_19360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2026/8rmf_19360.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2026/8rmf_19360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2026/8rmf_19360.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 0 Ad-hoc single atom residues: {'FE2': 1} Chain breaks: 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, 0 Ad-hoc single atom residues: {'FE2': 1} Chain breaks: 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: 4.28, per 1000 atoms: 0.36 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: 1.14 Conformation dependent library (CDL) restraints added in 977.9 milliseconds 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: 0.29 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: 1.87 Time building geometry restraints manager: 1.53 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 201) selection = (chain 'H' and resid 36 through 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: 1.780 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.490 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:9.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (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 ARG 0.008 0.000 ARG E 273 TYR 0.013 0.002 TYR A 80 PHE 0.013 0.002 PHE H 90 TRP 0.011 0.002 TRP H 108 HIS 0.014 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.24 (11823) covalent geometry : angle 0.70228 / 0.42 (15977) hydrogen bonds : bond 0.10992 / 7.37 ( 633) hydrogen bonds : angle 5.05249 / 3.76 ( 1844) metal coordination : bond 0.01658 / 0.84 ( 4) metal coordination : angle 8.27132 / 4.32 ( 6) Misc. bond : bond 0.04645 / 2.34 ( 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 : 0.468 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: 0.7680 (t0) REVERT: D 89 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7259 (mtp85) 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: 0.7223 (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: 0.7927 time to fit residues: 148.8772 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 : 0.460 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3735 r_free = 0.3735 target = 0.145420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.090797 restraints weight = 50459.653| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.57 r_work: 0.2893 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1096 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= 0.138 Angle : 0.521 7.748 15983 Z= 0.276 Chirality : 0.043 0.152 1807 Planarity : 0.004 0.052 2071 Dihedral : 11.412 160.258 1702 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.51 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.22), residues: 1469 helix: 1.70 (0.18), residues: 804 sheet: 0.52 (0.38), residues: 199 loop : 0.13 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 41 TYR 0.016 0.002 TYR E 80 PHE 0.010 0.002 PHE H 90 TRP 0.010 0.002 TRP E 440 HIS 0.014 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11823) covalent geometry : angle 0.51458 / 0.28 (15977) hydrogen bonds : bond 0.05266 / 3.58 ( 633) hydrogen bonds : angle 4.44800 / 3.32 ( 1844) metal coordination : bond 0.00945 / 0.48 ( 4) metal coordination : angle 4.17544 / 1.70 ( 6) Misc. bond : bond 0.00122 / 0.06 ( 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 173 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8447 (mmtp) cc_final: 0.7861 (mptt) REVERT: A 273 ARG cc_start: 0.7860 (tpt90) cc_final: 0.7440 (tmt-80) REVERT: A 316 GLU cc_start: 0.7931 (tt0) cc_final: 0.6835 (mp0) REVERT: A 364 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 416 GLU cc_start: 0.8110 (tt0) cc_final: 0.7134 (mp0) REVERT: A 417 GLU cc_start: 0.7909 (tt0) cc_final: 0.7143 (mp0) REVERT: B 37 ARG cc_start: 0.8288 (mtm110) cc_final: 0.7597 (mtm110) REVERT: D 37 LYS cc_start: 0.7466 (pttp) cc_final: 0.6879 (ptmt) REVERT: D 89 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7538 (mtp85) REVERT: I 81 GLN cc_start: 0.7676 (tt0) cc_final: 0.7471 (tt0) REVERT: I 166 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7952 (mt-10) REVERT: E 273 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7614 (ttp-110) REVERT: E 316 GLU cc_start: 0.8017 (mt-10) cc_final: 0.6925 (mp0) REVERT: E 327 GLU cc_start: 0.7579 (pt0) cc_final: 