Starting phenix.real_space_refine on Tue Jul 29 22:09:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmf_19360/07_2025/8rmf_19360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmf_19360/07_2025/8rmf_19360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2025/8rmf_19360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2025/8rmf_19360.map" model { file = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2025/8rmf_19360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmf_19360/07_2025/8rmf_19360.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 4 5.49 5 S 69 5.16 5 C 7282 2.51 5 N 2044 2.21 5 O 2483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11886 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3156 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3126 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 400, 3126 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 380} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3150 Chain: "B" Number of atoms: 689 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 674 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "D" Number of atoms: 939 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Conformer: "D" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} bond proxies already assigned to first conformer: 927 Chain: "I" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 9, 'TRANS': 108} Chain: "E" Number of atoms: 3082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 392, 3057 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 392, 3057 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 372} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3085 Chain: "F" Number of atoms: 689 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Conformer: "B" Number of residues, atoms: 81, 678 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} bond proxies already assigned to first conformer: 674 Chain: "H" Number of atoms: 939 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Conformer: "D" Number of residues, atoms: 123, 927 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} bond proxies already assigned to first conformer: 927 Chain: "G" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 576 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 112 Classifications: {'water': 112} Link IDs: {None: 111} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2553 SG CYS A 381 32.877 43.211 66.807 1.00 75.60 S ATOM 4899 SG CYS D 95 33.566 40.571 64.304 1.00 64.26 S ATOM 5660 SG CYS I 108 43.003 41.408 75.451 1.00 64.27 S ATOM 5699 SG CYS I 114 42.022 44.922 76.940 1.00 51.67 S ATOM 5718 SG CYS I 117 45.724 43.107 80.963 1.00 49.70 S ATOM 6015 SG CYS I 154 46.513 39.973 79.410 1.00 57.27 S ATOM 8821 SG CYS E 381 72.928 95.827 66.835 1.00 94.77 S ATOM 10522 SG CYS H 95 72.490 98.598 64.314 1.00 79.03 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N AASN A 83 " occ=0.77 ... (14 atoms not shown) pdb=" ND2BASN A 83 " occ=0.23 residue: pdb=" N AARG A 321 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG A 321 " occ=0.47 residue: pdb=" N ACYS A 426 " occ=0.39 ... (10 atoms not shown) pdb=" SG BCYS A 426 " occ=0.61 residue: pdb=" N AARG B 14 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG B 14 " occ=0.57 residue: pdb=" N BTYR D 35 " occ=0.56 ... (22 atoms not shown) pdb=" OH DTYR D 35 " occ=0.44 residue: pdb=" N AASN E 83 " occ=0.44 ... (14 atoms not shown) pdb=" ND2BASN E 83 " occ=0.56 residue: pdb=" N AARG E 321 " occ=0.82 ... (20 atoms not shown) pdb=" NH2BARG E 321 " occ=0.18 residue: pdb=" N ACYS E 426 " occ=0.37 ... (10 atoms not shown) pdb=" SG BCYS E 426 " occ=0.63 residue: pdb=" N AARG F 14 " occ=0.31 ... (20 atoms not shown) pdb=" NH2BARG F 14 " occ=0.69 residue: pdb=" N BTYR H 35 " occ=0.42 ... (22 atoms not shown) pdb=" OH DTYR H 35 " occ=0.58 Time building chain proxies: 12.14, per 1000 atoms: 1.02 Number of scatterers: 11886 At special positions: 0 Unit cell: (106.812, 142.416, 108.468, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 69 16.00 P 4 15.00 O 2483 8.00 N 2044 7.00 C 7282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES I 201 " pdb="FE1 FES I 201 " - pdb=" SG CYS I 108 " pdb="FE1 FES I 201 " - pdb=" SG CYS I 114 " pdb="FE2 FES I 201 " - pdb=" SG CYS I 154 " pdb="FE2 FES I 201 " - pdb=" SG CYS I 117 " Number of angles added : 6 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2762 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 9 sheets defined 55.