Starting phenix.real_space_refine on Fri Mar 15 12:16:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/03_2024/8go8_34173_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/03_2024/8go8_34173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/03_2024/8go8_34173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/03_2024/8go8_34173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/03_2024/8go8_34173_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8go8_34173/03_2024/8go8_34173_updated.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 74 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 38 5.16 5 C 7280 2.51 5 N 1938 2.21 5 O 2239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "L ASP 2": "OD1" <-> "OD2" Residue "L ASP 18": "OD1" <-> "OD2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 2": "OD1" <-> "OD2" Residue "M ASP 18": "OD1" <-> "OD2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11505 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2803 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2808 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 333} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1363 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 6.22, per 1000 atoms: 0.54 Number of scatterers: 11505 At special positions: 0 Unit cell: (112.238, 201.413, 99.9375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 10 15.00 O 2239 8.00 N 1938 7.00 C 7280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.8 seconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 30 sheets defined 4.5% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.849A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.850A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 123 through 128 Processing helix chain 'M' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.489A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 288 through 290 removed outlier: 4.825A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 87 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 55 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN A 85 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 57 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 83 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N CYS A 59 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL A 81 " --> pdb=" O CYS A 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 146 through 149 Processing sheet with id= E, first strand: chain 'A' and resid 183 through 189 Processing sheet with id= F, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.126A pdb=" N THR A 350 " --> pdb=" O TYR A 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 343 through 349 removed outlier: 3.560A pdb=" N PHE A 349 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 316 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 9 through 12 Processing sheet with id= I, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.489A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 288 through 290 removed outlier: 4.825A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 87 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 55 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 57 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N CYS B 59 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 81 " --> pdb=" O CYS B 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 146 through 149 Processing sheet with id= L, first strand: chain 'B' and resid 183 through 189 Processing sheet with id= M, first strand: chain 'B' and resid 207 through 209 removed outlier: 6.127A pdb=" N THR B 350 " --> pdb=" O TYR B 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 343 through 349 removed outlier: 3.560A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 316 " --> pdb=" O CYS B 242 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.868A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.580A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 161 through 164 Processing sheet with id= S, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.868A pdb=" N VAL I 8 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 117 through 119 removed outlier: 3.580A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 130 through 134 removed outlier: 4.014A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 