0.7192 (mt-10) REVERT: E 424 GLU cc_start: 0.7997 (tt0) cc_final: 0.7625 (tt0) REVERT: F 71 HIS cc_start: 0.8150 (t-90) cc_final: 0.7782 (t-90) REVERT: G 21 GLU cc_start: 0.6494 (mt-10) cc_final: 0.6252 (mp0) REVERT: G 61 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6257 (mp0) outliers start: 15 outliers final: 5 residues processed: 166 average time/residue: 0.8403 time to fit residues: 147.2718 Evaluate side-chains 158 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 259 ILE 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 14 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091724 restraints weight = 54437.408| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.90 r_work: 0.2893 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 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 = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11829 Z= 0.119 Angle : 0.479 6.904 15983 Z= 0.255 Chirality : 0.042 0.147 1807 Planarity : 0.004 0.042 2071 Dihedral : 10.364 157.253 1693 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.90 % Allowed : 14.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1469 helix: 1.93 (0.18), residues: 804 sheet: 0.49 (0.39), residues: 205 loop : 0.27 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 292 TYR 0.014 0.002 TYR E 80 PHE 0.009 0.001 PHE D 93 TRP 0.008 0.001 TRP E 440 HIS 0.011 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11823) covalent geometry : angle 0.47317 / 0.25 (15977) hydrogen bonds : bond 0.04840 / 3.29 ( 633) hydrogen bonds : angle 4.25331 / 3.17 ( 1844) metal coordination : bond 0.00801 / 0.40 ( 4) metal coordination : angle 3.71504 / 1.56 ( 6) Misc. bond : bond 0.00024 / 0.01 ( 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 169 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8491 (mmtp) cc_final: 0.7910 (mptt) REVERT: A 273 ARG cc_start: 0.7842 (tpt90) cc_final: 0.7393 (tmt-80) REVERT: A 316 GLU cc_start: 0.7921 (tt0) cc_final: 0.6812 (mp0) REVERT: A 335 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8001 (pttm) REVERT: A 364 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 416 GLU cc_start: 0.8165 (tt0) cc_final: 0.7079 (mp0) REVERT: A 417 GLU cc_start: 0.7915 (tt0) cc_final: 0.7138 (mp0) REVERT: B 37 ARG cc_start: 0.8255 (mtm110) cc_final: 0.7535 (mtm110) REVERT: D 37 LYS cc_start: 0.7441 (pttp) cc_final: 0.6899 (ptmt) REVERT: D 89 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7478 (mtp85) REVERT: D 143 GLU cc_start: 0.7549 (tt0) cc_final: 0.7305 (tt0) REVERT: I 81 GLN cc_start: 0.7618 (tt0) cc_final: 0.7399 (tt0) REVERT: I 135 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6624 (ttp80) REVERT: I 166 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8096 (mt-10) REVERT: E 273 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7608 (ttp-110) REVERT: E 316 GLU cc_start: 0.8028 (mt-10) cc_final: 0.6954 (mp0) REVERT: E 327 GLU cc_start: 0.7620 (pt0) cc_final: 0.7182 (mt-10) REVERT: E 424 GLU cc_start: 0.7978 (tt0) cc_final: 0.7157 (mp0) REVERT: E 442 MET cc_start: 0.7228 (mtm) cc_final: 0.7024 (mtp) REVERT: F 71 HIS cc_start: 0.8190 (t-90) cc_final: 0.7840 (t-90) REVERT: G 21 GLU cc_start: 0.6462 (mt-10) cc_final: 0.6210 (mp0) REVERT: G 61 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6202 (mp0) outliers start: 20 outliers final: 2 residues processed: 159 average time/residue: 0.7323 time to fit residues: 122.9890 Evaluate side-chains 153 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 120 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 71 optimal weight: 0.4980 chunk 59 optimal weight: 9.9990 chunk 54 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.088715 restraints weight = 62698.425| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.93 r_work: 0.2869 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11829 Z= 0.127 Angle : 0.486 7.063 15983 Z= 0.259 Chirality : 0.043 0.152 1807 Planarity : 0.004 0.036 2071 Dihedral : 10.041 156.890 1693 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.67 % Allowed : 14.