Starting phenix.real_space_refine on Fri Feb 16 05:40:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj9_23389/02_2024/7lj9_23389_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj9_23389/02_2024/7lj9_23389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj9_23389/02_2024/7lj9_23389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj9_23389/02_2024/7lj9_23389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj9_23389/02_2024/7lj9_23389_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lj9_23389/02_2024/7lj9_23389_updated.pdb" } resolution = 3.0 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= -0.005 sd= 0.129 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 96 5.16 5 C 9288 2.51 5 N 2461 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 891": "OE1" <-> "OE2" Residue "A ARG 986": "NH1" <-> "NH2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "B GLU 851": "OE1" <-> "OE2" Residue "B GLU 861": "OE1" <-> "OE2" Residue "B ARG 986": "NH1" <-> "NH2" Residue "B ARG 1085": "NH1" <-> "NH2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "C GLU 851": "OE1" <-> "OE2" Residue "C GLU 861": "OE1" <-> "OE2" Residue "C ARG 986": "NH1" <-> "NH2" Residue "C GLU 1046": "OE1" <-> "OE2" Residue "C GLU 1050": "OE1" <-> "OE2" Residue "C ARG 1085": "NH1" <-> "NH2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 137": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D GLU 523": "OE1" <-> "OE2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D GLU 718": "OE1" <-> "OE2" Residue "D GLU 847": "OE1" <-> "OE2" Residue "D GLU 851": "OE1" <-> "OE2" Residue "D GLU 891": "OE1" <-> "OE2" Residue "D ARG 986": "NH1" <-> "NH2" Residue "D ARG 995": "NH1" <-> "NH2" Residue "D GLU 1009": "OE1" <-> "OE2" Residue "D GLU 1047": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14516 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2160 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2160 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2160 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 266} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 7940 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1028, 7932 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 978} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 1028, 7932 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 47, 'TRANS': 978} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 8093 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OAA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'ACO': 1, 'OAA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 12.13, per 1000 atoms: 0.84 Number of scatterers: 14516 At special positions: 0 Unit cell: (96.57, 100.92, 142.68, 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 96 16.00 P 3 15.00 O 2668 8.00 N 2461 7.00 C 9288 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 - 3.50 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: 6.01 Conformation dependent library (CDL) restraints added in 4.3 seconds 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 8 sheets defined 46.8% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 859 through 864 Processing helix chain 'A' and resid 869 through 876 Processing helix chain 'A' and resid 884 through 896 Processing helix chain 'A' and resid 905 through 915 Processing helix chain 'A' and resid 920 through 930 removed outlier: 4.432A pdb=" N THR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 951 removed outlier: 3.523A pdb=" N PHE A 946 " --> pdb=" O ALA A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1002 through 1017 removed outlier: 3.940A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 4.030A pdb=" N GLY A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1054 removed outlier: 4.127A pdb=" N ILE A1052 " --> pdb=" O ALA A1048 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1078 removed outlier: 3.661A pdb=" N PHE A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A1067 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A1068 " --> pdb=" O GLY A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1090 No H-bonds generated for 'chain 'A' and resid 1088 through 1090' Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 859 through 864 Processing helix chain 'B' and resid 869 through 876 Processing