Starting phenix.real_space_refine on Thu Jun 27 12:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/06_2024/8ut9_42534_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/06_2024/8ut9_42534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/06_2024/8ut9_42534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/06_2024/8ut9_42534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/06_2024/8ut9_42534_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/06_2024/8ut9_42534_updated.pdb" } resolution = 3.3 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= 0.016 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7833 2.51 5 N 2266 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 163": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 12707 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "E" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "F" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.73, per 1000 atoms: 0.69 Number of scatterers: 12707 At special positions: 0 Unit cell: (83.375, 107.3, 143.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2542 8.00 N 2266 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 66 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.05 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.05 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 268 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 272 " - pdb=" SG CYS E 296 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 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 Links applied BETA1-3 " NAG I 1 " - " NAG I 2 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 401 " - " ASN A 28 " " NAG A 402 " - " ASN A 231 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 12 " " NAG C 402 " - " ASN C 28 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 28 " " NAG E 402 " - " ASN E 231 " " NAG F 301 " - " ASN F 154 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN D 82 " " NAG K 1 " - " ASN F 82 " Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 2.0 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 32 sheets defined 25.3% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 64 through 69 removed outlier: 5.700A pdb=" N GLN A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'B' and resid 38 through 55 Processing helix chain 'B' and resid 75 through 129 removed outlier: 6.726A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 160 through 168 removed outlier: 4.400A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 64 through 69 removed outlier: 3.916A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 68 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 179 through 185 Processing helix chain 'D' and resid 38 through 55 Processing helix chain 'D' and resid 75 through 129 removed outlier: 6.780A pdb=" N GLU D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 163 through 170 Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.871A pdb=" N THR E 61 " --> pdb=" O GLY E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 5.507A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 103 Processing helix chain 'E' and resid 179 through 186 Processing helix chain 'F' and resid 39 through 55 Processing helix chain 'F' and resid 75 through 129 removed outlier: 6.559A pdb=" N GLU F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 Processing helix chain 'F' and resid 163 through 170 Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'A' and resid 48 through 51 removed outlier: 6.679A pdb=" N LEU A 76 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 51 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A 78 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET A 256 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLU A 79 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 258 " --> pdb=" O GLU A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.551A pdb=" N ILE A 221 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 112 Processing sheet with id= E, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= F, first strand: chain 'A' and resid 155 through 160 Processing sheet with id= G, first strand: chain 'A' and resid 272 through 274 removed outlier: 4.031A pdb=" N CYS A 272 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 14 through 17 Processing sheet with id= I, first strand: chain 'B' and resid 23 through 27 Processing sheet with id= J, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= K, first strand: chain 'C' and resid 14 through 16 Processing