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.23), residues: 1469 helix: 2.01 (0.19), residues: 804 sheet: 0.54 (0.39), residues: 205 loop : 0.29 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 292 TYR 0.014 0.002 TYR A 80 PHE 0.008 0.001 PHE H 90 TRP 0.010 0.001 TRP E 440 HIS 0.010 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (11823) covalent geometry : angle 0.48083 / 0.26 (15977) hydrogen bonds : bond 0.05048 / 3.43 ( 633) hydrogen bonds : angle 4.23865 / 3.16 ( 1844) metal coordination : bond 0.01083 / 0.54 ( 4) metal coordination : angle 3.67967 / 1.52 ( 6) Misc. bond : bond 0.00023 / 0.01 ( 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 176 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8472 (mmtp) cc_final: 0.7870 (mptt) REVERT: A 273 ARG cc_start: 0.7833 (tpt90) cc_final: 0.7368 (tmt-80) REVERT: A 316 GLU cc_start: 0.7896 (tt0) cc_final: 0.6744 (mp0) REVERT: A 364 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 416 GLU cc_start: 0.8161 (tt0) cc_final: 0.6990 (mp0) REVERT: A 417 GLU cc_start: 0.7896 (tt0) cc_final: 0.7025 (mp0) REVERT: B 37 ARG cc_start: 0.8246 (mtm110) cc_final: 0.7525 (mtm110) REVERT: D 37 LYS cc_start: 0.7367 (pttp) cc_final: 0.6836 (ptmt) REVERT: D 89 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7504 (mtp85) REVERT: D 143 GLU cc_start: 0.7494 (tt0) cc_final: 0.7250 (tt0) REVERT: I 81 GLN cc_start: 0.7650 (tt0) cc_final: 0.7404 (tt0) REVERT: I 135 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.6619 (ttp80) REVERT: I 166 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8142 (mt-10) REVERT: E 208 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: E 273 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7528 (ttp-110) REVERT: E 291 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8731 (mtm) REVERT: E 316 GLU cc_start: 0.8017 (mt-10) cc_final: 0.6903 (mp0) REVERT: E 327 GLU cc_start: 0.7594 (pt0) cc_final: 0.7126 (mt-10) REVERT: E 424 GLU cc_start: 0.7941 (tt0) cc_final: 0.7073 (mp0) REVERT: E 442 MET cc_start: 0.7163 (mtm) cc_final: 0.6957 (mtp) REVERT: F 71 HIS cc_start: 0.8149 (t-90) cc_final: 0.7755 (t-90) REVERT: G 21 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6211 (mp0) REVERT: G 61 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6190 (mp0) outliers start: 17 outliers final: 2 residues processed: 169 average time/residue: 0.7655 time to fit residues: 136.9454 Evaluate side-chains 160 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU 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 E residue 291 MET 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 126 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.140974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085499 restraints weight = 57946.225| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.02 r_work: 0.2808 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11829 Z= 0.202 Angle : 0.580 9.291 15983 Z= 0.307 Chirality : 0.047 0.167 1807 Planarity : 0.005 0.037 2071 Dihedral : 10.523 162.519 1692 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.06 % Allowed : 14.35 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.22), residues: 1469 helix: 1.83 (0.18), residues: 805 sheet: 0.48 (0.38), residues: 204 loop : 0.23 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 292 TYR 0.018 0.003 TYR A 80 PHE 0.009 0.002 PHE A 408 TRP 0.015 0.002 TRP E 440 HIS 0.012 0.002 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (11823) covalent geometry : angle 0.57404 / 0.31 (15977) hydrogen bonds : bond 0.06204 / 4.21 ( 633) hydrogen bonds : angle 4.48277 / 3.34 ( 1844) metal coordination : bond 0.01628 / 0.80 ( 4) metal coordination : angle 4.14047 / 1.57 ( 6) Misc. bond : bond 0.00043 / 0.02 ( 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 175 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8458 (mmtp) cc_final: 0.7846 (mptt) REVERT: A 273 ARG cc_start: 0.7926 (tpt90) cc_final: 0.7416 (ttt180) REVERT: A 291 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.7420 (mtm) REVERT: A 316 GLU cc_start: 0.8047 (tt0) cc_final: 0.6892 (mp0) REVERT: A 327 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7763 (tt0) REVERT: A 364 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: A 416 GLU cc_start: 0.8368 (tt0) cc_final: 0.7957 (tt0) REVERT: A 417 GLU cc_start: 0.8034 (tt0) cc_final: 0.7085 (mp0) REVERT: D 89 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7631 (mtp85) REVERT: I 135 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6769 (ttp80) REVERT: I 166 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 208 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: E 273 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7665 (ttp-110) REVERT: E 316 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7010 (mp0) REVERT: E 327 GLU cc_start: 0.7718 (pt0) cc_final: 0.7194 (mt-10) REVERT: E 424 GLU cc_start: 0.8123 (tt0) cc_final: 0.7704 (tt0) REVERT: F 71 HIS cc_start: 0.8361 (t-90) cc_final: 0.7970 (t-90) REVERT: G 21 GLU cc_start: 0.6343 (mt-10) cc_final: 0.6061 (mt-10) REVERT: G 61 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6191 (mp0) outliers start: 22 outliers final: 8 residues processed: 164 average time/residue: 0.8426 time to fit residues: 146.0872 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 A residue 400 ASP Chi-restraints excluded: chain C residue 23 VAL 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 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP 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 106 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.144176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088654 restraints weight = 56205.841| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.72 r_work: 0.2878 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11829 Z= 0.113 Angle : 0.476 8.480 15983 Z= 0.251 Chirality : 0.042 0.145 1807 Planarity : 0.004 0.036 2071 Dihedral : 9.876 154.653 1692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.35 % Allowed : 15.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.23), residues: 1469 helix: 2.05 (0.19), residues: 804 sheet: 0.55 (0.39), residues: 205 loop : 0.27 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 292 TYR 0.013 0.002 TYR E 80 PHE 0.008 0.001 PHE D 93 TRP 0.007 0.001 TRP E 440 HIS 0.009 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (11823) covalent geometry : angle 0.47053 / 0.25 (15977) hydrogen bonds : bond 0.04787 / 3.26 ( 633) hydrogen bonds : angle 4.20993 / 3.14 ( 1844) metal coordination : bond 0.01059 / 0.53 ( 4) metal coordination : angle 3.63683 / 1.56 ( 6) Misc. bond : bond 0.00013 / 0.01 ( 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 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8547 (mmtp) cc_final: 0.7974 (mptt) REVERT: A 273 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7388 (ttt180) REVERT: A 316 GLU cc_start: 0.7938 (tt0) cc_final: 0.6837 (mp0) REVERT: A 364 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: A 416 GLU cc_start: 0.8263 (tt0) cc_final: 0.7901 (tt0) REVERT: A 417 GLU cc_start: 0.7978 (tt0) cc_final: 0.7162 (mp0) REVERT: B 37 ARG cc_start: 0.8286 (mtm110) cc_final: 0.7552 (mtm110) REVERT: D 37 LYS cc_start: 0.7455 (pttp) cc_final: 0.6926 (ptmt) REVERT: D 89 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7577 (mtp85) REVERT: I 81 GLN cc_start: 0.7800 (tt0) cc_final: 0.7555 (tt0) REVERT: I 135 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6668 (ttp80) REVERT: I 166 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8225 (mt-10) REVERT: E 273 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7591 (ttp-110) REVERT: E 316 GLU cc_start: 0.8074 (mt-10) cc_final: 0.6999 (mp0) REVERT: E 327 GLU cc_start: 0.7663 (pt0) cc_final: 0.7158 (mt-10) REVERT: E 424 GLU cc_start: 0.8000 (tt0) cc_final: 0.7183 (mp0) REVERT: F 71 HIS cc_start: 0.8223 (t-90) cc_final: 0.7885 (t-90) REVERT: G 5 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.4075 (tt0) REVERT: G 21 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6181 (mt-10) REVERT: G 61 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6249 (mp0) outliers start: 13 outliers final: 4 residues processed: 159 average time/residue: 0.7695 time to fit residues: 129.2073 Evaluate side-chains 157 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain G residue 5 GLU 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 121 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.089436 restraints weight = 56773.577| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.88 r_work: 0.2884 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11829 Z= 0.109 Angle : 0.462 8.310 15983 Z= 0.244 Chirality : 0.042 0.143 1807 Planarity : 0.003 0.034 2071 Dihedral : 9.367 143.777 1692 