161 through 164 Processing sheet with id= W, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= X, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.799A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.535A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.636A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 177 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 5 through 8 Processing sheet with id= AB, first strand: chain 'M' and resid 11 through 13 removed outlier: 5.798A pdb=" N LYS M 104 " --> pdb=" O LEU M 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.534A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.635A pdb=" N SER M 115 " --> pdb=" O ASN M 138 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER M 177 " --> pdb=" O SER M 163 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3708 1.34 - 1.46: 2688 1.46 - 1.58: 5291 1.58 - 1.69: 34 1.69 - 1.81: 48 Bond restraints: 11769 Sorted by residual: bond pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.92e+01 ... (remaining 11764 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 442 107.09 - 113.82: 6638 113.82 - 120.55: 4125 120.55 - 127.28: 4719 127.28 - 134.01: 133 Bond angle restraints: 16057 Sorted by residual: angle pdb=" CB TPO V 339 " pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 119.31 106.91 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB TPO U 339 " pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 119.31 106.94 12.37 3.00e+00 1.11e-01 1.70e+01 angle pdb=" CB TPO U 342 " pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO V 336 " pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 119.31 107.10 12.21 3.00e+00 1.11e-01 1.66e+01 angle pdb=" CB TPO U 336 " pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 119.31 107.12 12.19 3.00e+00 1.11e-01 1.65e+01 ... (remaining 16052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 6481 16.85 - 33.70: 458 33.70 - 50.54: 104 50.54 - 67.39: 14 67.39 - 84.24: 12 Dihedral angle restraints: 7069 sinusoidal: 2631 harmonic: 4438 Sorted by residual: dihedral pdb=" CB LYS A 226 " pdb=" CG LYS A 226 " pdb=" CD LYS A 226 " pdb=" CE LYS A 226 " ideal model delta sinusoidal sigma weight residual 60.00 116.52 -56.52 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CB LYS B 226 " pdb=" CG LYS B 226 " pdb=" CD LYS B 226 " pdb=" CE LYS B 226 " ideal model delta sinusoidal sigma weight residual 60.00 116.45 -56.45 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG ARG B 65 " pdb=" CD ARG B 65 " pdb=" NE ARG B 65 " pdb=" CZ ARG B 65 " ideal model delta sinusoidal sigma weight residual 180.00 139.48 40.52 2 1.50e+01 4.44e-03 9.00e+00 ... (remaining 7066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1026 0.026 - 0.052: 516 0.052 - 0.079: 102 0.079 - 0.105: 119 0.105 - 0.131: 73 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA VAL L 95 " pdb=" N VAL L 95 " pdb=" C VAL L 95 " pdb=" CB VAL L 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA PHE U 335 " pdb=" N PHE U 335 " pdb=" C PHE U 335 " pdb=" CB PHE U 335 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE B 233 " pdb=" N ILE B 233 " pdb=" C ILE B 233 " pdb=" CB ILE B 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1833 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 159 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 358 " 0.006 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C GLU B 358 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU B 358 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 359 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 158 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.75e+00 pdb=" N PRO I 159 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 159 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 159 " -0.017 5.00e-02 4.00e+02 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2153 2.78 - 3.31: 9830 3.31 - 3.84: 17832 3.84 - 4.37: 20140 4.37 - 4.90: 37099 Nonbonded interactions: 87054 Sorted by model distance: nonbonded pdb=" NE2 GLN L 125 " pdb=" O THR L 130 " model vdw 2.253 2.520 nonbonded pdb=" NE2 GLN M 125 " pdb=" O THR M 130 " model vdw 2.254 2.520 nonbonded pdb=" O ALA B 301 " pdb=" OH TYR B 321 " model vdw 2.278 2.440 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.278 2.440 nonbonded pdb=" O ALA B 263 " pdb=" OG SER B 266 " model