Starting phenix.real_space_refine on Mon Nov 20 11:29:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qq3_14121/11_2023/7qq3_14121_updated.pdb" } resolution = 2.1 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= 0.010 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3016 5.49 5 Mg 145 5.21 5 S 67 5.16 5 C 43087 2.51 5 N 16316 2.21 5 O 24962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 87594 Number of models: 1 Model: "" Number of chains: 35 Chain: "I" Number of atoms: 62225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 62225 Classifications: {'RNA': 2898} Modifications used: {'rna2p': 4, 'rna2p_pur': 278, 'rna2p_pyr': 153, 'rna3p': 14, 'rna3p_pur': 1389, 'rna3p_pyr': 1060} Link IDs: {'rna2p': 435, 'rna3p': 2462} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Chain: "J" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2531 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 58, 'rna3p_pyr': 48} Link IDs: {'rna2p': 12, 'rna3p': 105} Chain: "K" 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: "L" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" 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: "O" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "R" 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: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "U" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "V" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "X" 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: "Y" 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: "Z" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "a" 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: "b" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "d" 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: "e" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} 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: 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: "g" 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: "h" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "i" 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: "j" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" 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: "l" 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: "m" 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: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 119 Unusual residues: {'AG2': 1, 'IB9': 1, 'IVA': 1} Classifications: {'peptide': 13, 'undetermined': 3} Modifications used: {'PEPT-D': 6} Link IDs: {'TRANS': 11, None: 4} Not linked: pdbres="IVA B 1 " pdbres="RXL B 2 " Not linked: pdbres="DVA B 6 " pdbres="IB9 B 7 " Not linked: pdbres="IB9 B 7 " pdbres="DVA B 8 " Not linked: pdbres="DHV B 15 " pdbres="AG2 B 16 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'IVA:plan-1': 1, 'MAA:plan-1': 1, 'RX9:plan-1': 1, 'IB9:plan-2': 1, 'RXL:plan-1': 2, 'DHV:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 141 Unusual residues: {' MG': 141} Classifications: {'undetermined': 141} Link IDs: {None: 140} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 87084 SG CYS m 11 119.971 71.233 177.435 1.00 70.17 S ATOM 87109 SG CYS m 14 118.344 74.573 175.611 1.00 66.22 S ATOM 87212 SG CYS m 27 121.636 74.448 177.176 1.00 64.86 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG I3129 " occ=0.50 residue: pdb="MG MG I3130 " occ=0.50 Time building chain proxies: 33.00, per 1000 atoms: 0.38 Number of scatterers: 87594 At special positions: 0 Unit cell: (200.376, 196.236, 223.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 67 16.00 P 3016 15.00 Mg 145 11.99 O 24962 8.00 N 16316 7.00 C 43087 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.10 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" ND1 HIS m 33 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 27 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 11 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 14 " Number of angles added : 3 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA B 5 " pdb=" CB DVA B 6 " pdb=" CB DVA B 8 " pdb=" CB DAR B 10 " pdb=" CB DVA B 12 " pdb=" CB DAL B 14 " Input volumes are d-peptide like pdb=" CB RX9 B 13 " pdb=" CB DHV B 15 " Number of C-beta restraints generated: 5282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 46 sheets defined 26.2% alpha, 20.4% beta 1006 base pairs and 1615 stacking pairs defined. Time for finding SS restraints: 42.41 Creating SS restraints... Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 132 through 134 No H-bonds generated for 'chain 'K' and resid 132 through 134' Processing helix chain 'K' and resid 198 through 202 removed outlier: 4.157A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 264 through 266 No H-bonds generated for 'chain 'K' and resid 264 through 266' Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing helix chain 'L' and resid 62 through 71 removed outlier: 3.561A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 101 Processing helix chain 'L' and resid 121 through 125 Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 98 through 114 Processing helix chain 'M' and resid 131 through 140 Processing helix chain 'M' and resid 155 through 161 Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 Processing helix chain 'O' and resid 3 through 6 No H-bonds generated for 'chain 'O' and resid 3 through 6' Processing helix chain 'O' and resid 62 through 80 Processing helix chain 'O' and resid 138 through 152 removed outlier: 3.672A pdb=" N TYR O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 37 removed