Starting phenix.real_space_refine on Fri Feb 16 22:49:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3v_6883/02_2024/5z3v_6883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3v_6883/02_2024/5z3v_6883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3v_6883/02_2024/5z3v_6883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3v_6883/02_2024/5z3v_6883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3v_6883/02_2024/5z3v_6883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3v_6883/02_2024/5z3v_6883_updated.pdb" } resolution = 4.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 29 5.16 5 Be 1 3.05 5 C 9642 2.51 5 N 3087 2.21 5 O 3701 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 919": "NH1" <-> "NH2" Residue "O ARG 1076": "NH1" <-> "NH2" Residue "O ARG 1094": "NH1" <-> "NH2" Residue "O TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 1164": "NH1" <-> "NH2" Residue "O ARG 1196": "NH1" <-> "NH2" Residue "O ARG 1264": "NH1" <-> "NH2" Residue "O ARG 1349": "NH1" <-> "NH2" Residue "F ARG 17": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16758 Number of models: 1 Model: "" Number of chains: 12 Chain: "O" Number of atoms: 4729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4729 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 559} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.88, per 1000 atoms: 0.53 Number of scatterers: 16758 At special positions: 0 Unit cell: (142.56, 130.68, 124.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 29 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3701 8.00 N 3087 7.00 C 9642 6.00 Be 1 4.00 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: 8.37 Conformation dependent library (CDL) restraints added in 2.1 seconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 2 sheets defined 57.1% alpha, 1.5% beta 145 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 9.18 Creating SS restraints... Processing helix chain 'O' and resid 671 through 688 removed outlier: 4.142A pdb=" N ASP O 676 " --> pdb=" O GLN O 673 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR O 677 " --> pdb=" O THR O 674 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG O 678 " --> pdb=" O LYS O 675 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR O 680 " --> pdb=" O THR O 677 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN O 687 " --> pdb=" O ARG O 684 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA O 688 " --> pdb=" O GLN O 685 " (cutoff:3.500A) Processing helix chain 'O' and resid 744 through 747 No H-bonds generated for 'chain 'O' and resid 744 through 747' Processing helix chain 'O' and resid 770 through 783 Processing helix chain 'O' and resid 798 through 812 Processing helix chain 'O' and resid 829 through 834 Processing helix chain 'O' and resid 851 through 863 removed outlier: 5.573A pdb=" N ALA O 863 " --> pdb=" O ALA O 859 " (cutoff:3.500A) Processing helix chain 'O' and resid 873 through 883 removed outlier: 3.900A pdb=" N ILE O 877 " --> pdb=" O PHE O 873 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA O 881 " --> pdb=" O ILE O 877 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU O 882 " --> pdb=" O LYS O 878 " (cutoff:3.500A) Processing helix chain 'O' and resid 896 through 899 No H-bonds generated for 'chain 'O' and resid 896 through 899' Processing helix chain 'O' and resid 905 through 910 Processing helix chain 'O' and resid 934 through 940 Processing helix chain 'O' and resid 951 through 953 No H-bonds generated for 'chain 'O' and resid 951 through 953' Processing helix chain 'O' and resid 968 through 987 Processing helix chain 'O' and resid 996 through 999 No H-bonds generated for 'chain 'O' and resid 996 through 999' Processing helix chain 'O' and resid 1017 through 1029 removed outlier: 4.541A pdb=" N MET O1022 " --> pdb=" O LEU O1018 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR O1023 " --> pdb=" O GLN O1019 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN O1024 " --> pdb=" O GLN O1020 " (cutoff:3.500A) Processing helix chain 'O' and resid 1050 through 1060 removed outlier: 4.158A pdb=" N LEU O1055 " --> pdb=" O GLN O1051 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) Processing helix chain 'O' and resid 1066 through 1072 Processing helix chain 'O' and resid 1080 through 1082 No H-bonds generated for 'chain 'O' and resid 1080 through 1082' Processing helix chain 'O' and resid 1088 through 1102 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1114 through 1125 Processing helix chain 'O' and resid 1139 through 