vdw 2.290 2.440 ... (remaining 87049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 368)) selection = (chain 'B' and (resid 7 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 190)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 4.180 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.570 Find NCS groups from input model: 0.770 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: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.004 0.109 11769 Z= 0.299 Angle : 0.607 12.405 16057 Z= 0.270 Chirality : 0.042 0.131 1836 Planarity : 0.003 0.034 2058 Dihedral : 12.950 84.237 4191 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 1.03 (0.23), residues: 1478 helix: 0.56 (0.84), residues: 34 sheet: 1.29 (0.21), residues: 644 loop : 0.25 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.002 0.000 HIS B 353 PHE 0.008 0.001 PHE V 335 TYR 0.008 0.001 TYR M 50 ARG 0.005 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8525 (ttmt) REVERT: A 294 LYS cc_start: 0.8092 (mttp) cc_final: 0.7793 (mtpp) REVERT: B 147 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8411 (ttmt) REVERT: B 294 LYS cc_start: 0.8154 (mttp) cc_final: 0.7880 (mtpp) REVERT: H 86 MET cc_start: 0.7239 (mtm) cc_final: 0.7013 (mtp) REVERT: H 210 HIS cc_start: 0.5789 (t-90) cc_final: 0.5149 (t-90) REVERT: I 210 HIS cc_start: 0.6173 (t-90) cc_final: 0.5274 (t-90) REVERT: L 161 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7373 (mm110) REVERT: M 5 MET cc_start: 0.8295 (mmm) cc_final: 0.8080 (mmt) REVERT: M 82 GLU cc_start: 0.7357 (pt0) cc_final: 0.7045 (pm20) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2793 time to fit residues: 75.6393 Evaluate side-chains 127 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN B 248 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11769 Z= 0.200 Angle : 0.536 12.296 16057 Z= 0.268 Chirality : 0.043 0.134 1836 Planarity : 0.004 0.038 2058 Dihedral : 4.161 37.998 1658 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.07 % Allowed : 7.88 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.99 (0.23), residues: 1478 helix: -0.07 (0.70), residues: 46 sheet: 1.13 (0.20), residues: 706 loop : 0.32 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 164 HIS 0.003 0.001 HIS B 210 PHE 0.015 0.001 PHE M 117 TYR 0.025 0.001 TYR H 155 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8077 (mttp) cc_final: 0.7844 (mtpp) REVERT: B 294 LYS cc_start: 0.8077 (mttp) cc_final: 0.7799 (mtpp) REVERT: H 92 GLU cc_start: 0.7985 (pm20) cc_final: 0.7675 (pm20) REVERT: I 185 LEU cc_start: 0.7425 (mt) cc_final: 0.7218 (mm) REVERT: L 119 PHE cc_start: 0.5078 (m-80) cc_final: 0.4864 (m-80) REVERT: L 161 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7376 (mm110) REVERT: M 82 GLU cc_start: 0.7444 (pt0) cc_final: 0.7050 (pm20) REVERT: M 119 PHE cc_start: 0.5057 (m-80) cc_final: 0.4847 (m-80) REVERT: M 161 GLN cc_start: 0.7829 (mm-40) cc_final: 0.7413 (mm110) outliers start: 13 outliers final: 8 residues processed: 135 average time/residue: 0.2794 time to fit residues: 52.1010 Evaluate side-chains 119 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11769 Z= 0.216 Angle : 0.525 12.272 16057 Z= 0.262 Chirality : 0.044 0.176 1836 Planarity : 0.003 0.035 2058 Dihedral : 4.210 35.085 1658 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.23 % Allowed : 8.20 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.86 (0.22), residues: 1478 helix: -0.30 (0.68), residues: 46 sheet: 1.07 (0.20), residues: 686 loop : 0.25 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 164 HIS 0.003 0.001 HIS B 362 PHE 0.016 0.002 PHE M 117 TYR 0.025 0.001 TYR A 249 ARG 0.005 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.300 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6920 (ptt-90) cc_final: 0.6495 (ptp90) REVERT: A 294 LYS cc_start: 0.8403 (mttp) cc_final: 0.8117 (mtpp) REVERT: B 160 LYS cc_start: 0.7871 (tptp) cc_final: 0.7590 (tppt) REVERT: B 294 LYS cc_start: 0.8316 (mttp) cc_final: 0.8059 (mtpp) REVERT: H 92 GLU cc_start: 0.8013 (pm20) cc_final: 0.7789 (pm20) REVERT: I 49 GLU cc_start: 0.7219 (tt0) cc_final: 0.6908 (tt0) REVERT: L 82 GLU cc_start: 0.7473 (pt0) cc_final: 0.7014 (pm20) REVERT: L 119 PHE cc_start: 0.5325 (m-80) cc_final: 0.5029 (m-80) REVERT: L 161 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7382 (mm110) REVERT: M 82 