outlier: 3.785A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'R' and resid 68 through 71 No H-bonds generated for 'chain 'R' and resid 68 through 71' Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 97 through 108 removed outlier: 4.191A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 121 removed outlier: 4.112A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 135 No H-bonds generated for 'chain 'R' and resid 133 through 135' Processing helix chain 'S' and resid 113 through 118 Processing helix chain 'T' and resid 38 through 40 No H-bonds generated for 'chain 'T' and resid 38 through 40' Processing helix chain 'T' and resid 57 through 60 No H-bonds generated for 'chain 'T' and resid 57 through 60' Processing helix chain 'T' and resid 71 through 73 No H-bonds generated for 'chain 'T' and resid 71 through 73' Processing helix chain 'T' and resid 79 through 84 removed outlier: 3.656A pdb=" N ALA T 83 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 97 Processing helix chain 'T' and resid 129 through 137 Processing helix chain 'U' and resid 43 through 56 Processing helix chain 'U' and resid 110 through 123 removed outlier: 4.127A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 31 Processing helix chain 'V' and resid 38 through 56 removed outlier: 4.357A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Proline residue: V 50 - end of helix Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 73 through 81 Processing helix chain 'V' and resid 83 through 86 No H-bonds generated for 'chain 'V' and resid 83 through 86' Processing helix chain 'W' and resid 3 through 21 removed outlier: 4.643A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 61 removed outlier: 4.022A pdb=" N GLN W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 85 Processing helix chain 'W' and resid 102 through 113 Processing helix chain 'X' and resid 3 through 12 removed outlier: 4.003A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 56 No H-bonds generated for 'chain 'X' and resid 54 through 56' Processing helix chain 'X' and resid 98 through 102 Processing helix chain 'X' and resid 105 through 108 Processing helix chain 'Y' and resid 7 through 21 removed outlier: 3.539A pdb=" N GLN Y 20 " --> pdb=" O LYS Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 29 Processing helix chain 'Y' and resid 32 through 72 removed outlier: 3.646A pdb=" N GLN Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG Y 55 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 85 Processing helix chain 'Y' and resid 92 through 101 Processing helix chain 'Y' and resid 103 through 117 Processing helix chain 'a' and resid 14 through 24 removed outlier: 3.534A pdb=" N LEU a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 37 Processing helix chain 'a' and resid 42 through 61 Processing helix chain 'a' and resid 66 through 68 No H-bonds generated for 'chain 'a' and resid 66 through 68' Processing helix chain 'a' and resid 89 through 91 No H-bonds generated for 'chain 'a' and resid 89 through 91' Processing helix chain 'b' and resid 4 through 9 removed outlier: 3.845A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 27 Processing helix chain 'b' and resid 40 through 50 Processing helix chain 'c' and resid 67 through 69 No H-bonds generated for 'chain 'c' and resid 67 through 69' Processing helix chain 'd' and resid 14 through 23 Processing helix chain 'd' and resid 44 through 52 removed outlier: 3.603A pdb=" N ALA d 52 " --> pdb=" O MET d 48 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 57 Processing helix chain 'f' and resid 53 through 62 Processing helix chain 'f' and resid 64 through 74 Processing helix chain 'g' and resid 4 through 8 Processing helix chain 'g' and resid 11 through 34 Processing helix chain 'g' and resid 40 through 61 removed outlier: 4.836A pdb=" N VAL g 46 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG g 47 " --> pdb=" O LYS g 44 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG g 48 " --> pdb=" O GLN g 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 18 through 27 Processing helix chain 'h' and resid 42 through 54 removed outlier: 5.465A pdb=" N PHE h 53 " --> pdb=" O ASN h 49 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET h 54 " --> pdb=" O ALA h 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 19 removed outlier: 4.948A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 16 Processing helix chain 'k' and resid 18 through 23 Processing helix chain 'k' and resid 25 through 37 Processing helix chain 'l' and resid 8 through 12 Processing helix chain 'l' and resid 38 through 45 Processing helix chain 'l' and resid 52 through 61 removed outlier: 4.555A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) Processing helix chain 'm' and resid 31 through 33 No H-bonds generated for 'chain 'm' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.586A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 3.500A pdb=" N ALA K 166 " --> pdb=" O THR K 173 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 169 through 172 removed outlier: 4.721A pdb=" N THR L 112 " --> pdb=" O ASP L 200 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASP L 200 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL L 26 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET L 11 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL L 24 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG L 13 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE L 22 " --> pdb=" O ARG L 13 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS L 190 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL L 177 " --> pdb=" O LYS L 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 80 through 83 removed outlier: 6.380A pdb=" N THR L 51 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL L 34 " --> pdb=" O THR L 51 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.637A pdb=" N MET L 165 " --> pdb=" O LYS L 116 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE L 118 " --> pdb=" O GLY L 163 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY L 163 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 2 through 4 Processing sheet with id= J, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.330A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 16 through 20 Processing sheet with id= L, first strand: chain 'O' and resid 41 through 46 Processing sheet with id= M, first strand: chain 'O' and resid 161 through 164 removed outlier: 3.602A pdb=" N VAL O 90 " --> pdb=" O GLY O 161 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 95 through 99 Processing sheet with id= O, first strand: chain 'R' and resid 15 through 19 removed outlier: 6.518A pdb=" N TYR R 53 " --> pdb=" O TYR R 16 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL R 18 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE R 55 " --> pdb=" O VAL R 18 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'R' and resid 73 through 77 Processing sheet with id= Q, first strand: chain 'S' and resid 7 through 9 removed outlier: 6.623A pdb=" N LYS S 40 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N VAL S 24 " --> pdb=" O ILE S 38 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE S 38 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS S 59 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA S 83 " --> pdb=" O VAL S 63 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'T' and resid 74 through 78 removed outlier: 6.645A pdb=" N PHE T 107 " --> pdb=" O ALA T 75 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE T 77 " --> pdb=" O PHE T 107 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LYS T 109 " --> pdb=" O ILE T 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'T' and resid 121 through 123 removed outlier: 6.490A pdb=" N LYS T 141 " --> pdb=" O VAL T 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'U' and resid 128 through 132 removed outlier: 3.672A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA U 35 " --> pdb=" O VAL U 101 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL U 101 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'U' and resid 39 through 42 removed outlier: 6.844A pdb=" N ILE U 73 " --> pdb=" O GLU U 90 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TRP U 92 " --> pdb=" O LYS U 71 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS U 71 " --> pdb=" O TRP U 92 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 33 through 37 removed outlier: 3.840A pdb=" N GLY V 101 " --> pdb=" O MET V 110 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR V 112 " --> pdb=" O LYS V 99 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS V 99 " --> pdb=" O TYR V 112 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU V 114 " --> pdb=" O ILE V 97 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE V 97 " --> pdb=" O GLU V 114 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'W' and resid 91 through 93 removed outlier: 3.676A pdb=" N VAL W 28 " --> pdb=" O ASP W 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL W 49 " --> pdb=" O VAL W 39 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 83 through 88 removed outlier: 3.636A pdb=" N SER X 83 " --> pdb=" O LYS X 29 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N GLU X 44 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE X 64 " --> pdb=" O GLU X 44 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR X 60 " --> pdb=" O ILE X 48 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE X 50 " --> pdb=" O ALA X 58 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA X 58 " --> pdb=" O ILE X 50 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 11 through 15 removed outlier: 3.627A pdb=" N MET Z 40 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN Z 6 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL Z 38 " --> pdb=" O GLN Z 6 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 19 through 23 Processing sheet with id= AA, first strand: chain 'Z' and resid 32 through 35 removed outlier: 6.451A pdb=" N GLU Z 62 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE Z 98 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Z' and resid 72 through 78 removed outlier: 4.213A pdb=" N TYR Z 83 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'a' and resid 2 through 7 removed outlier: 6.757A pdb=" N SER a 108 " --> pdb=" O VAL a 71 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N VAL a 71 " --> pdb=" O SER a 108 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'a' and resid 82 through 87 Processing sheet with id= AE, first strand: chain 'b' and resid 11 through 14 removed outlier: 6.658A pdb=" N LYS b 33 " --> pdb=" O ARG b 12 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL b 31 " --> pdb=" O PRO b 14 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS b 81 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL b 57 " --> pdb=" O THR b 86 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'b' and resid 67 through 70 Processing sheet with id= AG, first strand: chain 'c' and resid 22 through 24 Processing sheet with id= AH, first strand: chain 'c' and resid 41 through 45 Processing sheet with id= AI, first strand: chain 