1149 Processing helix chain 'O' and resid 1163 through 1166 No H-bonds generated for 'chain 'O' and resid 1163 through 1166' Processing helix chain 'O' and resid 1187 through 1196 removed outlier: 3.701A pdb=" N ASP O1195 " --> pdb=" O LEU O1191 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG O1196 " --> pdb=" O GLN O1192 " (cutoff:3.500A) Processing helix chain 'O' and resid 1217 through 1234 Processing helix chain 'O' and resid 1248 through 1268 Processing helix chain 'O' and resid 1280 through 1288 removed outlier: 3.754A pdb=" N ILE O1286 " --> pdb=" O GLU O1282 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU O1287 " --> pdb=" O ILE O1283 " (cutoff:3.500A) Processing helix chain 'O' and resid 1291 through 1296 Processing helix chain 'O' and resid 1298 through 1300 No H-bonds generated for 'chain 'O' and resid 1298 through 1300' Processing helix chain 'O' and resid 1338 through 1348 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.968A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 Processing helix chain 'C' and resid 80 through 88 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.959A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 111 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL D 115 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 117 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.968A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.726A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.959A pdb=" N HIS H 106 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY H 111 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 115 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS H 117 " --> pdb=" O ALA H 114 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'O' and resid 868 through 871 removed outlier: 6.681A pdb=" N TYR O 819 " --> pdb=" O VAL O 869 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR O 871 " --> pdb=" O TYR O 819 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL O 821 " --> pdb=" O THR O 871 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'O' and resid 1160 through 1162 removed outlier: 8.354A pdb=" N LEU O1161 " --> pdb=" O VAL O1106 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE O1108 " --> pdb=" O LEU O1161 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR O1177 " --> pdb=" O LEU O1107 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE O1109 " --> pdb=" O THR O1177 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE O1179 " --> pdb=" O PHE O1109 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG O1207 " --> pdb=" O VAL O1178 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ILE O1180 " --> pdb=" O ARG O1207 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU O1209 " --> pdb=" O ILE O1180 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 485 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 8.74 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3687 1.33 - 1.45: 4803 1.45 - 1.57: 8509 1.57 - 1.69: 585 1.69 - 1.81: 56 Bond restraints: 17640 Sorted by residual: bond pdb=" BE BEF O1502 " pdb=" F2 BEF O1502 " ideal model delta sigma weight residual 1.476 1.709 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" BE BEF O1502 " pdb=" F1 BEF O1502 " ideal model delta sigma weight residual 1.476 1.705 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" BE BEF O1502 " pdb=" F3 BEF O1502 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.17e+00 ... (remaining 17635 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.55: 1449 105.55 - 113.15: 10000 113.15 - 120.74: 8416 120.74 - 128.34: 4851 128.34 - 135.94: 349 Bond angle restraints: 25065 Sorted by residual: angle pdb=" F1 BEF O1502 " pdb=" BE BEF O1502 " pdb=" F3 BEF O1502 " ideal model delta sigma weight residual 120.12 99.40 20.72 3.00e+00 1.11e-01 4.77e+01 angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.25 110.03 -6.78 1.05e+00 9.07e-01 4.16e+01 angle pdb=" F2 BEF O1502 " pdb=" BE BEF O1502 " pdb=" F3 BEF O1502 " ideal model delta sigma weight residual 119.96 104.79 15.17 3.00e+00 1.11e-01 2.56e+01 angle pdb=" CA THR O 958 " pdb=" C THR O 958 " pdb=" N PRO O 959 " ideal model delta sigma weight residual 120.77 117.09 3.68 9.70e-01 1.06e+00 1.44e+01 angle pdb=" C GLU O 793 " pdb=" N MET O 794 " pdb=" CA MET O 794 " ideal model delta sigma weight residual 122.19 130.80 -8.61 2.30e+00 1.89e-01 1.40e+01 ... (remaining 25060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 8557 33.91 - 67.82: 1343 67.82 - 101.73: 14 101.73 - 135.65: 1 135.65 - 169.56: 2 