Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 16:57:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cgv_16652/10_2023/8cgv_16652_updated.pdb" } resolution = 1.66 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= 0.006 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: 9 Type Number sf(0) Gaussians K 83 8.98 5 Zn 1 6.06 5 P 2743 5.49 5 Mg 219 5.21 5 S 69 5.16 5 C 40149 2.51 5 N 15147 2.21 5 O 29486 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 ARG 4": "NH1" <-> "NH2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "c TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 74": "OE1" <-> "OE2" Residue "d GLU 88": "OE1" <-> "OE2" Residue "d PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "i TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 86": "OE1" <-> "OE2" Residue "l PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 111": "OE1" <-> "OE2" Residue "l PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 20": "OE1" <-> "OE2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 25": "OE1" <-> "OE2" Residue "s GLU 54": "OE1" <-> "OE2" Residue "s GLU 56": "OE1" <-> "OE2" Residue "s GLU 89": "OE1" <-> "OE2" Residue "t GLU 37": "OE1" <-> "OE2" Residue "t PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 87899 Number of models: 1 Model: "" Number of chains: 67 Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 57720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2687, 57720 Classifications: {'RNA': 2687} Modifications used: {'rna2p': 7, 'rna2p_pur': 262, 'rna2p_pyr': 140, 'rna3p': 14, 'rna3p_pur': 1288, 'rna3p_pyr': 976} Link IDs: {'rna2p': 408, 'rna3p': 2278} Chain breaks: 7 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Chain: "b" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1209 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 18} Link IDs: {'rna2p': 8, 'rna3p': 47} Chain breaks: 1 Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1552 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "g" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1292 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "h" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 204 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain breaks: 1 Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 l 81 " pdbres="MS6 l 82 " Not linked: pdbres="MS6 l 82 " pdbres="GLY l 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 213 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 722 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "t" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 728 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 1 Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 444 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 400 Unusual residues: {' K': 76, ' MG': 210, 'MUL': 1, 'P8F': 2} Classifications: {'undetermined': 289} Link IDs: {None: 288} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' K': 4, ' MG': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "1" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "a" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5631, 5631 Classifications: {'water': 5631} Link IDs: {None: 5630} Chain: "b" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "c" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "e" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "j" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "k" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "l" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "m" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "n" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "p" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "q" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "r" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "t" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "u" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "v" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "w" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "x" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "z" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 23.284 73.297 153.054 1.00 39.35 S ATOM 1408 SG CYS 3 14 27.393 72.910 152.795 1.00 33.50 S ATOM 1511 SG CYS 3 27 24.752 70.326 151.558 1.00 37.42 S Time building chain proxies: 35.32, per 1000 atoms: 0.40 Number of scatterers: 87899 At special positions: 0 Unit cell: (194.549, 196.82, 213.474, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 K 83 19.00 S 69 16.00 P 2743 15.00 Mg 219 11.99 F 2 9.00 O 29486 8.00 N 15147 7.00 C 40149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 44.08 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " Number of angles added : 3 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 46 sheets defined 26.4% alpha, 21.0% beta 956 base pairs and 1435 stacking pairs defined. Time for finding SS restraints: 43.50 Creating SS restraints... Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 11 No H-bonds generated for 'chain '2' and resid 8 through 11' Processing helix chain '2' and resid 38 through 45 Processing helix chain '2' and resid 52 through 61 removed outlier: 4.578A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain 'c' and resid 31 through 33 No H-bonds generated for 'chain 'c' and resid 31 through 33' Processing helix chain 'c' and resid 132 through 134 No H-bonds generated for 'chain 'c' and resid 132 through 134' Processing helix chain 'c' and resid 198 through 202 removed outlier: 3.925A pdb=" N MET c 201 " --> pdb=" O ALA c 198 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 214 removed outlier: 3.597A pdb=" N ARG c 214 " --> pdb=" O ALA c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 222 through 224 No H-bonds generated for 'chain 'c' and resid 222 through 224' Processing helix chain 'c' and resid 264 through 266 No H-bonds generated for 'chain 'c' and resid 264 through 266' Processing helix chain 'd' and resid 40 through 43 No H-bonds generated for 'chain 'd' and resid 40 through 43' Processing helix chain 'd' and resid 57 through 59 No H-bonds generated for 'chain 'd' and resid 57 through 59' Processing helix chain 'd' and resid 62 through 71 removed outlier: 3.502A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 101 Processing helix chain 'd' and resid 121 through 125 Processing helix chain 'e' and resid 16 through 19 No H-bonds generated for 'chain 'e' and resid 16 through 19' Processing helix chain 'e' and resid 25 through 38 Processing helix chain 'e' and resid 98 through 114 Processing helix chain 'e' and resid 131 through 140 Processing helix chain 'e' and resid 155 through 161 Processing helix chain 'e' and resid 172 through 174 No H-bonds generated for 'chain 'e' and resid 172 through 174' Processing helix chain 'e' and resid 177 through 182 Processing helix chain 'e' and resid 190 through 200 Processing helix chain 'g' and resid 3 through 6 No H-bonds generated for 'chain 'g' and resid 3 through 6' Processing helix chain 'g' and resid 61 through 78 Processing helix chain 'g' and resid 138 through 152 removed outlier: 3.632A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 23 through 28 Processing helix chain 'i' and resid 25 through 37 removed outlier: 3.847A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 59 through 61 No H-bonds generated for 'chain 'i' and resid 59 through 61' Processing helix chain 'i' and resid 68 through 71 No H-bonds generated for 'chain 'i' and resid 68 through 71' Processing helix chain 'i' and resid 89 through 108 Proline residue: i 97 - end of helix removed outlier: 4.096A pdb=" N VAL i 100 " --> pdb=" O ARG i 96 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 113 through 121 removed outlier: 4.002A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 133 through 135 No H-bonds generated for 'chain 'i' and resid 133 through 135' Processing helix chain 'j' and resid 105 through 107 No H-bonds generated for 'chain 'j' and resid 105 through 107' Processing helix chain 'j' and resid 110 through 118 removed outlier: 3.778A pdb=" N MET j 113 " --> pdb=" O GLU j 110 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS j 114 " --> pdb=" O LYS j 111 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 40 No H-bonds generated for 'chain 'k' and resid 38 through 40' Processing helix chain 'k' and resid 57 through 60 No H-bonds generated for 'chain 'k' and resid 57 through 60' Processing helix chain 'k' and resid 69 through 73 removed outlier: 3.868A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 69 through 73' Processing helix chain 'k' and resid 79 through 84 removed outlier: 4.063A pdb=" N ALA k 83 " --> pdb=" O SER k 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 97 Processing helix chain 'k' and resid 129 through 137 Processing helix chain 'l' and resid 43 through 56 Processing helix chain 'l' and resid 110 through 123 removed outlier: 4.087A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 31 Processing helix chain 'm' and resid 38 through 56 removed outlier: 4.315A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix Processing helix chain 'm' and resid 60 through 70 Processing helix chain 'm' and resid 73 through 81 Processing helix chain 'm' and resid 83 through 86 No H-bonds generated for 'chain 'm' and resid 83 through 86' Processing helix chain 'n' and resid 4 through 21 removed outlier: 4.538A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 12 removed outlier: 4.089A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 56 No H-bonds generated for 'chain 'o' and resid 54 through 56' Processing helix chain 'o' and resid 98 through 102 Processing helix chain 'o' and resid 105 through 108 Processing helix chain 'p' and