helix chain 'B' and resid 884 through 896 Processing helix chain 'B' and resid 905 through 915 Processing helix chain 'B' and resid 920 through 930 removed outlier: 4.433A pdb=" N THR B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 951 removed outlier: 3.522A pdb=" N PHE B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1002 through 1011 removed outlier: 3.858A pdb=" N GLU B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1017 No H-bonds generated for 'chain 'B' and resid 1014 through 1017' Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 4.031A pdb=" N GLY B1030 " --> pdb=" O ASP B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1054 Processing helix chain 'B' and resid 1056 through 1078 removed outlier: 3.661A pdb=" N PHE B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET B1067 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY B1068 " --> pdb=" O GLY B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1090 No H-bonds generated for 'chain 'B' and resid 1088 through 1090' Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 859 through 864 Processing helix chain 'C' and resid 869 through 876 Processing helix chain 'C' and resid 884 through 896 Processing helix chain 'C' and resid 905 through 915 Processing helix chain 'C' and resid 920 through 930 removed outlier: 4.431A pdb=" N THR C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 951 removed outlier: 3.522A pdb=" N PHE C 946 " --> pdb=" O ALA C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1025 through 1039 removed outlier: 4.031A pdb=" N GLY C1030 " --> pdb=" O ASP C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1054 removed outlier: 3.873A pdb=" N TYR C1051 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE C1052 " --> pdb=" O ALA C1048 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1078 removed outlier: 3.662A pdb=" N PHE C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C1068 " --> pdb=" O GLY C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1088 through 1090 No H-bonds generated for 'chain 'C' and resid 1088 through 1090' Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 48 through 51 removed outlier: 4.007A pdb=" N LEU D 51 " --> pdb=" O PRO D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 51' Processing helix chain 'D' and resid 66 through 69 No H-bonds generated for 'chain 'D' and resid 66 through 69' Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 179 through 194 removed outlier: 3.883A pdb=" N SER D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.875A pdb=" N ASP D 226 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TYR D 227 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS D 230 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL D 231 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP D 233 " --> pdb=" O LYS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 4.358A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.743A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 328 removed outlier: 3.915A pdb=" N MET D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 384 through 398 Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 506 through 518 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 603 through 616 Processing helix chain 'D' and resid 643 through 648 Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.545A pdb=" N SER D 667 " --> pdb=" O GLY D 664 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN D 668 " --> pdb=" O GLY D 665 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 674 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 676 " --> pdb=" O ILE D 673 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 677 " --> pdb=" O ILE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 706 removed outlier: 3.665A pdb=" N LEU D 702 " --> pdb=" O MET D 698 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 772 through 782 Processing helix chain 'D' and resid 791 through 806 removed outlier: 4.014A pdb=" N GLY D 794 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 800 " --> pdb=" O ILE D 797 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA D 806 " --> pdb=" O ASP D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 830 Processing helix chain 'D' and resid 859 through 864 Processing helix chain 'D' and resid 