Dihedral angle restraints: 9917 sinusoidal: 6007 harmonic: 3910 Sorted by residual: dihedral pdb=" CA TYR O 810 " pdb=" C TYR O 810 " pdb=" N GLU O 811 " pdb=" CA GLU O 811 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA SER O 951 " pdb=" C SER O 951 " pdb=" N PHE O 952 " pdb=" CA PHE O 952 " ideal model delta harmonic sigma weight residual -180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA PHE O1110 " pdb=" C PHE O1110 " pdb=" N GLN O1111 " pdb=" CA GLN O1111 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 9914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2368 0.046 - 0.092: 397 0.092 - 0.138: 81 0.138 - 0.184: 4 0.184 - 0.230: 4 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA PRO O 959 " pdb=" N PRO O 959 " pdb=" C PRO O 959 " pdb=" CB PRO O 959 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ASP O1184 " pdb=" N ASP O1184 " pdb=" C ASP O1184 " pdb=" CB ASP O1184 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CG LEU O 820 " pdb=" CB LEU O 820 " pdb=" CD1 LEU O 820 " pdb=" CD2 LEU O 820 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 2851 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 48 " -0.019 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" N1 DT I 48 " 0.011 2.00e-02 2.50e+03 pdb=" C2 DT I 48 " 0.032 2.00e-02 2.50e+03 pdb=" O2 DT I 48 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 48 " -0.024 2.00e-02 2.50e+03 pdb=" O4 DT I 48 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT I 48 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 48 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DT I 48 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN O1073 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO O1074 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO O1074 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO O1074 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 100 " 0.017 2.00e-02 2.50e+03 1.33e-02 4.88e+00 pdb=" N9 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" C8 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DA J 100 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 100 " 0.030 2.00e-02 2.50e+03 pdb=" N6 DA J 100 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 100 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA J 100 " -0.023 2.00e-02 2.50e+03 pdb=" N3 DA J 100 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA J 100 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 768 2.71 - 3.26: 15802 3.26 - 3.80: 30394 3.80 - 4.35: 38538 4.35 - 4.90: 55815 Nonbonded interactions: 141317 Sorted by model distance: nonbonded pdb=" O3B ADP O1501 " pdb=" F3 BEF O1502 " model vdw 2.160 2.390 nonbonded pdb=" O ARG O 880 " pdb=" OG SER O 884 " model vdw 2.170 2.440 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.179 2.440 nonbonded pdb=" O2A ADP O1501 " pdb=" F3 BEF O1502 " model vdw 2.179 2.390 nonbonded pdb=" O ASP O1301 " pdb=" OG SER O1305 " model vdw 2.188 2.440 ... (remaining 141312 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 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ )) or resid 21 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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 group one per residue 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: 0.170 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: 1.820 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 55.460 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 17640 Z= 0.216 Angle : 0.630 20.720 25065 Z= 0.364 Chirality : 0.037 0.230 2854 Planarity : 0.004 0.058 2160 Dihedral : 22.976 169.558 7377 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.20), residues: 1309 helix: -1.72 (0.16), residues: 793 sheet: -2.78 (0.49), residues: 54 loop : -1.47 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 955 HIS 0.006 0.001 HIS O 984 PHE 0.028 0.002 PHE O 946 TYR 0.035 0.002 TYR O 810 ARG 0.005 0.000 ARG O 993 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6456 (tp) cc_final: 0.5684 (mt) REVERT: O 770 TYR cc_start: 0.6638 (p90) cc_final: 0.6225 (p90) REVERT: O 792 ASP cc_start: 0.7165 (p0) cc_final: 0.6469 (p0) REVERT: O 809 LEU cc_start: 0.5287 (mt) cc_final: 0.4960 (mt) REVERT: O 812 MET cc_start: 0.6557 (mtm) cc_final: 0.5779 (mmp) REVERT: O 852 ASN cc_start: 0.8762 (m110) cc_final: 0.8556 (m-40) REVERT: O 899 MET cc_start: 0.6788 (tpt) cc_final: 0.6486 (tpp) REVERT: O 981 ARG cc_start: 0.6569 (mtm-85) cc_final: 0.6259 (tpp80) REVERT: O 1024 GLN cc_start: 0.7364 (mp10) cc_final: 0.6397 (tm-30) REVERT: O 1115 ILE