GLU cc_start: 0.7477 (pt0) cc_final: 0.7044 (pm20) REVERT: M 119 PHE cc_start: 0.5186 (m-80) cc_final: 0.4881 (m-80) REVERT: M 161 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7512 (mm110) outliers start: 15 outliers final: 9 residues processed: 129 average time/residue: 0.2559 time to fit residues: 45.7968 Evaluate side-chains 115 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 70 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11769 Z= 0.272 Angle : 0.539 11.517 16057 Z= 0.270 Chirality : 0.044 0.168 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.305 36.283 1658 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.48 % Allowed : 9.84 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.71 (0.22), residues: 1478 helix: -0.55 (0.70), residues: 46 sheet: 0.99 (0.20), residues: 676 loop : 0.15 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 164 HIS 0.003 0.001 HIS B 362 PHE 0.015 0.002 PHE A 277 TYR 0.020 0.002 TYR H 155 ARG 0.005 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6978 (ptt-90) cc_final: 0.6500 (ptp90) REVERT: A 195 LYS cc_start: 0.8509 (mmmt) cc_final: 0.7726 (mtmt) REVERT: A 294 LYS cc_start: 0.8384 (mttp) cc_final: 0.8119 (mtpp) REVERT: B 195 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7694 (mtmt) REVERT: B 294 LYS cc_start: 0.8423 (mttp) cc_final: 0.8195 (mtpp) REVERT: H 92 GLU cc_start: 0.8059 (pm20) cc_final: 0.7823 (pm20) REVERT: I 49 GLU cc_start: 0.7255 (tt0) cc_final: 0.6960 (tt0) REVERT: L 82 GLU cc_start: 0.7511 (pt0) cc_final: 0.7016 (pm20) REVERT: L 119 PHE cc_start: 0.5408 (m-80) cc_final: 0.4971 (m-80) REVERT: L 161 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7452 (mm110) REVERT: L 189 LYS cc_start: 0.8081 (pttp) cc_final: 0.7755 (pttm) REVERT: M 82 GLU cc_start: 0.7502 (pt0) cc_final: 0.7035 (pm20) REVERT: M 119 PHE cc_start: 0.5271 (m-80) cc_final: 0.4865 (m-80) REVERT: M 161 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7614 (mm110) outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.2783 time to fit residues: 49.9343 Evaluate side-chains 118 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN L 38 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 11769 Z= 0.531 Angle : 0.672 11.664 16057 Z= 0.342 Chirality : 0.049 0.224 1836 Planarity : 0.004 0.030 2058 Dihedral : 4.754 39.069 1658 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.56 % Allowed : 13.04 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.21 (0.22), residues: 1478 helix: -0.76 (0.67), residues: 46 sheet: 0.58 (0.19), residues: 696 loop : -0.14 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP I 50 HIS 0.007 0.002 HIS B 362 PHE 0.015 0.002 PHE A 277 TYR 0.022 0.003 TYR M 50 ARG 0.009 0.001 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7030 (ptt-90) cc_final: 0.6533 (ptp90) REVERT: A 195 LYS cc_start: 0.8540 (mmmt) cc_final: 0.7772 (mtmt) REVERT: B 195 LYS cc_start: 0.8559 (mmmt) cc_final: 0.7777 (mtmt) REVERT: H 92 GLU cc_start: 0.7855 (pm20) cc_final: 0.7632 (pm20) REVERT: I 49 GLU cc_start: 0.7525 (tt0) cc_final: 0.7193 (tt0) REVERT: L 82 GLU cc_start: 0.7705 (pt0) cc_final: 0.7081 (pm20) REVERT: L 119 PHE cc_start: 0.5509 (m-80) cc_final: 0.4968 (m-80) REVERT: L 161 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7346 (mm110) REVERT: L 189 LYS cc_start: 0.8333 (pttp) cc_final: 0.7922 (ptpp) REVERT: M 82 GLU cc_start: 0.7693 (pt0) cc_final: 0.7095 (pm20) REVERT: M 119 PHE cc_start: 0.5298 (m-80) cc_final: 0.4783 (m-80) REVERT: M 161 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7454 (mm110) outliers start: 19 outliers final: 15 residues processed: 117 average time/residue: 0.2997 time to fit residues: 47.7048 Evaluate side-chains 116 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.0030 chunk 47 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN B 189 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11769 Z= 0.156 Angle : 0.509 10.529 16057 Z= 0.251 Chirality : 0.043 0.157 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.300 37.211 1658 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.90 % Allowed : 14.60 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.45 (0.22), residues: 1478 helix: -0.58 (0.72), residues: 46 sheet: 0.72 (0.20), residues: 684 loop : 0.06 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 164 HIS 0.002 0.000 HIS A 198 PHE 