869 through 876 Processing helix chain 'D' and resid 884 through 895 Processing helix chain 'D' and resid 905 through 915 Processing helix chain 'D' and resid 920 through 930 removed outlier: 4.469A pdb=" N THR D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 951 Processing helix chain 'D' and resid 956 through 965 removed outlier: 3.667A pdb=" N ASN D 961 " --> pdb=" O MET D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1002 through 1017 removed outlier: 3.950A pdb=" N SER D1016 " --> pdb=" O LYS D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1039 removed outlier: 4.136A pdb=" N GLY D1030 " --> pdb=" O ASP D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1054 removed outlier: 3.588A pdb=" N ILE D1052 " --> pdb=" O ALA D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1078 removed outlier: 3.525A pdb=" N PHE D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET D1067 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY D1068 " --> pdb=" O GLY D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1088 through 1090 No H-bonds generated for 'chain 'D' and resid 1088 through 1090' Processing sheet with id= A, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.405A pdb=" N ALA D 219 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP D 222 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE D 197 " --> pdb=" O ASP D 222 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR D 198 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 55 through 59 Processing sheet with id= C, first strand: chain 'D' and resid 92 through 95 Processing sheet with id= D, first strand: chain 'D' and resid 205 through 207 Processing sheet with id= E, first strand: chain 'D' and resid 263 through 265 Processing sheet with id= F, first strand: chain 'D' and resid 275 through 277 removed outlier: 6.356A pdb=" N ILE D 337 " --> pdb=" O TRP D 276 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL D 377 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N HIS D 403 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 619 through 621 removed outlier: 7.721A pdb=" N VAL D 501 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET D 529 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 14.231A pdb=" N ALA D 527 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N LEU D 549 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N MET D 529 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 546 " --> pdb=" O TRP D 543 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 739 through 744 removed outlier: 7.741A pdb=" N TYR D 659 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY D 684 " --> pdb=" O TYR D 659 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER D 661 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 686 " --> pdb=" O SER D 661 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1626 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: 4.44 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2420 1.30 - 1.43: 3748 1.43 - 1.56: 8473 1.56 - 1.69: 23 1.69 - 1.81: 160 Bond restraints: 14824 Sorted by residual: bond pdb=" N PRO D 36 " pdb=" CD PRO D 36 " ideal model delta sigma weight residual 1.473 1.330 0.143 1.40e-02 5.10e+03 1.04e+02 bond pdb=" C5A ACO D1201 " pdb=" N7A ACO D1201 " ideal model delta sigma weight residual 1.387 1.297 0.090 1.00e-02 1.00e+04 8.11e+01 bond pdb=" C VAL D 34 " pdb=" O VAL D 34 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.19e-02 7.06e+03 7.89e+01 bond pdb=" CA GLU B1011 " pdb=" C GLU B1011 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.34e-02 5.57e+03 5.48e+01 bond pdb=" C2P ACO D1201 " pdb=" S1P ACO D1201 " ideal model delta sigma weight residual 1.818 1.756 0.062 1.00e-02 1.00e+04 3.82e+01 ... (remaining 14819 not shown) Histogram of bond angle deviations from ideal: 92.19 - 101.22: 50 101.22 - 110.25: 3658 110.25 - 119.28: 8744 119.28 - 128.31: 7468 128.31 - 137.34: 124 Bond angle restraints: 20044 Sorted by residual: angle pdb=" P1A ACO D1201 " pdb=" O3A ACO D1201 " pdb=" P2A ACO D1201 " ideal model delta sigma weight residual 136.83 123.13 13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" N GLY D 832 " pdb=" CA GLY D 832 " pdb=" C GLY D 832 " ideal model delta sigma weight residual 113.48 129.42 -15.94 1.46e+00 4.69e-01 1.19e+02 