resid 7 through 21 Processing helix chain 'p' and resid 26 through 29 Processing helix chain 'p' and resid 32 through 72 removed outlier: 3.602A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 85 Processing helix chain 'p' and resid 92 through 101 Processing helix chain 'p' and resid 103 through 117 Processing helix chain 'r' and resid 14 through 24 removed outlier: 3.539A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 37 Processing helix chain 'r' and resid 42 through 62 Processing helix chain 'r' and resid 66 through 68 No H-bonds generated for 'chain 'r' and resid 66 through 68' Processing helix chain 'r' and resid 89 through 91 No H-bonds generated for 'chain 'r' and resid 89 through 91' Processing helix chain 's' and resid 4 through 10 removed outlier: 3.511A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 27 Processing helix chain 's' and resid 40 through 51 Processing helix chain 't' and resid 67 through 69 No H-bonds generated for 'chain 't' and resid 67 through 69' Processing helix chain 'u' and resid 14 through 22 Processing helix chain 'u' and resid 44 through 52 Processing helix chain 'u' and resid 54 through 58 removed outlier: 3.525A pdb=" N SER u 58 " --> pdb=" O GLU u 55 " (cutoff:3.500A) Processing helix chain 'w' and resid 53 through 62 Processing helix chain 'w' and resid 64 through 73 Processing helix chain 'x' and resid 3 through 8 removed outlier: 3.733A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 34 Processing helix chain 'x' and resid 40 through 61 removed outlier: 3.502A pdb=" N LYS x 44 " --> pdb=" O HIS x 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL x 46 " --> pdb=" O LEU x 43 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU x 57 " --> pdb=" O LYS x 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS x 60 " --> pdb=" O LEU x 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 27 Processing helix chain 'y' and resid 42 through 54 removed outlier: 5.479A pdb=" N PHE y 53 " --> pdb=" O ASN y 49 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET y 54 " --> pdb=" O ALA y 50 " (cutoff:3.500A) Processing helix chain 'z' and resid 10 through 19 removed outlier: 4.843A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 20 through 25 Processing sheet with id= B, first strand: chain '2' and resid 14 through 16 Processing sheet with id= C, first strand: chain '3' and resid 2 through 4 Processing sheet with id= D, first strand: chain '3' and resid 14 through 19 Processing sheet with id= E, first strand: chain 'c' and resid 3 through 5 Processing sheet with id= F, first strand: chain 'c' and resid 34 through 36 Processing sheet with id= G, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.336A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 129 through 131 Processing sheet with id= I, first strand: chain 'c' and resid 181 through 185 removed outlier: 6.583A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'd' and resid 169 through 172 removed outlier: 4.581A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS d 190 " --> pdb=" O VAL d 177 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL d 177 " --> pdb=" O LYS d 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.422A pdb=" N THR d 51 " --> pdb=" O VAL d 34 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL d 34 " --> pdb=" O THR d 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 115 through 119 removed outlier: 5.573A pdb=" N MET d 165 " --> pdb=" O LYS d 116 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE d 118 " --> pdb=" O GLY d 163 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY d 163 " --> pdb=" O PHE d 118 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'e' and resid 2 through 4 Processing sheet with id= N, first strand: chain 'e' and resid 118 through 121 removed outlier: 6.255A pdb=" N VAL e 186 " --> pdb=" O ILE e 119 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL e 121 " --> pdb=" O VAL e 186 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET e 188 " --> pdb=" O VAL e 121 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'g' and resid 17 through 19 Processing sheet with id= P, first strand: chain 'g' and resid 41 through 44 Processing sheet with id= Q, first strand: chain 'g' and resid 161 through 164 Processing sheet with id= R, first strand: chain 'g' and resid 95 through 99 Processing sheet with id= S, first strand: chain 'h' and resid 3 through 5 Processing sheet with id= T, first strand: chain 'i' and resid 15 through 19 removed outlier: 6.490A pdb=" N TYR i 53 " --> pdb=" O TYR i 16 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL i 18 " --> pdb=" O TYR i 53 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE i 55 " --> pdb=" O VAL i 18 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'i' and resid 73 through 77 Processing sheet with id= V, first strand: chain 