0.011 0.001 PHE A 349 TYR 0.019 0.001 TYR H 155 ARG 0.005 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6906 (ptt-90) cc_final: 0.6451 (ptp90) REVERT: A 195 LYS cc_start: 0.8523 (mmmt) cc_final: 0.7819 (mtmt) REVERT: B 160 LYS cc_start: 0.7959 (tptt) cc_final: 0.7741 (tptp) REVERT: B 195 LYS cc_start: 0.8526 (mmmt) cc_final: 0.7816 (mtmt) REVERT: H 92 GLU cc_start: 0.7861 (pm20) cc_final: 0.7617 (pm20) REVERT: I 49 GLU cc_start: 0.7236 (tt0) cc_final: 0.6937 (tt0) REVERT: I 90 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7316 (mtp180) REVERT: L 82 GLU cc_start: 0.7612 (pt0) cc_final: 0.7076 (pm20) REVERT: L 119 PHE cc_start: 0.5439 (m-80) cc_final: 0.4916 (m-80) REVERT: L 161 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7350 (mm110) REVERT: L 189 LYS cc_start: 0.8233 (pttp) cc_final: 0.7846 (ptpp) REVERT: M 82 GLU cc_start: 0.7600 (pt0) cc_final: 0.7087 (pm20) REVERT: M 119 PHE cc_start: 0.5289 (m-80) cc_final: 0.4744 (m-80) REVERT: M 161 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7485 (mm110) outliers start: 11 outliers final: 7 residues processed: 123 average time/residue: 0.2711 time to fit residues: 46.7365 Evaluate side-chains 117 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11769 Z= 0.266 Angle : 0.537 11.561 16057 Z= 0.268 Chirality : 0.044 0.140 1836 Planarity : 0.003 0.035 2058 Dihedral : 4.284 38.120 1658 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.90 % Allowed : 15.67 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.41 (0.22), residues: 1478 helix: -0.65 (0.71), residues: 46 sheet: 0.71 (0.20), residues: 680 loop : 0.02 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 164 HIS 0.004 0.001 HIS B 362 PHE 0.011 0.001 PHE H 105 TYR 0.023 0.002 TYR I 155 ARG 0.007 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.358 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6894 (ptt-90) cc_final: 0.6424 (ptp90) REVERT: A 195 LYS cc_start: 0.8567 (mmmt) cc_final: 0.7857 (mtmt) REVERT: B 160 LYS cc_start: 0.7901 (tptt) cc_final: 0.7672 (tptm) REVERT: B 195 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7832 (mtmt) REVERT: H 92 GLU cc_start: 0.7863 (pm20) cc_final: 0.7618 (pm20) REVERT: I 49 GLU cc_start: 0.7298 (tt0) cc_final: 0.6967 (tt0) REVERT: I 90 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7378 (mtp180) REVERT: L 82 GLU cc_start: 0.7632 (pt0) cc_final: 0.7110 (pm20) REVERT: L 119 PHE cc_start: 0.5460 (m-80) cc_final: 0.4910 (m-80) REVERT: L 161 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7432 (mm110) REVERT: L 189 LYS cc_start: 0.8260 (pttp) cc_final: 0.7859 (ptpp) REVERT: M 82 GLU cc_start: 0.7610 (pt0) cc_final: 0.7089 (pm20) REVERT: M 119 PHE cc_start: 0.5322 (m-80) cc_final: 0.4742 (m-80) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.2856 time to fit residues: 47.1094 Evaluate side-chains 114 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11769 Z= 0.165 Angle : 0.501 10.992 16057 Z= 0.248 Chirality : 0.043 0.160 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.118 37.448 1658 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.07 % Allowed : 15.83 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.54 (0.22), residues: 1478 helix: -0.55 (0.73), residues: 46 sheet: 0.88 (0.20), residues: 666 loop : 0.04 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 164 HIS 0.002 0.000 HIS B 362 PHE 0.011 0.001 PHE A 349 TYR 0.023 0.001 TYR I 155 ARG 0.007 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6840 (ptt-90) cc_final: 0.6424 (ptp90) REVERT: A 195 LYS cc_start: 0.8544 (mmmt) cc_final: 0.7823 (mtmt) REVERT: B 160 LYS cc_start: 0.7893 (tptt) cc_final: 0.7661 (tptm) REVERT: B 195 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7817 (mtmt) REVERT: H 92 GLU cc_start: 0.7862 (pm20) cc_final: 0.7610 (pm20) REVERT: I 49 GLU cc_start: 0.7215 (tt0) cc_final: 0.6913 (tt0) REVERT: I 90 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7346 (mtp180) REVERT: L 82 GLU cc_start: 0.7640 (pt0) cc_final: 0.7111 (pm20) REVERT: L 161 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7448 (mm110) REVERT: L 189 LYS cc_start: 0.8269 (pttp) cc_final: 0.7862 (ptpp) REVERT: M 82 GLU cc_start: 0.7649 (pt0) cc_final: 0.7095 (pm20) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.2800 time to fit residues: 45.7175 Evaluate side-chains 116 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.2980 