cc_start: 0.8583 (mp) cc_final: 0.8287 (tt) REVERT: O 1132 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.7868 (tmm160) REVERT: O 1140 ASP cc_start: 0.8112 (m-30) cc_final: 0.7237 (t0) REVERT: O 1160 ILE cc_start: 0.7703 (mt) cc_final: 0.7467 (mp) REVERT: O 1285 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7636 (tm-30) REVERT: A 81 ASP cc_start: 0.8924 (m-30) cc_final: 0.8652 (m-30) REVERT: A 129 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6705 (tpt170) REVERT: A 131 ARG cc_start: 0.6995 (mtt180) cc_final: 0.6767 (mtt90) REVERT: B 25 ASN cc_start: 0.8702 (m-40) cc_final: 0.8343 (m110) REVERT: C 84 GLN cc_start: 0.7920 (tp40) cc_final: 0.7610 (tp40) REVERT: C 99 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7028 (mtp85) REVERT: C 108 LEU cc_start: 0.8074 (mt) cc_final: 0.7708 (mt) REVERT: E 42 ARG cc_start: 0.7541 (ttm170) cc_final: 0.7128 (mtp85) REVERT: E 90 MET cc_start: 0.8054 (mmm) cc_final: 0.7294 (mmt) REVERT: F 72 TYR cc_start: 0.8378 (m-80) cc_final: 0.8017 (m-80) REVERT: F 91 LYS cc_start: 0.8588 (tttt) cc_final: 0.8381 (ttpt) REVERT: F 93 GLN cc_start: 0.7325 (mt0) cc_final: 0.7096 (mt0) REVERT: G 64 GLU cc_start: 0.7964 (tt0) cc_final: 0.7539 (tt0) REVERT: G 94 ASN cc_start: 0.8134 (t0) cc_final: 0.7881 (t0) REVERT: G 95 LYS cc_start: 0.7487 (tptm) cc_final: 0.6945 (mtpt) REVERT: G 104 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8743 (mm-40) REVERT: H 33 SER cc_start: 0.8514 (t) cc_final: 0.8265 (p) REVERT: H 42 LEU cc_start: 0.8694 (tp) cc_final: 0.8430 (tt) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.4253 time to fit residues: 205.6160 Evaluate side-chains 192 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 681 HIS O 749 HIS O 913 HIS O 915 HIS O1025 GLN O1071 GLN O1104 HIS A 39 HIS A 68 GLN B 25 ASN D 46 HIS D 79 HIS E 68 GLN F 93 GLN H 60 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17640 Z= 0.259 Angle : 0.654 8.777 25065 Z= 0.365 Chirality : 0.039 0.179 2854 Planarity : 0.005 0.070 2160 Dihedral : 28.119 174.370 4676 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.26 % Allowed : 2.62 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.98 (0.22), residues: 1309 helix: -0.05 (0.18), residues: 788 sheet: -2.01 (0.58), residues: 54 loop : -1.37 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 777 HIS 0.006 0.001 HIS D 46 PHE 0.021 0.002 PHE O1159 TYR 0.025 0.002 TYR O 810 ARG 0.008 0.001 ARG O1084 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6431 (tp) cc_final: 0.5704 (mt) REVERT: O 809 LEU cc_start: 0.6256 (mt) cc_final: 0.5970 (mt) REVERT: O 812 MET cc_start: 0.6637 (mtm) cc_final: 0.5769 (mmp) REVERT: O 981 ARG cc_start: 0.6598 (mtm-85) cc_final: 0.6302 (tpp80) REVERT: O 1024 GLN cc_start: 0.7133 (mp10) cc_final: 0.6741 (tm-30) REVERT: O 1096 LEU cc_start: 0.8337 (mt) cc_final: 0.8071 (mt) REVERT: O 1124 ARG cc_start: 0.8146 (ttt90) cc_final: 0.7830 (mtp-110) REVERT: O 1140 ASP cc_start: 0.8190 (m-30) cc_final: 0.7120 (t0) REVERT: O 1158 CYS cc_start: 0.7926 (p) cc_final: 0.7552 (p) REVERT: O 1160 ILE cc_start: 0.8286 (mt) cc_final: 0.7888 (mp) REVERT: O 1299 ARG cc_start: 0.5782 (ptt180) cc_final: 0.5396 (mmm-85) REVERT: A 81 ASP cc_start: 0.9030 (m-30) cc_final: 0.8779 (m-30) REVERT: A 129 ARG cc_start: 0.7166 (tpt90) cc_final: 0.6919 (tmt170) REVERT: B 25 ASN cc_start: 0.8737 (m110) cc_final: 0.8493 (m110) REVERT: B 74 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8158 (mt-10) REVERT: C 42 ARG cc_start: 0.8054 (mtp180) cc_final: 0.7473 (mtp-110) REVERT: C 99 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7232 (mtp85) REVERT: C 108 LEU cc_start: 0.7768 (mt) cc_final: 0.7561 (mt) REVERT: D 79 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7962 (t-90) REVERT: E 42 ARG cc_start: 0.7532 (ttm170) cc_final: 0.7113 (mtp85) REVERT: E 129 ARG cc_start: 0.7911 (tpt-90) cc_final: 0.6901 (tpt90) REVERT: F 44 LYS cc_start: 0.8165 (tttt) cc_final: 0.7821 (tttp) REVERT: F 72 TYR cc_start: 0.8352 (m-80) cc_final: 0.7804 (m-80) REVERT: F 93 GLN cc_start: 0.7633 (mt0) cc_final: 0.7415 (mt0) REVERT: G 56 GLU cc_start: 0.8391 (tt0) cc_final: 0.8184 (tt0) REVERT: G 95 LYS cc_start: 0.7482 (tptm) cc_final: 0.7013 (mtpt) outliers start: 3 outliers final: 2 residues processed: 242 average time/residue: 0.3635 time to fit residues: 122.2436 Evaluate side-chains 181 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1237 GLN A 39 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 17640 Z= 0.451 Angle : 0.751 8.427 25065 Z= 0.414 Chirality : 0.044 0.186 2854 Planarity : 0.006 0.075 2160 Dihedral : 28.694 172.975 4676 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1309 helix: -0.07 (0.18), residues: 802 sheet: -2.46 (0.55), residues: 61 loop : -1.37 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 777 HIS 0.011 0.002 HIS O 681 PHE 0.024 0.003 PHE O1159 TYR 0.025 0.003 TYR O 810 ARG 0.011 0.001 ARG O1304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6589 (tp) cc_final: 0.5888 (mt) REVERT: O 812 MET cc_start: 0.6565 (mtm) cc_final: 0.5699 (mmp) REVERT: O 981 ARG cc_start: 0.6599 (mtm-85) cc_final: 0.6272 (tpp80) REVERT: O 1026 MET cc_start: 0.6755 (mmp) cc_final: 0.6516 (mmp) REVERT: O 1061 HIS cc_start: 0.6578 (m-70) cc_final: 0.6356 (m-70) REVERT: O 1158 CYS cc_start: 0.7782 (p) cc_final: 0.7491 (p) REVERT: O 1215 ASN cc_start: 0.8330 (m-40) cc_final: 0.7856 (m-40) REVERT: O 1299 ARG cc_start: 0.6251 (ptt180) cc_final: 0.5611 (mmm-85) REVERT: A 59 GLU cc_start: 0.8140 (tt0) cc_final: 0.7927 (pt0) REVERT: A 65 LEU cc_start: 0.8154 (mt) cc_final: 0.7910 (mp) REVERT: A 81 ASP cc_start: 0.9027 (m-30) cc_final: 0.8814 (m-30) REVERT: A 129 ARG cc_start: 0.7111 (tpt90) cc_final: 0.6733 (tmt170) REVERT: C 75 LYS cc_start: 0.7322 (mmtt) cc_final: 0.7020 (mtmt) REVERT: C 99 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7515 (mtp85) REVERT: C 111 ILE cc_start: 0.7262 (mt) cc_final: 0.7056 (tt) REVERT: D 32 GLU cc_start: 0.6220 (pp20) cc_final: 0.5590 (pp20) REVERT: D 39 TYR cc_start: 0.8139 (t80) cc_final: 0.7833 (t80) REVERT: D 82 LYS cc_start: 0.8673 (mttm) cc_final: 0.8362 (mttm) REVERT: E 42 ARG cc_start: 0.7563 (ttm170) cc_final: 0.7184 (ttt90) REVERT: E 129 ARG cc_start: 0.7976 (tpt-90) cc_final: 0.6789 (tpt90) REVERT: F 44 LYS cc_start: 0.8327 (tttt) cc_final: 0.7985 (tttp) REVERT: F 93 GLN cc_start: 0.7488 (mt0) cc_final: 0.7220 (mt0) REVERT: G 56 GLU cc_start: 0.8493 (tt0) cc_final: 0.8245 (tt0) REVERT: G 95 LYS cc_start: 0.7622 (tptm) cc_final: 0.7219 (mtpt) REVERT: H 68 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8146 (tm-30) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3487 time to fit residues: 115.6613 Evaluate side-chains 167 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 126 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1071 GLN O1237 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17640 Z= 0.199 Angle : 0.585 8.839 25065 Z= 0.333 Chirality : 0.036 0.174 2854 Planarity : 0.004 0.047 2160 Dihedral : 28.088 174.083 4676 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.17 (0.23), residues: 1309 helix: 0.75 (0.19), residues: 794 sheet: -1.57 (0.62), residues: 55 loop : -1.39 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 777 HIS 0.004 0.001 HIS F 75 PHE 0.015 0.002 PHE O1241 TYR 0.020 0.002 TYR O 810 ARG 0.005 0.000 ARG O 988 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6855 (tp) cc_final: 0.6215 (mt) REVERT: O 812 MET cc_start: 0.6237 (mtm) cc_final: 0.5710 (mmp) REVERT: O 908 LEU cc_start: 0.6576 (tt) cc_final: 0.6029 (mp) REVERT: O 981 ARG cc_start: 0.6618 (mtm-85) cc_final: 0.6307 (tpp80) REVERT: O 1140 ASP cc_start: 0.8171 (m-30) cc_final: 0.6911 (t0) REVERT: O 1150 ASN cc_start: 0.8019 (m110) cc_final: 0.7629 (t0) REVERT: O 1158 CYS cc_start: 0.7704 (p) cc_final: 0.7386 (p) REVERT: O 1161 LEU cc_start: 0.8010 (tp) cc_final: 0.7699 (tp) REVERT: O 1215 ASN cc_start: 0.8292 (m-40) cc_final: 0.7943 (m-40) REVERT: O 1299 ARG cc_start: 0.6166 (ptt180) cc_final: 0.5748 (mmm-85) REVERT: A 59 GLU cc_start: 0.7685 (tt0) cc_final: 0.7354 (pt0) REVERT: A 81 ASP cc_start: 0.9048 (m-30) cc_final: 0.8813 (m-30) REVERT: B 25 ASN cc_start: 0.8546 (m110) cc_final: 0.8102 (m110) REVERT: C 99 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7463 (mtp85) REVERT: C 111 ILE cc_start: 0.7368 (mt) cc_final: 0.7048 (tt) REVERT: D 39 TYR cc_start: 0.8040 (t80) cc_final: 0.7662 (t80) REVERT: D 82 LYS cc_start: 0.8758 (mttm) cc_final: 0.8526 (mttm) REVERT: E 42 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7013 (ttt90) REVERT: E 59 GLU cc_start: 0.6362 (tt0) cc_final: 0.5864 (pt0) REVERT: E 129 ARG cc_start: 0.7952 (tpt-90) cc_final: 0.6884 (tpt90) REVERT: F 80 THR cc_start: 0.8072 (t) cc_final: 0.7663 (p) REVERT: G 56 GLU cc_start: 0.8331 (tt0) cc_final: 0.8044 (tt0) REVERT: G 95 LYS cc_start: 0.7538 (tptm) cc_final: 0.7120 (mtpt) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3339 time to fit residues: 102.5470 Evaluate side-chains 168 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 129 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 chunk 77 optimal weight: 0.4980 chunk 136 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 3.