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 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: 4.74 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 4650 1.40 - 1.60: 7059 1.60 - 1.80: 53 1.80 - 2.00: 57 2.00 - 2.19: 4 Bond restraints: 11823 Sorted by residual: bond pdb=" NZ LLP E 258 " pdb=" C4' LLP E 258 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" NZ LLP A 258 " pdb=" C4' LLP A 258 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" OP4 LLP E 258 " pdb=" P LLP E 258 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" OP4 LLP A 258 " pdb=" P LLP A 258 " ideal model delta sigma weight residual 1.726 1.612 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" CA LYS G 19 " pdb=" C LYS G 19 " ideal model delta sigma weight residual 1.523 1.583 -0.059 1.34e-02 5.57e+03 1.96e+01 ... (remaining 11818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 15925 3.96 - 7.93: 42 7.93 - 11.89: 4 11.89 - 15.86: 5 15.86 - 19.82: 1 Bond angle restraints: 15977 Sorted by residual: angle pdb=" S1 FES I 201 " pdb="FE2 FES I 201 " pdb=" S2 FES I 201 " ideal model delta sigma weight residual 104.33 90.93 13.40 1.14e+00 7.69e-01 1.38e+02 angle pdb="FE1 FES I 201 " pdb=" S2 FES I 201 " pdb="FE2 FES I 201 " ideal model delta sigma weight residual 75.66 89.01 -13.35 1.14e+00 7.69e-01 1.37e+02 angle pdb=" S1 FES I 201 " pdb="FE1 FES I 201 " pdb=" S2 FES I 201 " ideal model delta sigma weight residual 104.33 90.95 13.38 1.20e+00 6.94e-01 1.24e+02 angle pdb="FE1 FES I 201 " pdb=" S1 FES I 201 " pdb="FE2 FES I 201 " ideal model delta sigma weight residual 75.66 88.98 -13.32 1.20e+00 6.94e-01 1.23e+02 angle pdb=" NZ LLP A 258 " pdb=" C4' LLP A 258 " pdb=" C4 LLP A 258 " ideal model delta sigma weight residual 120.09 100.27 19.82 3.00e+00 1.11e-01 4.37e+01 ... (remaining 15972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.68: 6933 31.68 - 63.37: 303 63.37 - 95.05: 49 95.05 - 126.73: 1 126.73 - 158.41: 6 Dihedral angle restraints: 7292 sinusoidal: 3001 harmonic: 4291 Sorted by residual: dihedral pdb=" C39 8Q1 G 101 " pdb=" C42 8Q1 G 101 " pdb=" N41 8Q1 G 101 " pdb=" C43 8Q1 G 101 " ideal model delta sinusoidal sigma weight residual 89.93 -111.66 -158.41 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C LYS G 19 " pdb=" N LYS G 19 " pdb=" CA LYS G 19 " pdb=" CB LYS G 19 " ideal model delta harmonic sigma weight residual -122.60 -133.78 11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C39 8Q1 C 101 " pdb=" C42 8Q1 C 101 " pdb=" N41 8Q1 C 101 " pdb=" C43 8Q1 C 101 " ideal model delta sinusoidal sigma weight residual 89.93 -123.15 -146.92 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 7289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1491 0.057 - 0.115: 273 0.115 - 0.172: 39 0.172 - 0.230: 2 0.230 - 0.287: 2 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA LYS G 19 " pdb=" N LYS G 19 " pdb=" C LYS G 19 " pdb=" CB LYS G 19 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA TRP D 108 " pdb=" N TRP D 108 " pdb=" C TRP D 108 " pdb=" CB TRP D 108 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL D 109 " pdb=" N VAL D 109 " pdb=" C VAL D 109 " pdb=" CB VAL D 109 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.47e-01 ... (remaining 1804 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 8Q1 C 101 " -0.101 2.00e-02 2.50e+03 1.12e-01 1.58e+02 pdb=" C39 8Q1 C 101 " 0.038 2.00e-02 2.50e+03 pdb=" C42 8Q1 C 101 " -0.136 2.00e-02 2.50e+03 pdb=" N41 8Q1 C 101 " 0.180 2.00e-02 2.50e+03 pdb=" O40 8Q1 C 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 8Q1 C 101 " 0.049 2.00e-02 2.50e+03 5.94e-02 4.42e+01 pdb=" C34 8Q1 C 101 " -0.004 2.00e-02 2.50e+03 pdb=" C37 8Q1 C 101 " 0.072 2.00e-02 2.50e+03 pdb=" N36 8Q1 C 101 " -0.099 2.00e-02 2.50e+03 pdb=" O35 8Q1 C 101 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP E 258 " 0.058 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" NZ LLP E 258 " -0.064 2.00e-02 2.50e+03 pdb=" C4 LLP E 258 " 0.057 2.00e-02 2.50e+03 pdb=" C4' LLP E 258 " -0.051 2.00e-02 2.50e+03 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 176 2.63 - 3.20: 10477 3.20 - 3.76: 19995 3.76 - 4.33: 28935 4.33 - 4.90: 45270 Nonbonded interactions: 104853 Sorted by model distance: nonbonded pdb=" OD2 ASP H 71 " pdb="FE FE2 H 201 " model vdw 2.062 3.000 nonbonded pdb=" OD2 ASP D 71 " pdb="FE FE2 D 201 " model vdw 2.097 3.000 nonbonded pdb=" OH TYR B 13 " pdb=" OE2 GLU C 42 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR E 317 " pdb=" OD2 ASP F 38 " model vdw 2.167 3.040 nonbonded pdb=" OD1 ASP I 141 " pdb=" NH1 ARG E 277 " model vdw 2.214 3.120 ... (remaining 104848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 367 or resid 369 through 425 or resid 427 through 447)) selection = (chain 'E' and (resid 56 through 82 or resid 84 through 320 or resid 322 through \ 367 or resid 369 through 425 or resid 427 through 447)) } ncs_group { reference = (chain 'B' and (resid 5 through 13 or resid 15 through 85)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 85)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 36 through 157 or resid 201)) selection = (chain 'H' and (resid 36 through 157 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 38.790 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 11829 Z= 0.252 Angle : 0.720 19.823 15983 Z= 0.422 Chirality : 0.046 0.287 1807 Planarity : 0.006 0.112 2071 Dihedral : 18.077 158.413 4530 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.87 % Allowed : 15.94 % Favored : 83.