angle pdb=" C5A ACO D1201 " pdb=" C4A ACO D1201 " pdb=" N3A ACO D1201 " ideal model delta sigma weight residual 126.80 116.77 10.03 1.00e+00 1.00e+00 1.01e+02 angle pdb=" C2B ACO D1201 " pdb=" C1B ACO D1201 " pdb=" O4B ACO D1201 " ideal model delta sigma weight residual 106.53 95.02 11.51 1.18e+00 7.24e-01 9.60e+01 angle pdb=" CA GLU A1011 " pdb=" CB GLU A1011 " pdb=" CG GLU A1011 " ideal model delta sigma weight residual 114.10 133.14 -19.04 2.00e+00 2.50e-01 9.06e+01 ... (remaining 20039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7956 17.93 - 35.87: 745 35.87 - 53.80: 139 53.80 - 71.74: 27 71.74 - 89.67: 12 Dihedral angle restraints: 8879 sinusoidal: 3577 harmonic: 5302 Sorted by residual: dihedral pdb=" CA MET A 985 " pdb=" C MET A 985 " pdb=" N ARG A 986 " pdb=" CA ARG A 986 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET C 985 " pdb=" C MET C 985 " pdb=" N ARG C 986 " pdb=" CA ARG C 986 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA MET B 985 " pdb=" C MET B 985 " pdb=" N ARG B 986 " pdb=" CA ARG B 986 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1929 0.103 - 0.206: 250 0.206 - 0.308: 29 0.308 - 0.411: 6 0.411 - 0.514: 7 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA ARG B1045 " pdb=" N ARG B1045 " pdb=" C ARG B1045 " pdb=" CB ARG B1045 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA PRO D 36 " pdb=" N PRO D 36 " pdb=" C PRO D 36 " pdb=" CB PRO D 36 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" CB VAL D 904 " pdb=" CA VAL D 904 " pdb=" CG1 VAL D 904 " pdb=" CG2 VAL D 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 2218 not shown) Planarity restraints: 2569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P ACO D1201 " 0.315 2.00e-02 2.50e+03 2.65e-01 8.76e+02 pdb=" C5P ACO D1201 " -0.083 2.00e-02 2.50e+03 pdb=" C6P ACO D1201 " 0.184 2.00e-02 2.50e+03 pdb=" N4P ACO D1201 " -0.457 2.00e-02 2.50e+03 pdb=" O5P ACO D1201 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO D1201 " -0.188 2.00e-02 2.50e+03 1.51e-01 2.86e+02 pdb=" C9P ACO D1201 " 0.037 2.00e-02 2.50e+03 pdb=" CAP ACO D1201 " -0.132 2.00e-02 2.50e+03 pdb=" N8P ACO D1201 " 0.242 2.00e-02 2.50e+03 pdb=" O9P ACO D1201 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 86 " 0.123 5.00e-02 4.00e+02 1.89e-01 5.69e+01 pdb=" N PRO D 87 " -0.326 5.00e-02 4.00e+02 pdb=" CA PRO D 87 " 0.099 5.00e-02 4.00e+02 pdb=" CD PRO D 87 " 0.104 5.00e-02 4.00e+02 ... (remaining 2566 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 9 1.92 - 2.66: 357 2.66 - 3.41: 20198 3.41 - 4.15: 35127 4.15 - 4.90: 64951 Nonbonded interactions: 120642 Sorted by model distance: nonbonded pdb=" O ASN D 190 " pdb=" OD2 ASP D 194 " model vdw 1.171 3.040 nonbonded pdb=" OE2 GLU C 966 " pdb=" NZ LYS C 968 " model vdw 1.305 2.520 nonbonded pdb=" CG PRO D 36 " pdb=" CD1 LEU D 89 " model vdw 1.507 3.860 nonbonded pdb=" CH2 TRP D 49 " pdb=" CG PRO D 109 " model vdw 1.545 3.740 nonbonded pdb=" CB PRO D 36 " pdb=" CD1 LEU D 89 " model vdw 1.598 3.860 ... (remaining 120637 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' selection = chain 'B' selection = chain 'C' } 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=0.40 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: 0.610 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: 3.270 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 47.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.100 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 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 : 0.013 0.143 14824 Z= 0.858 Angle : 1.331 19.035 20044 Z= 0.742 Chirality : 0.076 0.514 2221 Planarity : 0.010 0.265 2569 Dihedral : 14.818 89.670 5507 Min Nonbonded Distance : 1.171 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.53 % Favored : 93.15 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -3.16 (0.17), residues: 1855 helix: -2.10 (0.13), residues: 951 sheet: -1.16 (0.45), residues: 142 loop : -2.08 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 49 HIS 0.008 0.002 HIS D 908 PHE 0.036 0.004 PHE A 840 TYR 0.042 0.004 TYR D 692 ARG 0.023 0.001 ARG A1045 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.580 Fit side-chains REVERT: B 865 GLU cc_start: 0.7387 (tt0) cc_final: 0.7127 (tm-30) REVERT: D 210 ASP cc_start: 0.7695 (t70) cc_final: 0.7192 (t0) REVERT: D 269 LEU cc_start: 0.7505 (mm) cc_final: 0.7152 (tm) REVERT: D 888 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7263 (tm-30) outliers start: 0 outliers final: 1 residues processed: 217 average time/residue: 1.2653 time to fit residues: 303.7877 Evaluate side-chains 163 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 522 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN B 909 ASN B1098 HIS ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 961 ASN D 172 HIS D 909 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14824 Z= 0.199 Angle : 0.643 8.801 20044 Z= 0.334 Chirality : 0.044 0.253 2221 Planarity : 0.005 0.124 2569 Dihedral : 8.261 87.534 2086 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.90 % Allowed : 9.57 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -2.15 (0.18), residues: 1855 helix: -1.04 (0.15), residues: 978 sheet: -1.15 (0.46), residues: 142 loop : -1.87 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 49 HIS 0.003 0.001 HIS C 900 PHE 0.011 0.001 PHE D 105 TYR 0.046 0.002 TYR D 304 ARG 0.003 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 191 time to evaluate : 1.729 Fit side-chains REVERT: B 888 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: B 976 ARG cc_start: 0.6898 (ptm160) cc_final: 0.6346 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: C 969 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6641 (mm) REVERT: D 194 ASP cc_start: 0.7719 (m-30) cc_final: 0.7275 (m-30) REVERT: D 210 ASP cc_start: 0.7730 (t70) cc_final: 0.7345 (t0) REVERT: D 269 LEU cc_start: 0.7864 (mm) cc_final: 0.7353 (tm) REVERT: D 408 GLU cc_start: 0.7010 (tp30) cc_final: 0.6578 (tp30) outliers start: 28 outliers final: 10 residues processed: 206 average time/residue: 1.0888 time to fit residues: 251.0378 Evaluate side-chains 176 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 1053 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN D 671 ASN D 909 ASN D1020 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14824 Z= 0.380 Angle : 0.678 9.173 20044 Z= 0.347 Chirality : 0.047 0.187 2221 Planarity : 0.005 0.107 2569 Dihedral : 7.742 84.468 2086 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.28 % Allowed : 12.78 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -1.64 (0.19), residues: 1855 helix: -0.56 (0.16), residues: 979 sheet: -1.19 (0.45), residues: 146 loop : -1.66 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 49 HIS 0.004 0.001 HIS C 900 PHE 0.029 0.002 PHE D 110 TYR 0.037 0.002 TYR D 307 ARG 0.005 0.001 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 1.880 Fit side-chains REVERT: A 925 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8744 (m) REVERT: B 888 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8064 (mm-40) REVERT: B 965 LYS cc_start: 0.8949 (tppt) cc_final: 0.8574 (mptm) REVERT: B 976 ARG cc_start: 0.6977 (ptm160) cc_final: 0.6407 (ptp-110) REVERT: B 1050 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: C 965 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7971 (tmmm) REVERT: C 969 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.5763 (mm) REVERT: D 210 ASP cc_start: 0.7745 (t70) cc_final: 0.7474 (t0) REVERT: D 408 GLU cc_start: 0.7098 (tp30) cc_final: 0.6628 (tp30) REVERT: D 1009 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7116 (mp0) outliers start: 49 outliers final: 16 residues processed: 198 average time/residue: 1.1291 time to fit residues: 249.6268 Evaluate side-chains 178 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1050 GLU Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 988 GLN D1020 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14824 Z= 0.209 Angle : 0.578 8.184 20044 Z= 0.296 Chirality : 0.043 0.180 2221 Planarity : 0.004 0.090 2569 Dihedral : 6.949 76.956 2086 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.62 % Allowed : 14.61 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -1.28 (0.19), residues: 1855 helix: -0.19 (0.16), residues: 988 sheet: -1.16 (0.45), residues: 146 loop : -1.59 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 49 HIS 0.004 0.001 HIS C 900 PHE 0.022 0.001 PHE D 110 TYR 0.036 0.002 TYR D 307 ARG 0.003 0.000 ARG C 976 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 1.757 Fit side-chains REVERT: A 925 