sheet with id= L, first strand: chain 'C' and resid 29 through 31 Processing sheet with id= M, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.832A pdb=" N LEU C 76 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE C 258 " --> pdb=" O GLU C 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 90 through 92 removed outlier: 6.594A pdb=" N ILE C 221 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 108 through 112 Processing sheet with id= P, first strand: chain 'C' and resid 155 through 159 Processing sheet with id= Q, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.879A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 23 through 28 Processing sheet with id= S, first strand: chain 'D' and resid 130 through 132 Processing sheet with id= T, first strand: chain 'E' and resid 14 through 16 Processing sheet with id= U, first strand: chain 'E' and resid 29 through 31 Processing sheet with id= V, first strand: chain 'E' and resid 48 through 51 removed outlier: 6.917A pdb=" N LEU E 76 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU E 51 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE E 78 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N MET E 256 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLU E 79 " --> pdb=" O MET E 256 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE E 258 " --> pdb=" O GLU E 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.128A pdb=" N ILE E 221 " --> pdb=" O LYS E 91 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 108 through 112 Processing sheet with id= Y, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= Z, first strand: chain 'F' and resid 23 through 28 Processing sheet with id= AA, first strand: chain 'F' and resid 130 through 132 Processing sheet with id= AB, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= AC, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.598A pdb=" N UNK G 92 " --> pdb=" O UNK G 123 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N UNK G 38 " --> pdb=" O UNK G 47 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N UNK G 47 " --> pdb=" O UNK G 38 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N UNK G 40 " --> pdb=" O UNK G 45 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N UNK G 45 " --> pdb=" O UNK G 40 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.869A pdb=" N UNK H 105 " --> pdb=" O UNK H 11 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N UNK H 13 " --> pdb=" O UNK H 105 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 107 " --> pdb=" O UNK H 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 19 through 24 Processing sheet with id= AF, first strand: chain 'H' and resid 86 through 91 removed outlier: 6.004A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1152 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: 3.53 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4373 1.34 - 1.48: 3084 1.48 - 1.61: 5355 1.61 - 1.75: 5 1.75 - 1.88: 92 Bond restraints: 12909 Sorted by residual: bond pdb=" N CYS A 268 " pdb=" CA CYS A 268 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA UNK H 67 " pdb=" CB UNK H 67 " ideal model delta sigma weight residual 1.530 1.471 0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" SD MET A 311 " pdb=" CE MET A 311 " ideal model delta sigma weight residual 1.791 1.722 0.069 2.50e-02 1.60e+03 7.65e+00 bond pdb=" CB PRO C 315 " pdb=" CG PRO C 315 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.37e+00 bond pdb=" N LYS B 161 " pdb=" CA LYS B 161 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.85e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.63: 141 104.63 - 111.96: 5849 111.96 - 119.29: 4882 119.29 - 126.63: 6453 126.63 - 133.96: 155 Bond angle restraints: 17480 Sorted by residual: angle pdb=" CA PRO C 315 " pdb=" N PRO C 315 " pdb=" CD PRO C 315 " ideal model delta sigma weight residual 112.00 100.59 11.41 1.40e+00 5.10e-01 6.65e+01 angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 132.20 -17.80 2.30e+00 1.89e-01 5.99e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" C GLU B 164 " ideal model delta sigma weight residual 111.33 103.52 7.81 1.21e+00 6.83e-01 4.16e+01 angle pdb=" CA CYS A 42 " pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " ideal model delta sigma weight residual 114.40 128.33 -13.93 2.30e+00 1.89e-01 3.67e+01 angle pdb=" CA CYS F 144 " pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " ideal model delta sigma weight residual 114.40 124.46 -10.06 2.30e+00 1.89e-01 