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1469 helix: 1.26 (0.18), residues: 799 sheet: 0.12 (0.36), residues: 204 loop : -0.10 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 108 HIS 0.014 0.001 HIS B 71 PHE 0.013 0.002 PHE H 90 TYR 0.013 0.002 TYR A 80 ARG 0.008 0.000 ARG E 273 Details of bonding type rmsd hydrogen bonds : bond 0.10992 ( 633) hydrogen bonds : angle 5.05249 ( 1844) metal coordination : bond 0.01658 ( 4) metal coordination : angle 8.27132 ( 6) covalent geometry : bond 0.00446 (11823) covalent geometry : angle 0.70228 (15977) Misc. bond : bond 0.04645 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 171 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7747 (mptt) REVERT: A 273 ARG cc_start: 0.7360 (tpt90) cc_final: 0.7074 (tmt-80) REVERT: A 316 GLU cc_start: 0.7514 (tt0) cc_final: 0.6515 (mp0) REVERT: A 416 GLU cc_start: 0.7626 (tt0) cc_final: 0.6961 (mp0) REVERT: A 417 GLU cc_start: 0.7647 (tt0) cc_final: 0.6905 (mp0) REVERT: B 44 LYS cc_start: 0.8025 (tttm) cc_final: 0.7782 (tttp) REVERT: B 71 HIS cc_start: 0.8142 (t70) cc_final: 0.7941 (t70) REVERT: C 42 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6773 (tt0) REVERT: D 37 LYS cc_start: 0.7266 (pttp) cc_final: 0.6637 (ptmt) REVERT: D 87 ASP cc_start: 0.8056 (t0) cc_final: 0.7692 (t0) REVERT: D 89 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7342 (mtt-85) REVERT: I 166 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7468 (mt-10) REVERT: E 164 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8020 (mtp180) REVERT: E 273 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7211 (ttp-110) REVERT: E 316 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6496 (mp0) REVERT: E 327 GLU cc_start: 0.7514 (pt0) cc_final: 0.7249 (pt0) REVERT: E 424 GLU cc_start: 0.7500 (tt0) cc_final: 0.7222 (tt0) REVERT: F 80 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8225 (mtmt) outliers start: 7 outliers final: 3 residues processed: 177 average time/residue: 1.7497 time to fit residues: 328.9373 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 159 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain H residue 44 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 37 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 112 optimal weight: 0.0060 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN A 194 GLN A 282 GLN B 45 ASN C 25 ASN D 122 ASN I 92 ASN E 64 GLN E 179 GLN E 194 GLN E 207 ASN H 42 HIS G 20 GLN G 25 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091291 restraints weight = 57427.718| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.89 r_work: 0.2888 rms_B_bonded: 3.58 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 = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11829 Z= 0.133 Angle : 0.515 7.345 15983 Z= 0.273 Chirality : 0.043 0.151 1807 Planarity : 0.004 0.052 2071 Dihedral : 11.229 160.364 1702 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.43 % Allowed : 15.15 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1469 helix: 1.73 (0.18), residues: 804 sheet: 0.53 (0.39), residues: 199 loop : 0.14 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 440 HIS 0.014 0.001 HIS B 71 PHE 0.011 0.002 PHE D 93 TYR 0.015 0.002 TYR A 80 ARG 0.004 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 633) hydrogen bonds : angle 4.39664 ( 1844) metal coordination : bond 0.00926 ( 4) metal coordination : angle 4.04665 ( 6) covalent geometry : bond 0.00294 (11823) covalent geometry : angle 0.50880 (15977) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2938 Ramachandran restraints generated. 1469 Oldfield, 0 Emsley, 1469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8468 (mmtp) cc_final: 0.7875 (mptt) REVERT: A 273 ARG cc_start: 0.7857 (tpt90) cc_final: 0.7430 (tmt-80) REVERT: A 316 GLU cc_start: 0.7933 (tt0) cc_final: 0.6825 (mp0) REVERT: A 364 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: A 416 GLU cc_start: 0.8126 (tt0) cc_final: 0.7124 (mp0) REVERT: A 417 GLU cc_start: 0.7895 (tt0) cc_final: 0.7111 (mp0) REVERT: B 37 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7599 (mtm110) REVERT: D 37 LYS cc_start: 0.7445 (pttp) cc_final: 0.6868 (ptmt) REVERT: D 89 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7495 (mtp85) REVERT: I 81 GLN cc_start: 0.7708 (tt0) cc_final: 0.7488 (tt0) REVERT: I 166 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8029 (mt-10) REVERT: E 273 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7611 (ttp-110) REVERT: E 316 GLU cc_start: 0.8031 (mt-10) cc_final: 0.6929 (mp0) REVERT: E 327 GLU cc_start: 0.7571 (pt0) cc_final: 0.7191 (mt-10) REVERT: E 424 GLU cc_start: 0.7977 (tt0) cc_final: 0.7631 (tt0) REVERT: F 71 HIS cc_start: 0.8160 (t-90) cc_final: 0.7807 (t-90) REVERT: G 21 GLU cc_start: 0.6491 (mt-10) cc_final: 0.6228 (mp0) REVERT: G 61 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6246 (mp0) outliers start: 14 outliers final: 4 residues processed: 163 average time/residue: 1.9189 time to fit residues: 330.6253 Evaluate side-chains 157 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086650 restraints weight = 49461.893| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.39 