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.59 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.23), residues: 1469 helix: 2.15 (0.19), residues: 804 sheet: 0.62 (0.39), residues: 205 loop : 0.32 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.013 0.002 TYR E 80 PHE 0.009 0.001 PHE D 93 TRP 0.008 0.001 TRP A 440 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (11823) covalent geometry : angle 0.45720 / 0.24 (15977) hydrogen bonds : bond 0.04573 / 3.11 ( 633) hydrogen bonds : angle 4.10707 / 3.06 ( 1844) metal coordination : bond 0.01057 / 0.53 ( 4) metal coordination : angle 3.57534 / 1.58 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 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 165 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8508 (mmtp) cc_final: 0.7927 (mptt) REVERT: A 273 ARG cc_start: 0.7857 (tpt90) cc_final: 0.7354 (ttt180) REVERT: A 316 GLU cc_start: 0.7886 (tt0) cc_final: 0.6771 (mp0) REVERT: A 364 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: A 416 GLU cc_start: 0.8222 (tt0) cc_final: 0.7077 (mp0) REVERT: A 417 GLU cc_start: 0.7925 (tt0) cc_final: 0.7117 (mp0) REVERT: B 37 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7508 (mtm110) REVERT: D 37 LYS cc_start: 0.7416 (pttp) cc_final: 0.6902 (ptmt) REVERT: D 89 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7582 (mtp85) REVERT: I 81 GLN cc_start: 0.7815 (tt0) cc_final: 0.7569 (tt0) REVERT: I 135 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6647 (ttp80) REVERT: E 273 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7572 (ttp-110) REVERT: E 316 GLU cc_start: 0.8019 (mt-10) cc_final: 0.6947 (mp0) REVERT: E 327 GLU cc_start: 0.7605 (pt0) cc_final: 0.7126 (mt-10) REVERT: E 424 GLU cc_start: 0.7966 (tt0) cc_final: 0.7148 (mp0) REVERT: E 442 MET cc_start: 0.7272 (mtm) cc_final: 0.7036 (mtp) REVERT: F 71 HIS cc_start: 0.8176 (t-90) cc_final: 0.7861 (t-90) REVERT: G 21 GLU cc_start: 0.6322 (mt-10) cc_final: 0.6021 (mt-10) REVERT: G 61 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6175 (mp0) outliers start: 16 outliers final: 5 residues processed: 156 average time/residue: 0.7736 time to fit residues: 127.1420 Evaluate side-chains 154 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER 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 55 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 134 optimal weight: 0.4980 chunk 75 optimal weight: 0.0070 chunk 79 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089484 restraints weight = 51681.733| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.80 r_work: 0.2888 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- 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 = 0.12 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 = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11829 Z= 0.113 Angle : 0.467 8.122 15983 Z= 0.247 Chirality : 0.042 0.145 1807 Planarity : 0.003 0.035 2071 Dihedral : 9.169 138.889 1692 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.27 % Allowed : 15.62 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.23), residues: 1469 helix: 2.16 (0.19), residues: 804 sheet: 0.63 (0.39), residues: 205 loop : 0.33 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 292 TYR 0.013 0.002 TYR E 80 PHE 0.008 0.001 PHE D 93 TRP 0.008 0.001 TRP A 440 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11823) covalent geometry : angle 0.46169 / 0.25 (15977) hydrogen bonds : bond 0.04692 / 3.20 ( 633) hydrogen bonds : angle 4.11129 / 3.06 ( 1844) metal coordination : bond 0.01032 / 0.52 ( 4) metal coordination : angle 3.57435 / 1.55 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 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 160 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8526 (mmtp) cc_final: 0.7952 (mptt) REVERT: A 273 ARG cc_start: 0.7878 (tpt90) cc_final: 0.7384 (ttt180) REVERT: A 316 GLU cc_start: 0.7902 (tt0) cc_final: 0.6810 (mp0) REVERT: A 364 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: A 416 GLU cc_start: 0.8228 (tt0) cc_final: 0.7101 (mp0) REVERT: A 417 GLU cc_start: 0.7938 (tt0) cc_final: 0.7137 (mp0) REVERT: B 37 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7587 (mtm110) REVERT: D 37 LYS cc_start: 0.7544 (pttp) cc_final: 0.7029 (ptmt) REVERT: D 89 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7646 (mtp85) REVERT: I 81 GLN cc_start: 0.7841 (tt0) cc_final: 0.7606 (tt0) REVERT: I 135 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6664 (ttp80) REVERT: I 161 GLU cc_start: 0.8104 (pm20) cc_final: 0.7291 (mp0) REVERT: E 273 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7580 (ttp-110) REVERT: E 316 GLU cc_start: 0.8037 (mt-10) cc_final: 0.6973 (mp0) REVERT: E 327 GLU cc_start: 0.7642 (pt0) cc_final: 0.7147 (mt-10) REVERT: E 335 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8265 (ttmm) REVERT: E 424 GLU cc_start: 0.7965 (tt0) cc_final: 0.7147 (mp0) REVERT: F 71 HIS cc_start: 0.8187 (t-90) cc_final: 0.7866 (t-90) REVERT: G 21 GLU cc_start: 0.6249 (mt-10) cc_final: 0.5945 (mt-10) REVERT: G 61 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6157 (mp0) outliers start: 12 outliers final: 5 residues processed: 155 average time/residue: 0.8683 time to fit residues: 141.9976 Evaluate side-chains 154 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER 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 75 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086358 restraints weight = 53796.369| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.88 r_work: 0.2832 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1920 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= 0.166 Angle : 0.532 8.019 15983 Z= 0.283 Chirality : 0.044 0.161 1807 Planarity : 0.004 0.035 2071 Dihedral : 9.716 145.891 1692 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.23), residues: 1469 helix: 1.99 (0.18), residues: 804 sheet: 0.56 (0.39), residues: 205 loop : 0.24 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 292 TYR 0.016 0.002 TYR E 80 PHE 0.009 0.002 PHE A 408 TRP 0.009 0.002 TRP E 440 HIS 0.009 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (11823) covalent geometry : angle 0.52679 / 0.28 (15977) hydrogen bonds : bond 0.05660 / 3.85 ( 633) hydrogen bonds : angle 4.32423 / 3.22 ( 1844) metal coordination : bond 0.01289 / 0.64 ( 4) metal coordination : angle 3.86534 / 1.50 ( 6) Misc. bond : bond 0.00026 / 0.01 ( 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 161 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8476 (mmtp) cc_final: 0.7896 (mptt) REVERT: A 273 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7411 (ttt180) REVERT: A 291 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7316 (mtm) REVERT: A 316 GLU cc_start: 0.7985 (tt0) cc_final: 0.6862 (mp0) REVERT: A 327 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7771 (tt0) REVERT: A 364 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: A 416 GLU cc_start: 0.8329 (tt0) cc_final: 0.7952 (tt0) REVERT: A 417 GLU cc_start: 0.8049 (tt0) cc_final: 0.7124 (mp0) REVERT: D 37 LYS cc_start: 0.7474 (pttp) cc_final: 0.6951 (ptmt) REVERT: D 89 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7652 (mtp85) REVERT: I 135 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6751 (ttp80) REVERT: I 141 ASP cc_start: 0.8447 (m-30) cc_final: 0.8143 (m-30) REVERT: I 161 GLU cc_start: 0.8130 (pm20) cc_final: 0.7346 (mp0) REVERT: I 166 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8173 (mt-10) REVERT: E 273 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7667 (ttp-110) REVERT: E 316 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7014 (mp0) REVERT: E 327 GLU cc_start: 0.7728 (pt0) cc_final: 0.7188 (mt-10) REVERT: E 335 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8333 (ttmm) REVERT: E 424 GLU cc_start: 0.8076 (tt0) cc_final: 0.7199 (mp0) REVERT: F 71 HIS cc_start: 0.8293 (t-90) cc_final: 0.7967 (t-90) REVERT: G 61 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6158 (mp0) outliers start: 12 outliers final: 7 residues processed: 156 average time/residue: 0.8497 time to fit residues: 139.7821 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 : 0.393 ------------------------------------------------------------------------------- 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 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 61 MET 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 40 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 91 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089748 restraints weight = 57558.736| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.94 r_work: 0.2878 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11829 Z= 0.108 Angle : 0.464 7.991 15983 Z= 0.245 Chirality : 0.041 0.143 1807 Planarity : 0.003 0.034 2071 Dihedral : 9.096 139.846 1692 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.27 % Allowed : 15.