'j' and resid 7 through 9 removed outlier: 6.448A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL j 24 " --> pdb=" O ILE j 38 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE j 38 " --> pdb=" O VAL j 24 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'k' and resid 74 through 78 removed outlier: 6.685A pdb=" N PHE k 107 " --> pdb=" O ALA k 75 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE k 77 " --> pdb=" O PHE k 107 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS k 109 " --> pdb=" O ILE k 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'k' and resid 121 through 123 removed outlier: 6.599A pdb=" N LYS k 141 " --> pdb=" O VAL k 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'l' and resid 128 through 132 removed outlier: 3.512A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA l 35 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL l 101 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'l' and resid 39 through 42 removed outlier: 6.923A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'm' and resid 33 through 37 Processing sheet with id= AB, first strand: chain 'o' and resid 83 through 88 removed outlier: 6.475A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS o 37 " --> pdb=" O GLU o 34 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLU o 44 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE o 64 " --> pdb=" O GLU o 44 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR o 60 " --> pdb=" O ILE o 48 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE o 50 " --> pdb=" O ALA o 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA o 58 " --> pdb=" O ILE o 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'q' and resid 10 through 14 removed outlier: 3.618A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN q 6 " --> pdb=" O VAL q 38 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL q 38 " --> pdb=" O GLN q 6 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'q' and resid 19 through 23 Processing sheet with id= AE, first strand: chain 'q' and resid 32 through 35 removed outlier: 6.418A pdb=" N GLU q 62 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE q 98 " --> pdb=" O GLU q 62 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'q' and resid 72 through 78 removed outlier: 4.208A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'r' and resid 2 through 7 removed outlier: 6.791A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'r' and resid 82 through 87 Processing sheet with id= AI, first strand: chain 's' and resid 11 through 14 removed outlier: 6.623A pdb=" N LYS s 33 " --> pdb=" O ARG s 12 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL s 31 " --> pdb=" O PRO s 14 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS s 81 " --> pdb=" O VAL s 34 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 's' and resid 67 through 69 Processing sheet with id= AK, first strand: chain 't' and resid 22 through 24 removed outlier: 6.010A pdb=" N GLU t 10 " --> pdb=" O PHE t 73 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE t 72 " --> pdb=" O ASP t 81 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 't' and resid 41 through 46 Processing sheet with id= AM, first strand: chain 't' and resid 83 through 88 Processing sheet with id= AN, first strand: chain 't' and resid 25 through 29 removed outlier: 6.570A pdb=" N ILE t 35 " --> pdb=" O LYS t 26 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL t 28 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS t 33 " --> pdb=" O VAL t 28 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'u' and resid 61 through 65 removed outlier: 6.275A pdb=" N PHE u 2 " --> pdb=" O THR u 62 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL u 64 " --> pdb=" O PHE u 2 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE u 4 " --> pdb=" O VAL u 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN u 5 " --> pdb=" O ASP u 43 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP u 43 " --> pdb=" O ASN u 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL u 92 " --> pdb=" O ALA u 74 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA u 74 " --> pdb=" O VAL u 92 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'v' and resid 45 through 47 removed outlier: 6.658A pdb=" N LYS v 78 " --> pdb=" O HIS v 46 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'v' and resid 51 through 53 Processing sheet with id= AR, first strand: chain 'w' and resid 13 through 18 Processing sheet with id= AS, first strand: chain 'w' and resid 33 through 40 Processing sheet with id= AT, first strand: chain 'y' and resid 35 through 39 736 hydrogen bonds defined for protein. 2010 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2399 hydrogen bonds 3718 hydrogen bond angles 0 basepair planarities 956 basepair parallelities 1435 stacking parallelities Total time for adding SS restraints: 498.78 Time building geometry restraints manager: 46.