1.91e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7301 17.98 - 35.96: 464 35.96 - 53.93: 133 53.93 - 71.91: 42 71.91 - 89.89: 19 Dihedral angle restraints: 7959 sinusoidal: 3137 harmonic: 4822 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -172.54 86.54 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CD ARG B 163 " pdb=" NE ARG B 163 " pdb=" CZ ARG B 163 " pdb=" NH1 ARG B 163 " ideal model delta sinusoidal sigma weight residual 0.00 -82.06 82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual 93.00 13.54 79.46 1 1.00e+01 1.00e-02 7.84e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1641 0.075 - 0.151: 303 0.151 - 0.226: 30 0.226 - 0.301: 7 0.301 - 0.377: 4 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB THR D 49 " pdb=" CA THR D 49 " pdb=" OG1 THR D 49 " pdb=" CG2 THR D 49 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA CYS C 296 " pdb=" N CYS C 296 " pdb=" C CYS C 296 " pdb=" CB CYS C 296 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1982 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 163 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG B 163 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 163 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 163 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 163 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 314 " -0.097 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO E 315 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO E 315 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO E 315 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 314 " -0.089 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C 315 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C 315 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 315 " -0.066 5.00e-02 4.00e+02 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 17 2.33 - 2.97: 6090 2.97 - 3.61: 18248 3.61 - 4.26: 28666 4.26 - 4.90: 48874 Nonbonded interactions: 101895 Sorted by model distance: nonbonded pdb=" NE2 GLN A 201 " pdb=" OD1 ASP E 222 " model vdw 1.682 2.520 nonbonded pdb=" OD2 ASP B 67 " pdb=" NH2 ARG B 85 " model vdw 1.886 2.520 nonbonded pdb=" OG SER E 43 " pdb=" OG1 THR E 48 " model vdw 2.062 2.440 nonbonded pdb=" NE2 HIS E 175 " pdb=" OD2 ASP E 222 " model vdw 2.141 2.520 nonbonded pdb=" OE2 GLU A 34 " pdb=" OG1 THR A 36 " model vdw 2.166 2.440 ... (remaining 101890 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 1 through 316 or resid 401 through 402)) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 20 through 127) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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=1.00 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: 3.940 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: 17.830 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.930 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.120 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.007 0.136 12909 Z= 0.429 Angle : 1.165 17.797 17480 Z= 0.632 Chirality : 0.060 0.377 1985 Planarity : 0.012 0.488 2315 Dihedral : 14.131 89.890 4810 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.20), residues: 1438 helix: 1.00 (0.25), residues: 329 sheet: 0.78 (0.30), residues: 262 loop : -0.35 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 142 HIS 0.013 0.003 HIS D 159 PHE 0.030 0.004 PHE A 250 TYR 0.043 0.003 TYR F 119 ARG 0.014 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.325 Fit side-chains REVERT: A 42 CYS cc_start: 0.5936 (m) cc_final: 0.5717 (m) REVERT: B 39 LYS cc_start: 0.7346 (ttmt) cc_final: 0.6690 (ttpt) REVERT: B 167 MET cc_start: 0.6540 (tmm) cc_final: 0.6056 (ttp) REVERT: B 168 GLN cc_start: 0.7363 (mm-40) cc_final: 0.7126 (mm-40) REVERT: C 185 LEU cc_start: 0.7320 (mp) cc_final: 0.7120 (mt) REVERT: C 303 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.7070 (ptm-80) REVERT: D 135 THR cc_start: 0.7938 (t) cc_final: 0.7714 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2683 time to fit residues: 60.2108 Evaluate side-chains 142 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 49 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN B 159 HIS C 37 ASN D 159 HIS E 239 ASN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12909 Z= 0.198 Angle : 0.597 6.885 17480 Z= 0.314 Chirality : 0.043 0.286 1985 Planarity : 0.004 0.081 2315 Dihedral : 5.471 44.408 2117 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.71 % Allowed : 11.97 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.20), residues: 