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.23), residues: 1469 helix: 2.14 (0.19), residues: 804 sheet: 0.62 (0.39), residues: 205 loop : 0.33 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.013 0.002 TYR A 80 PHE 0.008 0.001 PHE D 93 TRP 0.011 0.001 TRP A 440 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (11823) covalent geometry : angle 0.45923 / 0.25 (15977) hydrogen bonds : bond 0.04595 / 3.13 ( 633) hydrogen bonds : angle 4.12223 / 3.07 ( 1844) metal coordination : bond 0.01084 / 0.54 ( 4) metal coordination : angle 3.51175 / 1.53 ( 6) Misc. bond : bond 0.00015 / 0.01 ( 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 161 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8507 (mmtp) cc_final: 0.7921 (mptt) REVERT: A 273 ARG cc_start: 0.7890 (tpt90) cc_final: 0.7353 (ttt180) REVERT: A 291 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7295 (mtm) REVERT: A 316 GLU cc_start: 0.7889 (tt0) cc_final: 0.6774 (mp0) REVERT: A 364 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 416 GLU cc_start: 0.8243 (tt0) cc_final: 0.7858 (tt0) REVERT: A 417 GLU cc_start: 0.7936 (tt0) cc_final: 0.7098 (mp0) REVERT: B 37 ARG cc_start: 0.8152 (mtp-110) cc_final: 0.7382 (mtm110) REVERT: B 42 GLU cc_start: 0.7926 (tt0) cc_final: 0.7213 (pt0) REVERT: D 37 LYS cc_start: 0.7467 (pttp) cc_final: 0.6943 (ptmt) REVERT: D 89 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7663 (mtp85) REVERT: I 81 GLN cc_start: 0.7751 (tt0) cc_final: 0.7518 (tt0) REVERT: I 135 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6646 (ttp80) REVERT: I 161 GLU cc_start: 0.8032 (pm20) cc_final: 0.7247 (mp0) REVERT: E 273 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7554 (ttp-110) REVERT: E 316 GLU cc_start: 0.8049 (mt-10) cc_final: 0.6952 (mp0) REVERT: E 327 GLU cc_start: 0.7643 (pt0) cc_final: 0.7117 (mt-10) REVERT: E 335 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8221 (ttmm) REVERT: E 424 GLU cc_start: 0.7955 (tt0) cc_final: 0.7113 (mp0) REVERT: F 71 HIS cc_start: 0.8205 (t-90) cc_final: 0.7880 (t-90) REVERT: G 5 GLU cc_start: 0.5097 (tt0) cc_final: 0.4828 (tt0) REVERT: G 61 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6160 (mp0) outliers start: 12 outliers final: 5 residues processed: 156 average time/residue: 0.8171 time to fit residues: 134.3002 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 : 0.315 ------------------------------------------------------------------------------- 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 C residue 23 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER 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 54 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.090781 restraints weight = 54932.592| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.94 r_work: 0.2899 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- 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 = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11829 Z= 0.103 Angle : 0.453 7.941 15983 Z= 0.239 Chirality : 0.041 0.141 1807 Planarity : 0.003 0.034 2071 Dihedral : 8.341 125.262 1692 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.19 % Allowed : 16.02 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.23), residues: 1469 helix: 2.22 (0.19), residues: 804 sheet: 0.66 (0.39), residues: 205 loop : 0.38 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.013 0.001 TYR E 80 PHE 0.009 0.001 PHE D 93 TRP 0.011 0.001 TRP A 440 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (11823) covalent geometry : angle 0.44767 / 0.24 (15977) hydrogen bonds : bond 0.04363 / 2.98 ( 633) hydrogen bonds : angle 4.03125 / 3.00 ( 1844) metal coordination : bond 0.00993 / 0.50 ( 4) metal coordination : angle 3.51000 / 1.59 ( 6) Misc. bond : bond 0.00011 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5025.82 seconds wall clock time: 86 minutes 7.36 seconds (5167.36 seconds total)