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8152 1.32 - 1.45: 40258 1.45 - 1.58: 34380 1.58 - 1.70: 5477 1.70 - 1.83: 124 Bond restraints: 88391 Sorted by residual: bond pdb=" C9 P8F a3002 " pdb=" O5 P8F a3002 " ideal model delta sigma weight residual 0.000 1.329 -1.329 2.00e-02 2.50e+03 4.42e+03 bond pdb=" C9 P8F a3001 " pdb=" O5 P8F a3001 " ideal model delta sigma weight residual 0.000 1.327 -1.327 2.00e-02 2.50e+03 4.40e+03 bond pdb=" C11 P8F a3002 " pdb=" O6 P8F a3002 " ideal model delta sigma weight residual 0.132 1.261 -1.129 2.00e-02 2.50e+03 3.19e+03 bond pdb=" C11 P8F a3001 " pdb=" O6 P8F a3001 " ideal model delta sigma weight residual 0.132 1.258 -1.126 2.00e-02 2.50e+03 3.17e+03 bond pdb=" C29 P8F a3001 " pdb=" C3 P8F a3001 " ideal model delta sigma weight residual 0.954 1.552 -0.598 2.00e-02 2.50e+03 8.94e+02 ... (remaining 88386 not shown) Histogram of bond angle deviations from ideal: 86.73 - 96.35: 106 96.35 - 105.97: 16793 105.97 - 115.59: 58498 115.59 - 125.21: 46605 125.21 - 134.83: 10943 Bond angle restraints: 132945 Sorted by residual: angle pdb=" C1' 6MZ a1618 " pdb=" N9 6MZ a1618 " pdb=" C8 6MZ a1618 " ideal model delta sigma weight residual 91.39 128.49 -37.10 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C1' 6MZ a2030 " pdb=" N9 6MZ a2030 " pdb=" C8 6MZ a2030 " ideal model delta sigma weight residual 91.39 127.95 -36.56 3.00e+00 1.11e-01 1.49e+02 angle pdb=" O3' U a1971 " pdb=" P G a1972 " pdb=" O5' G a1972 " ideal model delta sigma weight residual 104.00 86.73 17.27 1.50e+00 4.44e-01 1.33e+02 angle pdb=" C1' 6MZ a1618 " pdb=" N9 6MZ a1618 " pdb=" C4 6MZ a1618 " ideal model delta sigma weight residual 154.15 124.78 29.37 3.00e+00 1.11e-01 9.58e+01 angle pdb=" C1' 6MZ a2030 " pdb=" N9 6MZ a2030 " pdb=" C4 6MZ a2030 " ideal model delta sigma weight residual 154.15 125.29 28.86 3.00e+00 1.11e-01 9.25e+01 ... (remaining 132940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 45463 36.00 - 72.00: 1182 72.00 - 108.00: 141 108.00 - 144.00: 6 144.00 - 180.00: 7 Dihedral angle restraints: 46799 sinusoidal: 38837 harmonic: 7962 Sorted by residual: dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 61.00 139.00 1 1.50e+01 4.44e-03 7.49e+01 dihedral pdb=" O4' U a2321 " pdb=" C1' U a2321 " pdb=" N1 U a2321 " pdb=" C2 U a2321 " ideal model delta sinusoidal sigma weight residual 200.00 63.77 136.23 1 1.50e+01 4.44e-03 7.35e+01 dihedral pdb=" O4' C a 323 " pdb=" C1' C a 323 " pdb=" N1 C a 323 " pdb=" C2 C a 323 " ideal model delta sinusoidal sigma weight residual 232.00 52.00 180.00 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 46796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.182: 15724 0.182 - 0.364: 1250 0.364 - 0.545: 8 0.545 - 0.727: 10 0.727 - 0.909: 2 Chirality restraints: 16994 Sorted by residual: chirality pdb=" C8 P8F a3001 " pdb=" C29 P8F a3001 " pdb=" C7 P8F a3001 " pdb=" C9 P8F a3001 " both_signs ideal model delta sigma weight residual True 1.74 -2.65 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C8 P8F a3002 " pdb=" C29 P8F a3002 " pdb=" C7 P8F a3002 " pdb=" C9 P8F a3002 " both_signs ideal model delta sigma weight residual True 1.74 -2.65 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" P A a2191 " pdb=" OP1 A a2191 " pdb=" OP2 A a2191 " pdb=" O5' A a2191 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.31e+00 ... (remaining 16991 not shown) Planarity restraints: 6593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M a2069 " 0.096 2.00e-02 2.50e+03 6.42e-01 9.28e+03 pdb=" C4' G7M a2069 " 0.485 2.00e-02 2.50e+03 pdb=" O4' G7M a2069 " 0.755 2.00e-02 2.50e+03 pdb=" C3' G7M a2069 " -0.611 2.00e-02 2.50e+03 pdb=" O3' G7M a2069 " -0.682 2.00e-02 2.50e+03 pdb=" C2' G7M a2069 " -0.162 2.00e-02 2.50e+03 pdb=" O2' G7M a2069 " 0.979 2.00e-02 2.50e+03 pdb=" C1' G7M a2069 " 0.164 2.00e-02 2.50e+03 pdb=" N9 G7M a2069 " -1.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 6MZ a1618 " 0.941 2.00e-02 2.50e+03 6.26e-01 8.81e+03 pdb=" C4' 6MZ a1618 " -0.200 2.00e-02 2.50e+03 pdb=" O4' 6MZ a1618 " -0.775 2.00e-02 2.50e+03 pdb=" C3' 6MZ a1618 " 0.183 2.00e-02 2.50e+03 pdb=" O3' 6MZ a1618 " -0.954 2.00e-02 2.50e+03 pdb=" C2' 6MZ a1618 " 0.646 2.00e-02 2.50e+03 pdb=" O2' 6MZ a1618 " 0.664 2.00e-02 2.50e+03 pdb=" C1' 6MZ a1618 " -0.439 2.00e-02 2.50e+03 pdb=" N9 6MZ a1618 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC a2498 " 0.059 2.00e-02 2.50e+03 6.03e-01 8.19e+03 pdb=" C4' OMC a2498 " 0.432 2.00e-02 2.50e+03 pdb=" O4' OMC a2498 " 0.674 2.00e-02 2.50e+03 pdb=" C3' OMC a2498 " -0.630 2.00e-02 2.50e+03 pdb=" O3' OMC a2498 " -0.635 2.00e-02 2.50e+03 pdb=" C2' OMC a2498 " -0.168 2.00e-02 2.50e+03 pdb=" O2' OMC a2498 " 0.960 2.00e-02 2.50e+03 pdb=" C1' OMC a2498 " 0.222 2.00e-02 2.50e+03 pdb=" N1 OMC a2498 " -0.913 2.00e-02 2.50e+03 ... (remaining 6590 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.46: 1260 2.46 - 3.13: 74727 3.13 - 3.80: 225088 3.80 - 4.47: 338231 4.47 - 5.14: 439323 Nonbonded interactions: 1078629 Sorted by model distance: nonbonded pdb=" OP2 A a2682 " pdb="MG MG a3032 " model vdw 1.795 2.170 nonbonded pdb="MG MG a3116 " pdb=" O HOH a4277 " model vdw 1.861 2.170 nonbonded pdb="MG MG a3175 " pdb=" O HOH a3320 " model vdw 1.880 2.170 nonbonded pdb=" OP1 U a1249 " pdb="MG MG a3138 " model vdw 1.889 2.170 nonbonded pdb=" OP2 A a 975 " pdb="MG MG a3147 " model vdw 1.890 2.170 ... (remaining 1078624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 24.330 Check model and map are aligned: 1.000 Set scattering table: 0.600 Process input model: 690.060 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:14.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 738.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.015 1.329 88391 Z= 0.924 Angle : 1.597 37.102 132945 Z= 0.953 Chirality : 0.106 0.909 16994 Planarity : 0.031 0.642 6593 Dihedral : 13.636 179.997 41673 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.35 % Allowed : 3.06 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 2753 helix: -0.17 (0.17), residues: 724 sheet: -0.52 (0.19), residues: 640 loop : -0.15 (0.15), residues: 1389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 614 time to evaluate : 3.926 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 621 average time/residue: 2.3518 time to fit residues: 1884.3780 Evaluate side-chains 532 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 530 time to evaluate : 3.971 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 4.2477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 458 optimal weight: 0.6980 chunk 411 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 425 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 316 optimal weight: 3.9990 chunk 493 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 21 ASN c 37 ASN d 32 ASN e 136 GLN i 138 GLN j 5 GLN j 88 ASN l 3 GLN m 18 GLN p 44 GLN p 71 GLN q 86 GLN r 31 GLN t 40 ASN u 75 GLN w 36 HIS x 27 ASN x 58 ASN z 42 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 88391 Z= 0.197 Angle : 0.790 20.018 132945 Z= 0.428 Chirality : 0.040 0.313 16994 Planarity : 0.009 0.152 6593 Dihedral : 13.454 176.653 36130 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.92 % Allowed : 7.78 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.30 (0.15), residues: 2753 helix: 0.91 (0.19), residues: 727 sheet: -0.22 (0.19), residues: 621 loop : 0.16 (0.15), residues: 1405 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 551 time to evaluate : 3.913 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 560 average time/residue: 2.3683 time to fit residues: 1710.1618 Evaluate side-chains 544 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 534 time to evaluate : 3.969 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.4019 time to fit residues: 12.6760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 274 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 493 optimal weight: 4.9990 chunk 533 optimal weight: 5.9990 chunk 439 optimal weight: 4.9990 chunk 489 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 21 ASN c 37 ASN d 32 ASN i 138 GLN j 88 ASN l 3 GLN m 18 GLN o 7 GLN q 86 GLN r 31 GLN t 40 ASN u 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 88391 Z= 0.199 Angle : 0.791 20.020 132945 Z= 0.428 Chirality : 0.040 0.313 16994 Planarity : 0.009 0.152 6593 Dihedral : 13.457 176.652 36130 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.31 % Allowed : 9.62 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.30 (0.15), residues: 2753 helix: 0.91 (0.19), residues: 727 sheet: -0.22 (0.19), residues: 621 loop : 0.16 (0.15), residues: 1405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 537 time to evaluate : 4.011 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 544 average time/residue: 2.4069 time to fit residues: 1689.1795 Evaluate side-chains 532 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 526 time to evaluate : 3.903 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 488 optimal weight: 2.9990 chunk 371 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 495 optimal weight: 8.9990 chunk 524 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 469 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 43 HIS c 37 ASN d 32 ASN j 88 ASN l 3 GLN m 18 GLN q 86 GLN r 31 GLN t 40 ASN u 5 ASN u 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 88391 Z= 0.440 Angle : 1.153 23.475 132945 Z= 0.578 Chirality : 0.052 0.355 16994 Planarity : 0.012 0.179 6593 Dihedral : 13.443 178.904 36130 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.18 % Allowed : 8.87 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.03 (0.15), residues: 2753 helix: 0.38 (0.18), residues: 725 sheet: -0.25 (0.19), residues: 632 loop : 0.04 (0.15), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 533 time to evaluate : 4.009 Fit side-chains outliers start: 27 outliers final: 15 residues processed: 547 average time/residue: 2.3383 time to fit residues: 1654.9692 Evaluate side-chains 542 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 527 time to evaluate : 3.918 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 7 residues processed: 8 average time/residue: 1.2474 time to fit residues: 19.6682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 437 optimal weight: 0.9980 chunk 297 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 390 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 447 optimal weight: 0.6980 chunk 362 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 471 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 37 ASN d 32 ASN d 49 GLN j 88 ASN l 3 GLN m 81 ASN o 7 GLN o 115 ASN q 86 GLN r 31 GLN t 40 ASN u 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 88391 Z= 0.223 Angle : 0.805 19.778 132945 Z= 0.436 Chirality : 0.041 0.299 16994 Planarity : 0.009 0.147 6593 Dihedral : 13.463 178.823 36130 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.96 % Allowed : 9.62 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.22 (0.15), residues: 2753 helix: 0.70 (0.18), residues: 723 sheet: -0.17 (0.19), residues: 621 loop : 0.15 (0.15), residues: 1409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 520 time to evaluate : 4.069 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 531 average time/residue: 2.3363 time to fit residues: 1608.5233 Evaluate side-chains 518 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 506 time to evaluate : 3.900 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 1.1522 time to fit residues: 15.1684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 176 optimal weight: 9.9990 chunk 472 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 308 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 525 optimal weight: 5.9990 chunk 436 optimal weight: 2.9990 chunk 243 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN g 20 ASN j 88 ASN l 3 GLN m 81 ASN o 7 GLN q 86 GLN r 31 GLN t 40 ASN u 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 88391 Z= 0.326 Angle : 0.971 19.961 132945 Z= 0.502 Chirality : 0.046 0.328 16994 Planarity : 0.010 0.153 6593 Dihedral : 13.433 179.030 36130 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.92 % Allowed : 10.31 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.13 (0.15), residues: 2753 helix: 0.55 (0.18), residues: 723 sheet: -0.21 (0.19), residues: 634 loop : 0.14 (0.15), residues: 1396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 524 time to evaluate : 3.964 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 537 average time/residue: 2.3358 time to fit residues: 1624.3322 Evaluate side-chains 537 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 527 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 1.2447 time to fit residues: 13.9593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 506 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 383 optimal weight: 0.3980 chunk 297 optimal weight: 5.9990 chunk 442 optimal weight: 4.9990 chunk 293 optimal weight: 2.9990 chunk 523 optimal weight: 2.9990 chunk 327 optimal weight: 0.0060 chunk 319 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN j 88 ASN l 3 GLN m 81 ASN q 86 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 ASN u 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 88391 Z= 0.192 Angle : 0.754 16.668 132945 Z= 0.415 Chirality : 0.039 0.298 16994 Planarity : 0.008 0.144 6593 Dihedral : 13.452 179.018 36130 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.70 % Allowed : 10.45 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.32 (0.15), residues: 2753 helix: 0.79 (0.19), residues: 725 sheet: -0.11 (0.20), residues: 611 loop : 0.21 (0.15), residues: 1417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 528 time to evaluate : 3.980 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 538 average time/residue: 2.3416 time to fit residues: 1636.0921 Evaluate side-chains 528 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 519 time to evaluate : 3.899 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.7246 time to fit residues: 9.8541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 323 optimal weight: 0.5980 chunk 209 optimal weight: 10.0000 chunk 312 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN j 88 ASN l 3 GLN m 81 ASN o 7 GLN q 86 GLN r 31 GLN t 40 ASN u 75 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 88391 Z= 0.308 Angle : 0.932 18.346 132945 Z= 0.484 Chirality : 0.045 0.306 16994 Planarity : 0.010 0.152 6593 Dihedral : 13.417 178.846 