1438 helix: 1.54 (0.26), residues: 335 sheet: 0.60 (0.31), residues: 254 loop : -0.48 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.005 0.001 HIS D 159 PHE 0.014 0.002 PHE C 136 TYR 0.017 0.001 TYR F 119 ARG 0.005 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.421 Fit side-chains REVERT: B 25 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7363 (tpp80) REVERT: B 39 LYS cc_start: 0.7542 (ttmt) cc_final: 0.6823 (ttpt) REVERT: C 75 ASP cc_start: 0.6666 (m-30) cc_final: 0.6445 (m-30) REVERT: D 135 THR cc_start: 0.7940 (t) cc_final: 0.7733 (t) REVERT: E 108 ILE cc_start: 0.8454 (mt) cc_final: 0.8217 (mm) REVERT: E 171 TRP cc_start: 0.8731 (p90) cc_final: 0.8497 (p90) outliers start: 21 outliers final: 16 residues processed: 180 average time/residue: 0.2493 time to fit residues: 64.3921 Evaluate side-chains 159 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN D 42 GLN D 159 HIS E 263 GLN F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12909 Z= 0.307 Angle : 0.613 6.666 17480 Z= 0.323 Chirality : 0.045 0.345 1985 Planarity : 0.004 0.063 2315 Dihedral : 5.230 42.308 2117 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.77 % Allowed : 12.46 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.21), residues: 1438 helix: 1.58 (0.27), residues: 327 sheet: 0.25 (0.30), residues: 270 loop : -0.76 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 92 HIS 0.006 0.002 HIS F 142 PHE 0.021 0.002 PHE C 238 TYR 0.015 0.002 TYR F 119 ARG 0.006 0.001 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7862 (ptt180) cc_final: 0.7652 (ptt90) REVERT: A 238 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: B 25 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7601 (tpp80) REVERT: B 39 LYS cc_start: 0.7603 (ttmt) cc_final: 0.6888 (ttpt) outliers start: 34 outliers final: 21 residues processed: 190 average time/residue: 0.2538 time to fit residues: 68.4604 Evaluate side-chains 181 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN E 53 GLN E 201 GLN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 12909 Z= 0.445 Angle : 0.711 8.400 17480 Z= 0.369 Chirality : 0.047 0.335 1985 Planarity : 0.005 0.058 2315 Dihedral : 5.642 40.767 2117 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.83 % Allowed : 13.19 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.21), residues: 1438 helix: 1.00 (0.27), residues: 327 sheet: -0.66 (0.30), residues: 282 loop : -1.23 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 142 HIS 0.010 0.002 HIS A 7 PHE 0.027 0.003 PHE C 238 TYR 0.016 0.002 TYR F 119 ARG 0.008 0.001 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7563 (tpp80) REVERT: B 39 LYS cc_start: 0.7674 (ttmt) cc_final: 0.6948 (ttpt) REVERT: C 27 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8689 (t) REVERT: D 120 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: E 22 ARG cc_start: 0.6409 (mmp80) cc_final: 0.6191 (mmp80) REVERT: E 217 GLN cc_start: 0.7409 (tp40) cc_final: 0.7144 (mt0) REVERT: E 271 ASP cc_start: 0.7842 (p0) cc_final: 0.7300 (t0) outliers start: 47 outliers final: 29 residues processed: 211 average time/residue: 0.2543 time to fit residues: 75.2610 Evaluate side-chains 188 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 128 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 0.0070 chunk 117 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN E 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12909 Z= 0.179 Angle : 0.533 6.180 17480 Z= 0.282 Chirality : 0.041 0.306 1985 Planarity : 0.003 0.052 2315 Dihedral : 5.085 39.258 2117 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.61 % Allowed : 15.47 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.61 (0.21), residues: 1438 helix: 1.51 (0.28), residues: 324 sheet: -0.50 (0.31), residues: 274 loop : -1.18 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE F 9 TYR 0.022 0.002 TYR F 119 ARG 0.006 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: B 25 ARG cc_start: 0.7816 (ttm170) cc_final: 0.7594 (tpp80) REVERT: B 39 LYS cc_start: 0.7670 (ttmt) cc_final: 0.6945 (ttpt) REVERT: C 27 VAL cc_start: 0.8835 (p) cc_final: 0.8471 (t) REVERT: D 115 MET cc_start: 0.8549 (tpt) cc_final: 0.8317 (mmm) REVERT: E 217 GLN cc_start: 0.7275 (tp40) cc_final: 0.6986 (mt0) REVERT: F 157 TYR cc_start: 0.6427 (t80) cc_final: 0.6097 (t80) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 0.2638 time to fit residues: 70.4898 Evaluate side-chains 179 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12909 