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1071 GLN O1237 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17640 Z= 0.307 Angle : 0.644 7.866 25065 Z= 0.362 Chirality : 0.039 0.214 2854 Planarity : 0.004 0.049 2160 Dihedral : 28.378 174.840 4676 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.25 (0.23), residues: 1309 helix: 0.65 (0.19), residues: 804 sheet: -1.86 (0.59), residues: 61 loop : -1.33 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP O 777 HIS 0.004 0.001 HIS F 75 PHE 0.022 0.002 PHE O1159 TYR 0.025 0.002 TYR O 810 ARG 0.005 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6889 (tp) cc_final: 0.6247 (mt) REVERT: O 812 MET cc_start: 0.6357 (mtm) cc_final: 0.5650 (mmp) REVERT: O 981 ARG cc_start: 0.6636 (mtm-85) cc_final: 0.6340 (tpp-160) REVERT: O 1112 MET cc_start: 0.7121 (ttm) cc_final: 0.6476 (mtt) REVERT: O 1140 ASP cc_start: 0.8060 (m-30) cc_final: 0.7500 (p0) REVERT: O 1215 ASN cc_start: 0.8315 (m-40) cc_final: 0.8094 (m-40) REVERT: O 1299 ARG cc_start: 0.6149 (ptt180) cc_final: 0.5531 (mmm-85) REVERT: A 60 LEU cc_start: 0.8143 (mt) cc_final: 0.7868 (mt) REVERT: A 81 ASP cc_start: 0.9045 (m-30) cc_final: 0.8806 (m-30) REVERT: C 99 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7233 (mtp85) REVERT: D 32 GLU cc_start: 0.6039 (pp20) cc_final: 0.5465 (pp20) REVERT: D 39 TYR cc_start: 0.8195 (t80) cc_final: 0.7795 (t80) REVERT: E 42 ARG cc_start: 0.7283 (ttm170) cc_final: 0.6854 (ttt90) REVERT: E 59 GLU cc_start: 0.6986 (tt0) cc_final: 0.6253 (pt0) REVERT: E 129 ARG cc_start: 0.8049 (tpt-90) cc_final: 0.6870 (tpt90) REVERT: F 44 LYS cc_start: 0.8374 (tttt) cc_final: 0.7943 (tttp) REVERT: G 56 GLU cc_start: 0.8423 (tt0) cc_final: 0.8172 (tt0) REVERT: G 92 GLU cc_start: 0.8900 (mp0) cc_final: 0.8688 (mp0) REVERT: G 95 LYS cc_start: 0.7622 (tptm) cc_final: 0.7155 (mtpt) REVERT: H 68 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8097 (tm-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3145 time to fit residues: 92.9643 Evaluate side-chains 174 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN A 39 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS F 25 ASN F 93 GLN G 73 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17640 Z= 0.383 Angle : 0.694 9.378 25065 Z= 0.387 Chirality : 0.041 0.209 2854 Planarity : 0.005 0.048 2160 Dihedral : 28.569 173.672 4676 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1309 helix: 0.56 (0.18), residues: 793 sheet: -1.85 (0.60), residues: 61 loop : -1.45 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 777 HIS 0.006 0.001 HIS D 79 PHE 0.027 0.002 PHE O1159 TYR 0.026 0.002 TYR D 80 ARG 0.007 0.001 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6443 (tp) cc_final: 0.5833 (mt) REVERT: O 812 MET cc_start: 0.6619 (mtm) cc_final: 0.5846 (mmp) REVERT: O 952 PHE cc_start: 0.6194 (m-10) cc_final: 0.5948 (m-10) REVERT: O 981 ARG cc_start: 0.6574 (mtm-85) cc_final: 0.6309 (tpp-160) REVERT: O 1140 ASP cc_start: 0.7911 (m-30) cc_final: 0.7406 (p0) REVERT: O 1299 ARG cc_start: 0.6038 (ptt180) cc_final: 0.5288 (ttm170) REVERT: A 39 HIS cc_start: 0.7581 (t-170) cc_final: 0.7030 (m-70) REVERT: A 60 LEU cc_start: 0.8397 (mt) cc_final: 0.7859 (mt) REVERT: C 73 ASN cc_start: 0.8659 (t0) cc_final: 0.8288 (t0) REVERT: C 75 LYS cc_start: 0.7691 (mtmt) cc_final: 0.7246 (mtmt) REVERT: C 99 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7320 (mtp85) REVERT: D 32 GLU cc_start: 0.6034 (pp20) cc_final: 0.5431 (pp20) REVERT: E 42 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6817 (ttt90) REVERT: E 59 GLU cc_start: 0.6792 (tt0) cc_final: 0.6320 (pt0) REVERT: E 120 MET cc_start: 0.8200 (mtp) cc_final: 0.7968 (mtp) REVERT: E 129 ARG cc_start: 0.8037 (tpt-90) cc_final: 0.6848 (tpt90) REVERT: F 44 LYS cc_start: 0.8428 (tttt) cc_final: 0.8028 (tttp) REVERT: F 93 GLN cc_start: 0.7506 (mt0) cc_final: 0.7304 (mt0) REVERT: G 56 GLU cc_start: 0.8398 (tt0) cc_final: 0.8194 (tt0) REVERT: G 92 GLU cc_start: 0.8935 (mp0) cc_final: 0.8724 (mp0) REVERT: G 95 LYS cc_start: 0.7623 (tptm) cc_final: 0.7236 (mtpt) REVERT: H 68 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8188 (tm-30) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3147 time to fit residues: 89.8898 Evaluate side-chains 166 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN A 68 GLN D 81 ASN F 18 HIS F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17640 Z= 0.238 Angle : 0.605 8.880 25065 Z= 0.342 Chirality : 