r_work: 0.2832 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11829 Z= 0.202 Angle : 0.579 8.692 15983 Z= 0.309 Chirality : 0.047 0.169 1807 Planarity : 0.005 0.042 2071 Dihedral : 11.058 171.260 1693 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.38 % Allowed : 13.72 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1469 helix: 1.71 (0.18), residues: 806 sheet: 0.55 (0.38), residues: 198 loop : 0.16 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 440 HIS 0.014 0.002 HIS B 71 PHE 0.010 0.002 PHE E 141 TYR 0.019 0.003 TYR A 80 ARG 0.007 0.001 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.06247 ( 633) hydrogen bonds : angle 4.53662 ( 1844) metal coordination : bond 0.01475 ( 4) metal coordination : angle 4.24020 ( 6) covalent geometry : bond 0.00480 (11823) covalent geometry : angle 0.57318 (15977) Misc. bond : bond 0.00053 ( 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 189 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7837 (mptt) REVERT: A 273 ARG cc_start: 0.7863 (tpt90) cc_final: 0.7394 (ttt180) REVERT: A 316 GLU cc_start: 0.8013 (tt0) cc_final: 0.6893 (mp0) REVERT: A 364 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: A 416 GLU cc_start: 0.8303 (tt0) cc_final: 0.7115 (mp0) REVERT: A 417 GLU cc_start: 0.7992 (tt0) cc_final: 0.7070 (mp0) REVERT: B 37 ARG cc_start: 0.8299 (mtm110) cc_final: 0.7547 (mtm110) REVERT: D 89 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7544 (mtp85) REVERT: I 81 GLN cc_start: 0.7630 (tt0) cc_final: 0.7399 (tt0) REVERT: I 135 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6748 (ttp80) REVERT: I 166 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8103 (mt-10) REVERT: E 208 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: E 273 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7666 (ttp-110) REVERT: E 316 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7030 (mp0) REVERT: E 327 GLU cc_start: 0.7677 (pt0) cc_final: 0.7201 (mt-10) REVERT: E 424 GLU cc_start: 0.8030 (tt0) cc_final: 0.7633 (tt0) REVERT: F 42 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: F 71 HIS cc_start: 0.8324 (t-90) cc_final: 0.7927 (t-90) REVERT: G 21 GLU cc_start: 0.6419 (mt-10) cc_final: 0.6200 (mp0) REVERT: G 61 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: G 74 ASN cc_start: 0.4710 (OUTLIER) cc_final: 0.4403 (p0) outliers start: 26 outliers final: 5 residues processed: 179 average time/residue: 1.8195 time to fit residues: 345.5286 Evaluate side-chains 169 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 78 GLN Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.085426 restraints weight = 55923.326| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.25 r_work: 0.2809 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- 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 = 0.19 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 = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11829 Z= 0.241 Angle : 0.627 9.066 15983 Z= 0.334 Chirality : 0.049 0.173 1807 Planarity : 0.005 0.041 2071 Dihedral : 11.189 179.443 1693 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.46 % Allowed : 14.35 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.22), residues: 1469 helix: 1.57 (0.18), residues: 806 sheet: 0.54 (0.38), residues: 197 loop : 0.03 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 440 HIS 0.014 0.002 HIS B 71 PHE 0.011 0.002 PHE E 141 TYR 0.020 0.003 TYR A 80 ARG 0.008 0.001 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.06671 ( 633) hydrogen bonds : angle 4.61273 ( 1844) metal coordination : bond 0.01975 ( 4) metal coordination : angle 4.42608 ( 6) covalent geometry : bond 0.00586 (11823) covalent geometry : angle 0.62152 (15977) Misc. bond : bond 0.00058 ( 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 185 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8438 (mmtp) cc_final: 0.7832 (mptt) REVERT: A 226 LYS cc_start: 0.8487 (mptt) cc_final: 0.7876 (mppt) REVERT: A 273 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7337 (ttt180) REVERT: A 316 GLU cc_start: 0.8052 (tt0) cc_final: 0.6933 (mp0) REVERT: A 320 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7646 (ttpp) REVERT: A 364 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: A 416 GLU cc_start: 0.8339 (tt0) cc_final: 0.7953 (tt0) REVERT: A 417 GLU cc_start: 0.8054 (tt0) cc_final: 0.7120 (mp0) REVERT: B 54 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7862 (t) REVERT: D 89 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7573 (mtp85) REVERT: I 135 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6722 (ttp80) REVERT: I 166 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8197 (mt-10) REVERT: E 208 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: E 273 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7663 (ttp-110) REVERT: E 316 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7034 (mp0) REVERT: E 327 GLU cc_start: 0.7710 (pt0) cc_final: 0.7389 (pt0) REVERT: E 424 GLU cc_start: 0.8072 (tt0) cc_final: 0.7678 (tt0) REVERT: F 42 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7544 (pt0) REVERT: F 71 HIS cc_start: 0.8380 (t-90) cc_final: 0.8006 (t-90) REVERT: G 5 GLU cc_start: 0.4463 (OUTLIER) cc_final: 0.4056 (tt0) REVERT: G 21 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6206 (mp0) REVERT: G 61 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6211 (mp0) outliers start: 27 outliers final: 10 residues processed: 173 average time/residue: 1.9661 time to fit residues: 360.4399 Evaluate side-chains 174 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 54 THR 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 61 MET Chi-restraints excluded: chain E residue 208 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 64 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN F 74 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.143071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.087772 restraints weight = 57169.426| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.28 r_work: 0.2858 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11829 Z= 0.135 Angle : 0.509 8.320 15983 Z= 0.270 Chirality : 0.043 0.151 1807 Planarity : 0.004 0.039 2071 Dihedral : 10.714 177.773 1693 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.82 % Allowed : 14.75 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1469 helix: 1.89 (0.19), residues: 804 sheet: 0.45 (0.38), residues: 204 loop : 0.18 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 440 HIS 0.010 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.016 0.002 TYR E 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05255 ( 633) hydrogen bonds : angle 4.33242 ( 1844) metal coordination : bond 0.01302 ( 4) metal coordination : angle 3.84467 ( 6) covalent geometry : bond 0.00303 (11823) covalent geometry : angle 0.50336 (15977) Misc. bond : bond 0.00033 ( 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 170 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.784 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8534 (mmtp) cc_final: 0.7940 (mptt) REVERT: A 273 ARG cc_start: 0.7895 (tpt90) cc_final: 0.7404 (ttt180) REVERT: A 316 GLU cc_start: 0.7974 (tt0) cc_final: 0.6862 (mp0) REVERT: A 364 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: A 416 GLU cc_start: 0.8292 (tt0) cc_final: 0.7899 (tt0) REVERT: A 417 GLU cc_start: 0.8004 (tt0) cc_final: 0.7163 (mp0) REVERT: B 37 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7406 (mtm110) REVERT: D 37 LYS cc_start: 0.7414 (pttm) cc_final: 0.6871 (ptmt) REVERT: D 89 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7504 (mtp85) REVERT: I 81 GLN cc_start: 0.7755 (tt0) cc_final: 0.7541 (tt0) REVERT: I 135 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.6698 (ttp80) REVERT: I 166 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8208 (mt-10) REVERT: E 273 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7661 (ttp-110) REVERT: E 316 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7007 (mp0) REVERT: E 327 GLU cc_start: 0.7669 (pt0) cc_final: 0.7193 (mt-10) REVERT: E 424 GLU cc_start: 0.8045 (tt0) cc_final: 0.7209 (mp0) REVERT: F 42 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: F 71 HIS cc_start: 0.8277 (t-90) cc_final: 0.7932 (t-90) REVERT: G 5 GLU cc_start: 0.4371 (OUTLIER) cc_final: 0.4005 (tt0) REVERT: G 21 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6157 (mp0) REVERT: G 61 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6146 (mp0) outliers start: 19 outliers final: 9 residues processed: 161 average time/residue: 2.5646 time to fit residues: 437.1495 Evaluate side-chains 166 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 C residue 37 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 0.0030 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 143 optimal weight: 20.0000 chunk 134 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088688 restraints weight = 49222.605| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.53 r_work: 0.2882 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11829 Z= 0.117 Angle : 0.478 7.898 15983 Z= 0.253 Chirality : 0.042 0.145 1807 Planarity : 0.004 0.038 2071 Dihedral : 10.303 174.174 1693 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.90 % Allowed : 14.91 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.23), residues: 1469 helix: 2.05 (0.19), residues: 804 sheet: 0.52 (0.38), residues: 205 loop : 0.26 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 440 HIS 0.009 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.014 0.002 TYR A 80 ARG 0.002 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 633) hydrogen bonds : angle 4.20621 ( 1844) metal coordination : bond 0.01198 ( 4) metal coordination : angle 3.65079 ( 6) covalent geometry : bond 0.00256 (11823) covalent geometry : angle 0.47282 (15977) Misc. bond : bond 0.00019 ( 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 170 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.711 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8541 (mmtp) cc_final: 0.7949 (mptt) REVERT: A 273 ARG cc_start: 0.7880 (tpt90) cc_final: 0.7381 (ttt180) REVERT: A 316 GLU cc_start: 0.7925 (tt0) cc_final: 0.6799 (mp0) REVERT: A 364 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: A 416 GLU cc_start: 0.8271 (tt0) cc_final: 0.7899 (tt0) REVERT: A 417 GLU cc_start: 0.7942 (tt0) cc_final: 0.7144 (mp0) REVERT: B 37 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7413 (mtm110) REVERT: B 54 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7594 (t) REVERT: D 37 LYS cc_start: 0.7351 (pttm) cc_final: 0.6812 (ptmt) REVERT: D 89 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7563 (mtp85) REVERT: I 81 GLN cc_start: 0.7773 (tt0) cc_final: 0.7548 (tt0) REVERT: I 135 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6656 (ttp80) REVERT: I 166 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8197 (mt-10) REVERT: E 273 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7586 (ttp-110) REVERT: E 291 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8729 (mtm) REVERT: E 316 GLU cc_start: 0.8026 (mt-10) cc_final: 0.6974 (mp0) REVERT: E 327 GLU cc_start: 0.7635 (pt0) cc_final: 0.7143 (mt-10) REVERT: E 424 GLU cc_start: 0.7975 (tt0) cc_final: 0.7161 (mp0) REVERT: F 42 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: F 71 HIS cc_start: 0.8242 (t-90) cc_final: 0.7914 (t-90) REVERT: G 5 GLU cc_start: 0.4455 (OUTLIER) cc_final: 0.4195 (tt0) REVERT: G 21 GLU cc_start: 0.6468 (mt-10) cc_final: 0.6189 (mt-10) REVERT: G 61 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6223 (mp0) outliers start: 20 outliers final: 8 residues processed: 162 average time/residue: 2.2414 time to fit residues: 384.3156 Evaluate side-chains 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.087412 restraints weight = 46120.972| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.45 r_work: 0.2864 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 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 = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11829 Z= 0.138 Angle : 0.502 7.625 15983 Z= 0.267 Chirality : 0.043 0.153 1807 Planarity : 0.004 0.038 2071 Dihedral : 10.248 170.780 1692 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.90 % Allowed : 14.83 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.22), residues: 1469 helix: 2.01 (0.19), residues: 804 sheet: 0.53 (0.38), residues: 205 loop : 0.23 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 440 HIS 0.009 0.001 HIS B 71 PHE 0.008 0.001 PHE D 93 TYR 0.016 0.002 TYR A 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05252 ( 633) hydrogen bonds : angle 4.28042 ( 1844) metal coordination : bond 0.01244 ( 4) metal coordination : angle 3.80213 ( 6) covalent geometry : bond 0.00314 (11823) covalent geometry : angle 0.49652 (15977) Misc. bond : bond 0.00018 ( 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 172 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 2.222 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8457 (mmtp) cc_final: 0.7877 (mptt) REVERT: A 273 ARG cc_start: 0.7889 (tpt90) cc_final: 0.7408 (ttt180) REVERT: A 291 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7288 (mtm) REVERT: A 316 GLU cc_start: 0.7955 (tt0) cc_final: 0.6833 (mp0) REVERT: A 364 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: A 416 GLU cc_start: 0.8295 (tt0) cc_final: 0.7899 (tt0) REVERT: A 417 GLU cc_start: 0.7992 (tt0) cc_final: 0.7153 (mp0) REVERT: B 37 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7352 (mtm110) REVERT: B 54 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7638 (t) REVERT: D 37 LYS cc_start: 0.7366 (pttm) cc_final: 0.6821 (ptmt) REVERT: D 89 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7591 (mtp85) REVERT: I 135 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.6692 (ttp80) REVERT: I 161 GLU cc_start: 0.8115 (pm20) cc_final: 0.7368 (mp0) REVERT: I 166 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8215 (mt-10) REVERT: E 273 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7613 (ttp-110) REVERT: E 291 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8772 (mtm) REVERT: E 316 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6982 (mp0) REVERT: E 327 GLU cc_start: 0.7628 (pt0) cc_final: 0.7136 (mt-10) REVERT: E 424 GLU cc_start: 0.8021 (tt0) cc_final: 0.7187 (mp0) REVERT: F 42 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: F 71 HIS cc_start: 0.8220 (t-90) cc_final: 0.7897 (t-90) REVERT: G 5 GLU cc_start: 0.4453 (OUTLIER) cc_final: 0.4205 (tt0) REVERT: G 21 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5958 (mt-10) REVERT: G 61 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6215 (mp0) outliers start: 20 outliers final: 11 residues processed: 162 average time/residue: 2.2611 time to fit residues: 390.0927 Evaluate side-chains 171 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 335 LYS Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 400 ASP Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 61 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 143 optimal weight: 0.0470 chunk 93 