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8650 (m) REVERT: B 888 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7996 (tm-30) REVERT: B 965 LYS cc_start: 0.8912 (tppt) cc_final: 0.8564 (mptm) REVERT: B 976 ARG cc_start: 0.6943 (ptm160) cc_final: 0.6382 (ptp-110) REVERT: C 969 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.5493 (mm) REVERT: D 86 LYS cc_start: 0.6414 (mmmt) cc_final: 0.5549 (mttt) REVERT: D 210 ASP cc_start: 0.7728 (t70) cc_final: 0.7445 (t0) REVERT: D 408 GLU cc_start: 0.7052 (tp30) cc_final: 0.6665 (tp30) outliers start: 39 outliers final: 14 residues processed: 190 average time/residue: 1.1449 time to fit residues: 243.0268 Evaluate side-chains 173 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 156 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1089 ASP Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 919 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 909 ASN D1020 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14824 Z= 0.360 Angle : 0.641 8.581 20044 Z= 0.326 Chirality : 0.046 0.164 2221 Planarity : 0.005 0.077 2569 Dihedral : 6.962 74.536 2086 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.15 % Allowed : 15.14 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -1.15 (0.19), residues: 1855 helix: -0.10 (0.16), residues: 991 sheet: -1.24 (0.45), residues: 146 loop : -1.50 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 49 HIS 0.005 0.001 HIS D 113 PHE 0.023 0.001 PHE D 110 TYR 0.033 0.002 TYR D 307 ARG 0.004 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 163 time to evaluate : 1.696 Fit side-chains REVERT: A 925 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8711 (m) REVERT: B 888 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8056 (mm-40) REVERT: B 965 LYS cc_start: 0.8944 (tppt) cc_final: 0.8586 (mptm) REVERT: B 976 ARG cc_start: 0.6980 (ptm160) cc_final: 0.6462 (ptp-110) REVERT: B 1035 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: C 965 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7981 (tmmm) REVERT: C 969 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5140 (mm) REVERT: D 210 ASP cc_start: 0.7791 (t70) cc_final: 0.7346 (t0) REVERT: D 408 GLU cc_start: 0.7008 (tp30) cc_final: 0.6653 (tp30) outliers start: 47 outliers final: 19 residues processed: 190 average time/residue: 1.1869 time to fit residues: 250.5219 Evaluate side-chains 179 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 940 ASP Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 977 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 919 ASP Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 0.9990 chunk 159 optimal weight: 0.0040 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN D 909 ASN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14824 Z= 0.207 Angle : 0.572 9.172 20044 Z= 0.292 Chirality : 0.043 0.146 2221 Planarity : 0.004 0.068 2569 Dihedral : 6.434 69.812 2084 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.49 % Allowed : 16.84 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -0.89 (0.19), residues: 1855 helix: 0.14 (0.16), residues: 996 sheet: -1.13 (0.46), residues: 146 loop : -1.42 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 49 HIS 0.004 0.001 HIS D 113 PHE 0.021 0.001 PHE D 110 TYR 0.033 0.002 TYR D 307 ARG 0.004 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 165 time to evaluate : 1.721 Fit side-chains REVERT: A 925 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8675 (m) REVERT: B 965 LYS cc_start: 0.8913 (tppt) cc_final: 0.8580 (mptm) REVERT: B 976 ARG cc_start: 0.7009 (ptm160) cc_final: 0.6472 (ptp-110) REVERT: B 1035 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: C 904 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8164 (m) REVERT: C 969 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5276 (mm) REVERT: D 86 LYS cc_start: 0.6367 (mmmt) cc_final: 0.5399 (mttt) REVERT: D 194 ASP cc_start: 0.7644 (m-30) cc_final: 0.7174 (m-30) REVERT: D 210 ASP cc_start: 0.7760 (t70) cc_final: 0.7463 (t0) outliers start: 37 outliers final: 14 residues processed: 188 average time/residue: 1.1762 time to fit residues: 246.2715 Evaluate side-chains 176 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 176 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 107 