0.037 0.211 2854 Planarity : 0.004 0.046 2160 Dihedral : 28.238 172.991 4676 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.00 (0.23), residues: 1309 helix: 0.88 (0.19), residues: 797 sheet: -1.80 (0.61), residues: 61 loop : -1.27 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP O 777 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.002 PHE O1159 TYR 0.026 0.002 TYR D 80 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6627 (tp) cc_final: 0.6035 (mt) REVERT: O 812 MET cc_start: 0.6493 (mtm) cc_final: 0.5931 (mmp) REVERT: O 981 ARG cc_start: 0.6465 (mtm-85) cc_final: 0.6196 (tpp-160) REVERT: O 1112 MET cc_start: 0.7099 (ttm) cc_final: 0.6447 (mtt) REVERT: O 1150 ASN cc_start: 0.8103 (m110) cc_final: 0.7555 (t0) REVERT: O 1194 GLN cc_start: 0.7725 (tp-100) cc_final: 0.7487 (tp-100) REVERT: O 1299 ARG cc_start: 0.6107 (ptt180) cc_final: 0.5352 (ttm170) REVERT: A 39 HIS cc_start: 0.7546 (t-170) cc_final: 0.7099 (m-70) REVERT: A 60 LEU cc_start: 0.8262 (mt) cc_final: 0.7820 (mt) REVERT: C 99 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7297 (mtp85) REVERT: D 32 GLU cc_start: 0.6034 (pp20) cc_final: 0.5392 (pp20) REVERT: D 44 GLN cc_start: 0.8906 (tt0) cc_final: 0.8663 (tt0) REVERT: E 129 ARG cc_start: 0.8111 (tpt-90) cc_final: 0.6897 (tpt90) REVERT: F 44 LYS cc_start: 0.8462 (tttt) cc_final: 0.7998 (tttp) REVERT: F 80 THR cc_start: 0.8121 (t) cc_final: 0.7851 (p) REVERT: G 56 GLU cc_start: 0.8317 (tt0) cc_final: 0.8059 (tt0) REVERT: G 95 LYS cc_start: 0.7652 (tptm) cc_final: 0.7191 (mtpt) REVERT: H 68 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8111 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3106 time to fit residues: 89.7623 Evaluate side-chains 168 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 18 HIS G 73 ASN H 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17640 Z= 0.168 Angle : 0.568 8.497 25065 Z= 0.322 Chirality : 0.035 0.206 2854 Planarity : 0.004 0.045 2160 Dihedral : 27.930 172.912 4676 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.09 % Allowed : 1.05 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1309 helix: 1.21 (0.19), residues: 796 sheet: -1.09 (0.72), residues: 48 loop : -1.22 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP O 777 HIS 0.005 0.001 HIS O1061 PHE 0.013 0.002 PHE O1241 TYR 0.021 0.001 TYR O 810 ARG 0.006 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6676 (tp) cc_final: 0.6039 (mt) REVERT: O 812 MET cc_start: 0.6734 (mtm) cc_final: 0.6152 (mmp) REVERT: O 908 LEU cc_start: 0.6826 (tt) cc_final: 0.6389 (mp) REVERT: O 1112 MET cc_start: 0.7028 (ttm) cc_final: 0.6279 (mtt) REVERT: O 1150 ASN cc_start: 0.7983 (m110) cc_final: 0.7343 (t0) REVERT: O 1157 LEU cc_start: 0.7338 (mt) cc_final: 0.7137 (mt) REVERT: O 1184 ASP cc_start: 0.4353 (p0) cc_final: 0.4078 (p0) REVERT: O 1299 ARG cc_start: 0.6007 (ptt180) cc_final: 0.5262 (ttm170) REVERT: A 39 HIS cc_start: 0.7584 (t-170) cc_final: 0.7132 (m-70) REVERT: A 60 LEU cc_start: 0.8302 (mt) cc_final: 0.7798 (mt) REVERT: C 27 VAL cc_start: 0.8929 (t) cc_final: 0.8659 (p) REVERT: C 99 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7238 (mtp85) REVERT: D 118 TYR cc_start: 0.8503 (t80) cc_final: 0.8229 (t80) REVERT: E 129 ARG cc_start: 0.8040 (tpt-90) cc_final: 0.6816 (tpt90) REVERT: F 44 LYS cc_start: 0.8441 (tttt) cc_final: 0.8235 (mtpt) REVERT: F 80 THR cc_start: 0.8015 (t) cc_final: 0.7705 (p) REVERT: G 50 TYR cc_start: 0.8626 (t80) cc_final: 0.8329 (t80) REVERT: G 56 GLU cc_start: 0.8265 (tt0) cc_final: 0.8024 (tt0) REVERT: G 84 GLN cc_start: 0.7721 (tp40) cc_final: 0.7299 (tp40) REVERT: G 89 ASN cc_start: 0.7785 (t0) cc_final: 0.7205 (t0) REVERT: G 95 LYS cc_start: 0.7504 (tptm) cc_final: 0.7047 (mtpt) REVERT: G 100 VAL cc_start: 0.8376 (t) cc_final: 0.7943 (p) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2964 time to fit residues: 87.5082 Evaluate side-chains 167 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 79 HIS D 81 ASN E 68 GLN F 18 HIS F 93 GLN G 38 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17640 Z= 0.408 Angle : 0.711 8.102 25065 Z= 0.396 Chirality : 0.043 0.215 2854 Planarity : 0.005 0.048 2160 Dihedral : 28.624 172.875 4676 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.09 % Allowed : 1.40 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.26 (0.23), residues: 1309 helix: 0.65 (0.19), residues: 799 sheet: -1.86 (0.67), residues: 54 loop : -1.36 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 777 HIS 0.008 0.002 HIS D 46 PHE 0.025 0.003 PHE O1159 TYR 0.030 0.002 