chunk 124 optimal weight: 0.0070 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11769 Z= 0.315 Angle : 0.559 10.617 16057 Z= 0.280 Chirality : 0.045 0.178 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.285 38.349 1658 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.15 % Allowed : 15.75 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.40 (0.22), residues: 1478 helix: -0.57 (0.73), residues: 46 sheet: 0.71 (0.20), residues: 670 loop : -0.00 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 164 HIS 0.004 0.001 HIS B 362 PHE 0.013 0.002 PHE H 105 TYR 0.024 0.002 TYR H 155 ARG 0.009 0.001 ARG M 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6860 (ptt-90) cc_final: 0.6438 (ptp90) REVERT: A 195 LYS cc_start: 0.8573 (mmmt) cc_final: 0.7857 (mtmt) REVERT: B 160 LYS cc_start: 0.7920 (tptt) cc_final: 0.7715 (tptm) REVERT: B 195 LYS cc_start: 0.8569 (mmmt) cc_final: 0.7847 (mtmt) REVERT: H 92 GLU cc_start: 0.7855 (pm20) cc_final: 0.7605 (pm20) REVERT: I 49 GLU cc_start: 0.7285 (tt0) cc_final: 0.6990 (tt0) REVERT: I 90 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7387 (mtp180) REVERT: L 82 GLU cc_start: 0.7645 (pt0) cc_final: 0.7118 (pm20) REVERT: L 161 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7479 (mm110) REVERT: L 189 LYS cc_start: 0.8372 (pttp) cc_final: 0.7987 (ptpp) REVERT: M 82 GLU cc_start: 0.7629 (pt0) cc_final: 0.7107 (pm20) outliers start: 14 outliers final: 14 residues processed: 116 average time/residue: 0.2841 time to fit residues: 45.7357 Evaluate side-chains 118 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 147 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11769 Z= 0.195 Angle : 0.514 10.350 16057 Z= 0.255 Chirality : 0.043 0.168 1836 Planarity : 0.003 0.033 2058 Dihedral : 4.166 37.639 1658 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.31 % Allowed : 15.83 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.47 (0.22), residues: 1478 helix: -0.55 (0.73), residues: 46 sheet: 0.79 (0.20), residues: 668 loop : 0.01 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 164 HIS 0.002 0.000 HIS B 362 PHE 0.010 0.001 PHE A 277 TYR 0.023 0.001 TYR H 155 ARG 0.008 0.000 ARG M 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.6804 (ptt-90) cc_final: 0.6394 (ptp90) REVERT: A 195 LYS cc_start: 0.8557 (mmmt) cc_final: 0.7838 (mtmt) REVERT: A 307 ARG cc_start: 0.6689 (tmm-80) cc_final: 0.6331 (tmm-80) REVERT: B 195 LYS cc_start: 0.8555 (mmmt) cc_final: 0.7834 (mtmt) REVERT: H 92 GLU cc_start: 0.7864 (pm20) cc_final: 0.7610 (pm20) REVERT: I 49 GLU cc_start: 0.7217 (tt0) cc_final: 0.6911 (tt0) REVERT: I 90 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7370 (mtp180) REVERT: L 82 GLU cc_start: 0.7635 (pt0) cc_final: 0.7113 (pm20) REVERT: L 161 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7393 (mm110) REVERT: L 189 LYS cc_start: 0.8409 (pttp) cc_final: 0.8085 (ptpp) REVERT: M 79 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8687 (tt) REVERT: M 82 GLU cc_start: 0.7626 (pt0) cc_final: 0.7122 (pm20) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.3047 time to fit residues: 51.2396 Evaluate side-chains 123 residues out of total 1320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 TRP Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 149 TRP Chi-restraints excluded: chain M residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 21 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.165170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113750 restraints weight = 16443.603| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.34 r_work: 0.3194 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11769 Z= 0.169 Angle : 0.505 10.164 16057 Z= 0.248 Chirality : 0.043 0.162 1836 Planarity : 0.003 0.035 2058 Dihedral : 4.056 37.593 1658 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.90 % Allowed : 16.16 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.56 (0.22), residues: 1478 helix: -0.51 (0.74), residues: 46 sheet: 0.89 (0.20), residues: 666 loop : 0.05 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 164 HIS 0.002 0.000 HIS B 362 PHE 0.012 0.001 PHE L 117 TYR 0.024 0.001 TYR H 155 ARG 0.007 0.000 ARG M 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.32 seconds wall clock time: 45 minutes 2.95 seconds (2702.95 seconds total)