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14824 Z= 0.234 Angle : 0.583 10.464 20044 Z= 0.296 Chirality : 0.043 0.148 2221 Planarity : 0.004 0.063 2569 Dihedral : 6.302 68.326 2084 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.36 % Allowed : 17.63 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.71 (0.20), residues: 1855 helix: 0.29 (0.16), residues: 996 sheet: -1.05 (0.46), residues: 146 loop : -1.34 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 49 HIS 0.003 0.001 HIS D 113 PHE 0.020 0.001 PHE D 110 TYR 0.027 0.002 TYR D 307 ARG 0.002 0.000 ARG A 848 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.730 Fit side-chains REVERT: A 925 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8680 (m) REVERT: B 965 LYS cc_start: 0.8929 (tppt) cc_final: 0.8611 (mptm) REVERT: B 976 ARG cc_start: 0.6979 (ptm160) cc_final: 0.6446 (ptp-110) REVERT: C 969 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5277 (mm) REVERT: D 86 LYS cc_start: 0.6363 (mmmt) cc_final: 0.5518 (mttt) REVERT: D 194 ASP cc_start: 0.7673 (m-30) cc_final: 0.7202 (m-30) REVERT: D 201 GLU cc_start: 0.6973 (tp30) cc_final: 0.6769 (tm-30) REVERT: D 210 ASP cc_start: 0.7763 (t70) cc_final: 0.7464 (t0) REVERT: D 244 ARG cc_start: 0.5727 (ppt170) cc_final: 0.5491 (pmt-80) REVERT: D 408 GLU cc_start: 0.7218 (tp30) cc_final: 0.6666 (tp30) outliers start: 35 outliers final: 17 residues processed: 191 average time/residue: 1.1529 time to fit residues: 245.7569 Evaluate side-chains 179 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 0.0060 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 888 GLN C 996 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14824 Z= 0.246 Angle : 0.594 10.298 20044 Z= 0.301 Chirality : 0.044 0.149 2221 Planarity : 0.004 0.060 2569 Dihedral : 6.234 68.471 2084 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.29 % Allowed : 18.09 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.65 (0.20), residues: 1855 helix: 0.36 (0.16), residues: 996 sheet: -1.05 (0.46), residues: 146 loop : -1.34 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 49 HIS 0.003 0.001 HIS C 900 PHE 0.019 0.001 PHE D 110 TYR 0.025 0.002 TYR D 692 ARG 0.005 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.588 Fit side-chains REVERT: A 925 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8628 (m) REVERT: B 965 LYS cc_start: 0.8924 (tppt) cc_final: 0.8617 (mptm) REVERT: B 976 ARG cc_start: 0.6987 (ptm160) cc_final: 0.6458 (ptp-110) REVERT: C 969 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5255 (mm) REVERT: D 194 ASP cc_start: 0.7642 (m-30) cc_final: 0.7159 (m-30) REVERT: D 210 ASP cc_start: 0.7766 (t70) cc_final: 0.7472 (t0) REVERT: D 244 ARG cc_start: 0.5790 (ppt170) cc_final: 0.5541 (pmt-80) REVERT: D 408 GLU cc_start: 0.7175 (tp30) cc_final: 0.6613 (tp30) REVERT: D 780 LYS cc_start: 0.8322 (tttt) cc_final: 0.7913 (tptt) outliers start: 34 outliers final: 19 residues processed: 186 average time/residue: 1.1656 time to fit residues: 241.2459 Evaluate side-chains 179 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 45 GLN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14824 Z= 0.288 Angle : 0.617 10.863 20044 Z= 0.313 Chirality : 0.045 0.168 2221 Planarity : 0.004 0.059 2569 Dihedral : 6.264 68.958 2084 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.16 % Allowed : 18.87 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.63 (0.20), residues: 1855 helix: 0.35 (0.16), residues: 995 sheet: -1.05 (0.45), residues: 148 loop : -1.29 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 49 HIS 0.003 0.001 HIS D 47 PHE 0.020 0.001 PHE D 110 TYR 0.028 0.002 TYR D 692 ARG 0.008 0.000 ARG C 829 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.531 Fit side-chains REVERT: A 925 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8647 (m) REVERT: B 888 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: B 965 LYS cc_start: 0.8924 (tppt) cc_final: 0.8608 (mptm) REVERT: B 976 ARG cc_start: 0.6980 (ptm160) cc_final: 0.6424 (ptp-110) REVERT: C 969 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5286 (mm) REVERT: D 86 LYS cc_start: 0.6124 (mmmt) cc_final: 0.5203 (mttt) REVERT: D 194 ASP cc_start: 0.7641 (m-30) cc_final: 0.7175 (m-30) REVERT: D 210 ASP cc_start: 0.7779 (t70) cc_final: 0.7328 (t0) REVERT: D 244 