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091188 restraints weight = 56564.914| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.82 r_work: 0.2914 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1922 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= 0.096 Angle : 0.443 7.413 15983 Z= 0.234 Chirality : 0.041 0.137 1807 Planarity : 0.003 0.036 2071 Dihedral : 9.481 159.231 1692 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.43 % Allowed : 15.31 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.23), residues: 1469 helix: 2.18 (0.19), residues: 804 sheet: 0.68 (0.39), residues: 204 loop : 0.33 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 440 HIS 0.007 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.011 0.001 TYR A 80 ARG 0.002 0.000 ARG E 275 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 633) hydrogen bonds : angle 4.05102 ( 1844) metal coordination : bond 0.01042 ( 4) metal coordination : angle 3.36558 ( 6) covalent geometry : bond 0.00197 (11823) covalent geometry : angle 0.43807 (15977) Misc. bond : bond 0.00014 ( 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 168 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8524 (mmtp) cc_final: 0.7923 (mptt) REVERT: A 273 ARG cc_start: 0.7858 (tpt90) cc_final: 0.7344 (ttt180) REVERT: A 291 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7275 (mtm) REVERT: A 316 GLU cc_start: 0.7846 (tt0) cc_final: 0.6742 (mp0) REVERT: A 416 GLU cc_start: 0.8228 (tt0) cc_final: 0.7098 (mp0) REVERT: A 417 GLU cc_start: 0.7898 (tt0) cc_final: 0.7123 (mp0) REVERT: B 37 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7394 (mtm110) REVERT: D 37 LYS cc_start: 0.7348 (pttm) cc_final: 0.6817 (ttmt) REVERT: D 89 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7581 (mtp85) REVERT: I 81 GLN cc_start: 0.7814 (tt0) cc_final: 0.7611 (tt0) REVERT: I 135 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6564 (ttp80) REVERT: I 161 GLU cc_start: 0.8055 (pm20) cc_final: 0.7267 (mp0) REVERT: I 166 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8188 (mt-10) REVERT: E 273 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7542 (ttp-110) REVERT: E 316 GLU cc_start: 0.8021 (mt-10) cc_final: 0.6932 (mp0) REVERT: E 327 GLU cc_start: 0.7577 (pt0) cc_final: 0.7081 (mt-10) REVERT: E 335 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8180 (ttmm) REVERT: E 424 GLU cc_start: 0.7939 (tt0) cc_final: 0.7118 (mp0) REVERT: F 71 HIS cc_start: 0.8146 (t-90) cc_final: 0.7837 (t-90) REVERT: G 21 GLU cc_start: 0.6317 (mt-10) cc_final: 0.6014 (mt-10) outliers start: 14 outliers final: 5 residues processed: 163 average time/residue: 1.9193 time to fit residues: 330.5095 Evaluate side-chains 154 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain G residue 37 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 98 GLN F 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088779 restraints weight = 58752.818| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.02 r_work: 0.2859 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11829 Z= 0.121 Angle : 0.474 7.365 15983 Z= 0.252 Chirality : 0.042 0.147 1807 Planarity : 0.004 0.036 2071 Dihedral : 9.458 153.592 1692 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.35 % Allowed : 15.46 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.23), residues: 1469 helix: 2.13 (0.19), residues: 804 sheet: 0.67 (0.39), residues: 205 loop : 0.31 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 440 HIS 0.008 0.001 HIS B 71 PHE 0.009 0.001 PHE D 93 TYR 0.015 0.002 TYR A 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 633) hydrogen bonds : angle 4.15250 ( 1844) metal coordination : bond 0.01161 ( 4) metal coordination : angle 3.64053 ( 6) covalent geometry : bond 0.00266 (11823) covalent geometry : angle 0.46893 (15977) Misc. bond : bond 0.00013 ( 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 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8534 (mmtp) cc_final: 0.7951 (mptt) REVERT: A 273 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7392 (ttt180) REVERT: A 291 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7273 (mtm) REVERT: A 316 GLU cc_start: 0.7938 (tt0) cc_final: 0.6810 (mp0) REVERT: A 327 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7721 (tt0) REVERT: A 416 GLU cc_start: 0.8302 (tt0) cc_final: 0.7140 (mp0) REVERT: A 417 GLU cc_start: 0.7980 (tt0) cc_final: 0.7153 (mp0) REVERT: B 37 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7444 (mtm110) REVERT: D 37 LYS cc_start: 0.7334 (pttm) cc_final: 0.6789 (ttmt) REVERT: D 89 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7626 (mtp85) REVERT: I 81 GLN cc_start: 0.7781 (tt0) cc_final: 0.7580 (tt0) REVERT: I 135 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.6685 (ttp80) REVERT: I 161 GLU cc_start: 0.8036 (pm20) cc_final: 0.7290 (mp0) REVERT: I 166 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8214 (mt-10) REVERT: E 273 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7611 (ttp-110) REVERT: E 291 