Z= 0.247 Angle : 0.552 6.947 17480 Z= 0.290 Chirality : 0.042 0.321 1985 Planarity : 0.003 0.051 2315 Dihedral : 4.938 34.886 2117 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.77 % Allowed : 15.80 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.21), residues: 1438 helix: 1.57 (0.28), residues: 324 sheet: -0.62 (0.31), residues: 276 loop : -1.17 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 142 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.002 PHE C 238 TYR 0.041 0.002 TYR E 186 ARG 0.005 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8020 (ptt180) cc_final: 0.7647 (ptt90) REVERT: A 185 LEU cc_start: 0.6161 (OUTLIER) cc_final: 0.5200 (mp) REVERT: A 238 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 25 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7577 (tpp80) REVERT: B 39 LYS cc_start: 0.7694 (ttmt) cc_final: 0.6971 (ttpt) REVERT: C 27 VAL cc_start: 0.8871 (p) cc_final: 0.8516 (t) REVERT: C 37 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8123 (p0) REVERT: D 115 MET cc_start: 0.8567 (tpt) cc_final: 0.8340 (mmm) REVERT: D 120 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: E 217 GLN cc_start: 0.7304 (tp40) cc_final: 0.6998 (mt0) REVERT: F 157 TYR cc_start: 0.6492 (t80) cc_final: 0.6177 (t80) outliers start: 34 outliers final: 22 residues processed: 187 average time/residue: 0.2681 time to fit residues: 70.2214 Evaluate side-chains 180 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12909 Z= 0.199 Angle : 0.526 7.133 17480 Z= 0.276 Chirality : 0.042 0.316 1985 Planarity : 0.003 0.050 2315 Dihedral : 4.854 37.017 2117 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.77 % Allowed : 16.29 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.56 (0.21), residues: 1438 helix: 1.68 (0.28), residues: 324 sheet: -0.62 (0.31), residues: 276 loop : -1.14 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.003 0.001 HIS A 7 PHE 0.014 0.001 PHE C 238 TYR 0.049 0.002 TYR E 186 ARG 0.005 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7989 (ptt180) cc_final: 0.7778 (ptt90) REVERT: A 238 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 25 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7587 (tpp80) REVERT: B 39 LYS cc_start: 0.7681 (ttmt) cc_final: 0.6964 (ttpt) REVERT: C 27 VAL cc_start: 0.8836 (p) cc_final: 0.8492 (t) REVERT: C 37 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.8009 (p0) REVERT: C 220 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.5842 (ttm170) REVERT: D 115 MET cc_start: 0.8569 (tpt) cc_final: 0.8343 (mmm) REVERT: D 120 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: D 149 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5168 (ttm) REVERT: E 217 GLN cc_start: 0.7269 (tp40) cc_final: 0.6974 (mt0) REVERT: F 157 TYR cc_start: 0.6492 (t80) cc_final: 0.6218 (t80) outliers start: 34 outliers final: 25 residues processed: 183 average time/residue: 0.2867 time to fit residues: 73.7890 Evaluate side-chains 190 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12909 Z= 0.372 Angle : 0.614 7.391 17480 Z= 0.320 Chirality : 0.045 0.345 1985 Planarity : 0.004 0.052 2315 Dihedral : 5.066 35.415 2117 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.42 % Allowed : 16.21 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.21), residues: 1438 helix: 1.44 (0.28), residues: 319 sheet: -0.91 (0.31), residues: 276 loop : -1.29 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 142 HIS 0.005 0.001 HIS C 7 PHE 0.019 0.002 PHE C 238 TYR 0.061 0.002 TYR E 186 ARG 0.006 0.001 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8123 (ptt180) cc_final: 0.7828 (ptt90) REVERT: A 185 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5266 (mp) REVERT: A 238 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: B 25 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7573 (tpp80) REVERT: B 39 LYS cc_start: 0.7718 (ttmt) cc_final: 0.6989 (ttpt) REVERT: C 27 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8635 (t) REVERT: C 37 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8078 (p0) REVERT: C 220 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6046 (ttm170) REVERT: D 19 ASP cc_start: 0.7984 (p0) cc_final: 0.7666 (p0) REVERT: D 116 ASP cc_start: 0.7216 (m-30) cc_final: 0.6969 (m-30) REVERT: D 120 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: E 217 GLN cc_start: 0.7326 (tp40) cc_final: 0.7012 (mt0) REVERT: F 157 TYR cc_start: 0.6667 (t80) cc_final: 0.6373 (t80) outliers start: 42 outliers final: 30 residues processed: 