36130 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.79 % Allowed : 10.62 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.15), residues: 2753 helix: 0.66 (0.18), residues: 723 sheet: -0.16 (0.19), residues: 632 loop : 0.21 (0.16), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 525 time to evaluate : 4.199 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 534 average time/residue: 2.3662 time to fit residues: 1642.8735 Evaluate side-chains 529 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 519 time to evaluate : 3.901 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.0020 time to fit residues: 10.8666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 476 optimal weight: 7.9990 chunk 501 optimal weight: 1.9990 chunk 457 optimal weight: 0.8980 chunk 487 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 382 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 440 optimal weight: 0.6980 chunk 461 optimal weight: 6.9990 chunk 486 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN j 88 ASN l 3 GLN m 81 ASN o 7 GLN q 86 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 ASN u 75 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 88391 Z= 0.308 Angle : 0.932 18.348 132945 Z= 0.484 Chirality : 0.045 0.306 16994 Planarity : 0.010 0.152 6593 Dihedral : 13.418 178.846 36130 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.39 % Allowed : 11.10 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 (0.15), residues: 2753 helix: 0.66 (0.18), residues: 723 sheet: -0.16 (0.19), residues: 632 loop : 0.21 (0.16), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 520 time to evaluate : 3.999 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 527 average time/residue: 2.3612 time to fit residues: 1613.5524 Evaluate side-chains 525 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 519 time to evaluate : 3.973 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.2910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 320 optimal weight: 8.9990 chunk 515 optimal weight: 0.9990 chunk 314 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 358 optimal weight: 9.9990 chunk 540 optimal weight: 3.9990 chunk 497 optimal weight: 10.0000 chunk 430 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 332 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN j 88 ASN l 3 GLN m 81 ASN o 7 GLN q 86 GLN ** r 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 ASN u 75 GLN x 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 88391 Z= 0.237 Angle : 0.833 18.197 132945 Z= 0.446 Chirality : 0.041 0.300 16994 Planarity : 0.009 0.150 6593 Dihedral : 13.431 178.926 36130 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.61 % Allowed : 10.88 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: 0.27 (0.15), residues: 2753 helix: 0.71 (0.19), residues: 723 sheet: -0.16 (0.19), residues: 632 loop : 0.22 (0.16), residues: 1398 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5506 Ramachandran restraints generated. 2753 Oldfield, 0 Emsley, 2753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 517 time to evaluate : 4.094 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 528 average time/residue: 2.3793 time to fit residues: 1629.3154 Evaluate side-chains 522 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 514 time to evaluate : 3.940 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.7633 time to fit residues: 6.7127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 543 random chunks: chunk 342 optimal weight: 4.9990 chunk 458 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 397 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 431 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 443 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 79 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 32 ASN j 88 ASN l 3 GLN m 81 ASN q 86 GLN r 31 GLN t 40 ASN u 75 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.161030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.127799 restraints weight = 45433.414| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 0.35 r_work: 0.3107 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 1.36 restraints_weight: 0.2500 r_work: 0.2933 rms_B_bonded: 2.47 restraints_weight: 0.1250 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.140 88391 Z= 0.512 Angle : 1.266 24.967 132945 Z= 0.621 Chirality : 0.056 0.363 16994 Planarity : 0.012 0.187 6593 Dihedral : 13.480 178.767 36130 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.79 % Allowed : 10.49 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.10 (0.15), residues: 2753 helix: 0.22 (0.18), residues: 723 sheet: -0.24 (0.19), residues: 648 loop : 0.03 (0.15), residues: 1382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30325.59 seconds wall clock time: 530 minutes 44.87 seconds (31844.87 seconds total)