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8811 (mtm) REVERT: E 316 GLU cc_start: 0.8043 (mt-10) cc_final: 0.6956 (mp0) REVERT: E 327 GLU cc_start: 0.7641 (pt0) cc_final: 0.7141 (mt-10) REVERT: E 335 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8264 (ttmm) REVERT: E 424 GLU cc_start: 0.8023 (tt0) cc_final: 0.7167 (mp0) REVERT: F 71 HIS cc_start: 0.8209 (t-90) cc_final: 0.7884 (t-90) REVERT: G 21 GLU cc_start: 0.6205 (mt-10) cc_final: 0.5903 (mt-10) outliers start: 13 outliers final: 6 residues processed: 158 average time/residue: 1.9625 time to fit residues: 327.4754 Evaluate side-chains 159 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain G residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN I 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087139 restraints weight = 56503.003| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.90 r_work: 0.2846 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11829 Z= 0.139 Angle : 0.499 7.358 15983 Z= 0.266 Chirality : 0.043 0.153 1807 Planarity : 0.004 0.037 2071 Dihedral : 9.555 152.717 1692 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.23), residues: 1469 helix: 2.05 (0.19), residues: 804 sheet: 0.62 (0.39), residues: 205 loop : 0.27 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 440 HIS 0.008 0.001 HIS B 71 PHE 0.008 0.001 PHE D 93 TYR 0.016 0.002 TYR A 80 ARG 0.003 0.000 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 633) hydrogen bonds : angle 4.25476 ( 1844) metal coordination : bond 0.01235 ( 4) metal coordination : angle 3.76341 ( 6) covalent geometry : bond 0.00316 (11823) covalent geometry : angle 0.49353 (15977) Misc. bond : bond 0.00015 ( 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 168 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 180 LYS cc_start: 0.8535 (mmtp) cc_final: 0.7955 (mptt) REVERT: A 273 ARG cc_start: 0.7904 (tpt90) cc_final: 0.7394 (ttt180) REVERT: A 291 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7297 (mtm) REVERT: A 316 GLU cc_start: 0.7968 (tt0) cc_final: 0.6820 (mp0) REVERT: A 327 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7730 (tt0) REVERT: A 416 GLU cc_start: 0.8314 (tt0) cc_final: 0.7913 (tt0) REVERT: A 417 GLU cc_start: 0.7982 (tt0) cc_final: 0.7102 (mp0) REVERT: B 37 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7354 (mtm110) REVERT: D 37 LYS cc_start: 0.7328 (pttm) cc_final: 0.6799 (ptmt) REVERT: D 89 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.7678 (mtp85) REVERT: I 135 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6710 (ttp80) REVERT: I 161 GLU cc_start: 0.8045 (pm20) cc_final: 0.7306 (mp0) REVERT: I 166 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8215 (mt-10) REVERT: E 226 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7822 (mtmm) REVERT: E 273 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7622 (ttp-110) REVERT: E 291 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8810 (mtm) REVERT: E 316 GLU cc_start: 0.8051 (mt-10) cc_final: 0.6974 (mp0) REVERT: E 327 GLU cc_start: 0.7652 (pt0) cc_final: 0.7130 (mt-10) REVERT: E 335 LYS cc_start: 0.8591 (ttmt) cc_final: 0.8319 (ttmm) REVERT: E 424 GLU cc_start: 0.8036 (tt0) cc_final: 0.7147 (mp0) REVERT: F 71 HIS cc_start: 0.8235 (t-90) cc_final: 0.7891 (t-90) REVERT: G 21 GLU cc_start: 0.6223 (mt-10) cc_final: 0.5916 (mt-10) outliers start: 12 outliers final: 6 residues processed: 163 average time/residue: 1.9634 time to fit residues: 337.9188 Evaluate side-chains 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 155 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 335 LYS Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain I residue 135 ARG Chi-restraints excluded: chain E residue 291 MET Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain G residue 37 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN I 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.138991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.083656 restraints weight = 57266.731| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.81 r_work: 0.2788 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 11829 Z= 0.267 Angle : 0.644 9.250 15983 Z= 0.342 Chirality : 0.050 0.177 1807 Planarity : 0.005 0.039 2071 Dihedral : 10.451 164.630 1692 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.59 % Allowed : 15.70 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1469 helix: 1.67 (0.18), residues: 806 sheet: 0.46 (0.37), residues: 204 loop : 0.13 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 440 HIS 0.011 0.002 HIS B 71 PHE 0.011 0.002 PHE A 408 TYR 0.022 0.003 TYR A 80 ARG 0.008 0.001 ARG E 292 Details of bonding type rmsd hydrogen bonds : bond 0.06863 ( 633) hydrogen bonds : angle 4.60505 ( 1844) metal coordination : bond 0.02065 ( 4) metal coordination : angle 4.42343 ( 6) covalent geometry : bond 0.00651 (11823) covalent geometry : angle 0.63828 (15977) Misc. bond : bond 0.00044 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14039.04 seconds wall clock time: 250 minutes 40.36 seconds (15040.36 seconds total)