TYR D 80 ARG 0.007 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6689 (tp) cc_final: 0.6067 (mt) REVERT: O 812 MET cc_start: 0.6713 (mtm) cc_final: 0.5996 (mmp) REVERT: O 908 LEU cc_start: 0.6666 (tt) cc_final: 0.6255 (mp) REVERT: O 1150 ASN cc_start: 0.7782 (m110) cc_final: 0.7270 (t0) REVERT: O 1299 ARG cc_start: 0.5976 (ptt180) cc_final: 0.5210 (ttm170) REVERT: A 39 HIS cc_start: 0.7527 (t-170) cc_final: 0.7118 (m-70) REVERT: A 60 LEU cc_start: 0.8356 (mt) cc_final: 0.7971 (mt) REVERT: C 99 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7249 (mtp85) REVERT: D 118 TYR cc_start: 0.8586 (t80) cc_final: 0.8219 (t80) REVERT: E 90 MET cc_start: 0.7600 (mmt) cc_final: 0.6989 (ttp) REVERT: E 129 ARG cc_start: 0.8066 (tpt-90) cc_final: 0.6897 (tpt90) REVERT: F 44 LYS cc_start: 0.8411 (tttt) cc_final: 0.8019 (tttp) REVERT: F 80 THR cc_start: 0.8195 (t) cc_final: 0.7794 (p) REVERT: G 56 GLU cc_start: 0.8534 (tt0) cc_final: 0.8318 (tt0) REVERT: G 92 GLU cc_start: 0.8821 (mp0) cc_final: 0.8531 (mp0) REVERT: G 95 LYS cc_start: 0.7637 (tptm) cc_final: 0.7171 (mtpt) REVERT: H 68 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8190 (tm-30) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.3047 time to fit residues: 87.6899 Evaluate side-chains 169 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 156 optimal weight: 20.0000 chunk 143 optimal weight: 30.0000 chunk 124 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17640 Z= 0.186 Angle : 0.591 7.881 25065 Z= 0.334 Chirality : 0.037 0.210 2854 Planarity : 0.004 0.045 2160 Dihedral : 28.099 171.762 4676 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.16 (0.24), residues: 1309 helix: 1.02 (0.19), residues: 797 sheet: -1.67 (0.68), residues: 54 loop : -1.27 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP O 777 HIS 0.004 0.001 HIS O1198 PHE 0.014 0.002 PHE O1159 TYR 0.024 0.002 TYR O 810 ARG 0.006 0.000 ARG H 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 762 LEU cc_start: 0.6698 (tp) cc_final: 0.6073 (mt) REVERT: O 812 MET cc_start: 0.6576 (mtm) cc_final: 0.6186 (mmp) REVERT: O 908 LEU cc_start: 0.6842 (tt) cc_final: 0.6450 (mp) REVERT: O 1112 MET cc_start: 0.6886 (ttm) cc_final: 0.6282 (mtt) REVERT: O 1150 ASN cc_start: 0.7888 (m110) cc_final: 0.7348 (t0) REVERT: O 1184 ASP cc_start: 0.4131 (p0) cc_final: 0.3893 (p0) REVERT: O 1299 ARG cc_start: 0.5912 (ptt180) cc_final: 0.4930 (ttm170) REVERT: A 39 HIS cc_start: 0.7544 (t-170) cc_final: 0.7134 (m-70) REVERT: B 25 ASN cc_start: 0.8472 (m110) cc_final: 0.7974 (m110) REVERT: C 41 GLU cc_start: 0.8741 (tt0) cc_final: 0.8476 (tt0) REVERT: C 75 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7774 (mtmm) REVERT: C 99 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7270 (mtp85) REVERT: D 32 GLU cc_start: 0.5800 (pp20) cc_final: 0.5245 (pp20) REVERT: D 118 TYR cc_start: 0.8507 (t80) cc_final: 0.8058 (t80) REVERT: E 129 ARG cc_start: 0.8076 (tpt-90) cc_final: 0.6867 (tpt90) REVERT: F 44 LYS cc_start: 0.8454 (tttt) cc_final: 0.8206 (mtpt) REVERT: F 80 THR cc_start: 0.8112 (t) cc_final: 0.7806 (p) REVERT: G 56 GLU cc_start: 0.8397 (tt0) cc_final: 0.8121 (tt0) REVERT: G 89 ASN cc_start: 0.7770 (t0) cc_final: 0.7351 (t0) REVERT: G 95 LYS cc_start: 0.7533 (tptm) cc_final: 0.7007 (mtpt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3250 time to fit residues: 90.1818 Evaluate side-chains 163 residues out of total 1161 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 897 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 913 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1071 GLN ** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 81 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114107 restraints weight = 27976.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112941 restraints weight = 53213.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112697 restraints weight = 54118.548| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17640 Z= 0.323 Angle : 0.662 9.734 25065 Z= 0.370 Chirality : 0.040 0.211 2854 Planarity : 0.005 0.080 2160 Dihedral : 28.434 179.898 4676 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.09 (0.24), residues: 1309 helix: 0.80 (0.19), residues: 788 sheet: -1.77 (0.68), residues: 54 loop : -1.28 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 777 HIS 0.006 0.001 HIS D 46 PHE 0.022 0.002 PHE O1159 TYR 0.055 0.002 TYR D 80 ARG 0.006 0.001 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2750.97 seconds wall clock time: 51 minutes 16.78 seconds (3076.78 seconds total)