ARG cc_start: 0.5797 (ppt170) cc_final: 0.5545 (pmt-80) REVERT: D 408 GLU cc_start: 0.7192 (tp30) cc_final: 0.6657 (tp30) REVERT: D 780 LYS cc_start: 0.8335 (tttt) cc_final: 0.7917 (tptt) outliers start: 32 outliers final: 20 residues processed: 176 average time/residue: 1.2204 time to fit residues: 238.2620 Evaluate side-chains 178 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 888 GLN Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 966 GLU Chi-restraints excluded: chain B residue 977 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 182 optimal weight: 0.7980 chunk 167 optimal weight: 0.6980 chunk 145 optimal weight: 0.0030 chunk 15 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1024 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 996 GLN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 GLN ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14824 Z= 0.192 Angle : 0.588 11.001 20044 Z= 0.298 Chirality : 0.043 0.150 2221 Planarity : 0.004 0.073 2569 Dihedral : 6.032 67.579 2084 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.03 % Allowed : 19.46 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.49 (0.20), residues: 1855 helix: 0.48 (0.17), residues: 991 sheet: -0.98 (0.45), residues: 148 loop : -1.24 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 49 HIS 0.003 0.001 HIS D 113 PHE 0.018 0.001 PHE D 110 TYR 0.022 0.001 TYR D 307 ARG 0.007 0.000 ARG C 829 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3710 Ramachandran restraints generated. 1855 Oldfield, 0 Emsley, 1855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.770 Fit side-chains REVERT: A 925 THR cc_start: 0.8859 (OUTLIER) cc_final: 0.8626 (m) REVERT: A 1075 ASP cc_start: 0.8068 (t0) cc_final: 0.7787 (t0) REVERT: B 965 LYS cc_start: 0.8891 (tppt) cc_final: 0.8583 (mptm) REVERT: B 976 ARG cc_start: 0.6929 (ptm160) cc_final: 0.6360 (ptp-110) REVERT: C 969 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5315 (mm) REVERT: D 86 LYS cc_start: 0.6077 (mmmt) cc_final: 0.5177 (mttt) REVERT: D 194 ASP cc_start: 0.7649 (m-30) cc_final: 0.7235 (m-30) REVERT: D 210 ASP cc_start: 0.7747 (t70) cc_final: 0.7464 (t0) REVERT: D 244 ARG cc_start: 0.5762 (ppt170) cc_final: 0.5559 (pmt-80) REVERT: D 327 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5820 (mmt) REVERT: D 355 LYS cc_start: 0.6149 (mmtm) cc_final: 0.5340 (tppt) REVERT: D 408 GLU cc_start: 0.7119 (tp30) cc_final: 0.6624 (tp30) REVERT: D 690 ASP cc_start: 0.7586 (t70) cc_final: 0.7384 (t70) REVERT: D 780 LYS cc_start: 0.8295 (tttt) cc_final: 0.7873 (tptt) outliers start: 30 outliers final: 22 residues processed: 182 average time/residue: 1.2671 time to fit residues: 257.1100 Evaluate side-chains 185 residues out of total 1549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 919 ASP Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain B residue 919 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 955 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 969 LEU Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 696 THR Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 867 MET Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 1009 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 0.0050 chunk 44 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 ASN ** C 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1024 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.133820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102115 restraints weight = 28457.815| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.58 r_work: 0.3207 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14824 Z= 0.211 Angle : 0.593 12.814 20044 Z= 0.299 Chirality : 0.043 0.151 2221 Planarity : 0.004 0.065 2569 Dihedral : 5.960 67.660 2084 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.16 % Allowed : 19.40 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.42 (0.20), residues: 1855 helix: 0.55 (0.17), residues: 991 sheet: -0.97 (0.45), residues: 148 loop : -1.22 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 49 HIS 0.002 0.001 HIS D 997 PHE 0.019 0.001 PHE D 110 TYR 0.024 0.001 TYR D 692 ARG 0.007 0.000 ARG C 829 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4886.79 seconds wall clock time: 88 minutes 0.36 seconds (5280.36 seconds total)