198 average time/residue: 0.2684 time to fit residues: 75.4068 Evaluate side-chains 202 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12909 Z= 0.296 Angle : 0.577 7.138 17480 Z= 0.300 Chirality : 0.044 0.335 1985 Planarity : 0.004 0.052 2315 Dihedral : 5.019 35.380 2117 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.26 % Allowed : 16.53 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.21), residues: 1438 helix: 1.47 (0.28), residues: 319 sheet: -0.99 (0.31), residues: 276 loop : -1.33 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 142 HIS 0.004 0.001 HIS C 7 PHE 0.017 0.002 PHE C 238 TYR 0.039 0.002 TYR E 186 ARG 0.005 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 171 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8112 (ptt180) cc_final: 0.7793 (ptt90) REVERT: A 185 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5254 (mp) REVERT: A 238 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: B 25 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7579 (tpp80) REVERT: B 39 LYS cc_start: 0.7716 (ttmt) cc_final: 0.6996 (ttpt) REVERT: C 27 VAL cc_start: 0.8934 (OUTLIER) cc_final: 0.8624 (t) REVERT: C 37 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.8049 (p0) REVERT: C 70 LEU cc_start: 0.7573 (mt) cc_final: 0.7192 (mt) REVERT: C 220 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6028 (ttm170) REVERT: D 19 ASP cc_start: 0.7961 (p0) cc_final: 0.7657 (p0) REVERT: D 120 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: E 217 GLN cc_start: 0.7339 (tp40) cc_final: 0.7023 (mt0) REVERT: F 157 TYR cc_start: 0.6678 (t80) cc_final: 0.6412 (t80) outliers start: 40 outliers final: 25 residues processed: 199 average time/residue: 0.2635 time to fit residues: 73.7067 Evaluate side-chains 197 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12909 Z= 0.348 Angle : 0.606 7.428 17480 Z= 0.315 Chirality : 0.044 0.344 1985 Planarity : 0.004 0.053 2315 Dihedral : 5.105 35.597 2117 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.85 % Allowed : 17.02 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1438 helix: 1.40 (0.28), residues: 319 sheet: -1.08 (0.31), residues: 276 loop : -1.39 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 142 HIS 0.011 0.001 HIS D 142 PHE 0.018 0.002 PHE C 238 TYR 0.016 0.002 TYR E 186 ARG 0.006 0.001 ARG F 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8129 (ptt180) cc_final: 0.7743 (ptt90) REVERT: A 185 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5245 (mp) REVERT: A 238 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 25 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7587 (tpp80) REVERT: B 39 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7181 (mtpt) REVERT: C 27 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8668 (t) REVERT: C 37 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8038 (p0) REVERT: C 70 LEU cc_start: 0.7576 (mt) cc_final: 0.7219 (mt) REVERT: C 179 THR cc_start: 0.7749 (m) cc_final: 0.7417 (p) REVERT: C 220 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6042 (ttm170) REVERT: D 19 ASP cc_start: 0.7962 (p0) cc_final: 0.7653 (p0) REVERT: D 120 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: E 217 GLN cc_start: 0.7352 (tp40) cc_final: 0.7044 (mt0) REVERT: F 157 TYR cc_start: 0.6739 (t80) cc_final: 0.6482 (t80) REVERT: F 161 LYS cc_start: 0.6571 (pttm) cc_final: 0.6363 (pttm) outliers start: 35 outliers final: 27 residues processed: 201 average time/residue: 0.2707 time to fit residues: 76.5499 Evaluate side-chains 206 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN B 60 ASN C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.167205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.146298 restraints weight = 16632.797| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.37 r_work: 0.3591 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12909 Z= 0.250 Angle : 0.560 7.066 17480 Z= 0.292 Chirality : 0.043 0.333 1985 Planarity : 0.003 0.052 2315 Dihedral : 4.976 34.926 2117 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.18 % Allowed : 17.43 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.21), residues: 1438 helix: 1.52 (0.28), residues: 325 sheet: -0.95 (0.32), residues: 266 loop : -1.38 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.008 0.001 HIS D 142 PHE 0.016 0.002 PHE C 238 TYR 0.016 0.002 TYR E 186 ARG 0.004 0.000 ARG D 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.64 seconds wall clock time: 51 minutes 18.36 seconds (3078.36 seconds total)