'c' and resid 83 through 88 Processing sheet with id= AJ, first strand: chain 'c' and resid 25 through 29 removed outlier: 6.826A pdb=" N ILE c 35 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL c 28 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS c 33 " --> pdb=" O VAL c 28 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'd' and resid 62 through 65 removed outlier: 7.927A pdb=" N ASN d 5 " --> pdb=" O ASP d 43 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASP d 43 " --> pdb=" O ASN d 5 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE d 89 " --> pdb=" O ILE d 29 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR d 31 " --> pdb=" O ILE d 89 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE d 91 " --> pdb=" O TYR d 31 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL d 92 " --> pdb=" O ALA d 74 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ALA d 74 " --> pdb=" O VAL d 92 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'e' and resid 45 through 47 removed outlier: 6.709A pdb=" N LYS e 78 " --> pdb=" O HIS e 46 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'e' and resid 51 through 53 Processing sheet with id= AN, first strand: chain 'f' and resid 13 through 18 Processing sheet with id= AO, first strand: chain 'f' and resid 33 through 40 Processing sheet with id= AP, first strand: chain 'h' and resid 35 through 38 Processing sheet with id= AQ, first strand: chain 'j' and resid 6 through 12 Processing sheet with id= AR, first strand: chain 'j' and resid 36 through 40 Processing sheet with id= AS, first strand: chain 'm' and resid 2 through 4 Processing sheet with id= AT, first strand: chain 'm' and resid 14 through 19 746 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2530 hydrogen bonds 3964 hydrogen bond angles 0 basepair planarities 1006 basepair parallelities 1615 stacking parallelities Total time for adding SS restraints: 159.12 Time building geometry restraints manager: 37.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 6507 1.27 - 1.40: 30674 1.40 - 1.54: 51926 1.54 - 1.67: 6255 1.67 - 1.81: 122 Bond restraints: 95484 Sorted by residual: bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.802 1.437 0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.438 0.364 2.00e-02 2.50e+03 3.31e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.635 1.368 0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.635 1.369 0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" N3 5MU I 747 " pdb=" C4 5MU I 747 " ideal model delta sigma weight residual 1.182 1.373 -0.191 2.00e-02 2.50e+03 9.16e+01 ... (remaining 95479 not shown) Histogram of bond angle deviations from ideal: 99.26 - 107.09: 19829 107.09 - 114.93: 60725 114.93 - 122.76: 45704 122.76 - 130.60: 16461 130.60 - 138.43: 1163 Bond angle restraints: 143882 Sorted by residual: angle pdb=" CG1 RXL B 2 " pdb=" CB RXL B 2 " pdb=" CG2 RXL B 2 " ideal model delta sigma weight residual 68.18 113.73 -45.55 3.00e+00 1.11e-01 2.31e+02 angle pdb=" CG1 RXL B 9 " pdb=" CB RXL B 9 " pdb=" CG2 RXL B 9 " ideal model delta sigma weight residual 68.18 113.55 -45.37 3.00e+00 1.11e-01 2.29e+02 angle pdb=" CA RXL B 9 " pdb=" CB RXL B 9 " pdb=" CG2 RXL B 9 " ideal model delta sigma weight residual 85.86 125.57 -39.71 3.00e+00 1.11e-01 1.75e+02 angle pdb=" CA RXL B 2 " pdb=" CB RXL B 2 " pdb=" CG2 RXL B 2 " ideal model delta sigma weight residual 85.86 124.60 -38.74 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C8 1MG I 745 " ideal model delta sigma weight residual 100.16 138.43 -38.27 3.00e+00 1.11e-01 1.63e+02 ... (remaining 143877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 48302 35.64 - 71.28: 1922 71.28 - 106.92: 146 106.92 - 142.57: 5 142.57 - 178.21: 12 Dihedral angle restraints: 50387 sinusoidal: 42175 harmonic: 8212 Sorted by residual: dihedral pdb=" N IB9 B 7 " pdb=" C IB9 B 7 " pdb=" CA IB9 B 7 " pdb=" CB IB9 B 7 " ideal model delta harmonic sigma weight residual 122.80 32.75 90.05 0 2.50e+00 1.60e-01 1.30e+03 dihedral pdb=" C RXL B 9 " pdb=" N RXL B 9 " pdb=" CA RXL B 9 " pdb=" CB RXL B 9 " ideal model delta harmonic sigma weight residual -122.60 -179.86 57.26 0 2.50e+00 1.60e-01 5.25e+02 dihedral pdb=" N RXL B 9 " pdb=" C RXL B 9 " pdb=" CA RXL B 9 " pdb=" CB RXL B 9 " ideal model delta harmonic sigma weight residual 122.80 179.84 -57.04 0 2.50e+00 1.60e-01 5.20e+02 ... (remaining 50384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 17450 0.088 - 0.176: 957 0.176 - 0.264: 55 0.264 - 0.352: 3 0.352 - 0.440: 1 Chirality restraints: 18466 Sorted by residual: chirality pdb=" CA DAR B 10 " pdb=" N DAR B 10 " pdb=" C DAR B 10 " pdb=" CB DAR B 10 " both_signs ideal model delta sigma weight residual False -2.51 -2.07 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" C3' A I2425 " pdb=" C4' A I2425 " pdb=" O3' A I2425 " pdb=" C2' A I2425 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" P G I1842 " pdb=" OP1 G I1842 " pdb=" OP2 G I1842 " pdb=" O5' G I1842 " both_signs ideal model delta sigma weight residual True 2.41 -2.69 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 18463 not shown) Planarity restraints: 6987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MG I 745 " 0.032 2.00e-02 2.50e+03 5.97e-01 8.01e+03 pdb=" C4' 1MG I 745 " 0.456 2.00e-02 2.50e+03 pdb=" O4' 1MG I 745 " 0.718 2.00e-02 2.50e+03 pdb=" C3' 1MG I 745 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 1MG I 745 " -0.588 2.00e-02 2.50e+03 pdb=" C2' 1MG I 745 " -0.212 2.00e-02 2.50e+03 pdb=" O2' 1MG I 745 " 0.907 2.00e-02 2.50e+03 pdb=" C1' 1MG I 745 " 0.212 2.00e-02 2.50e+03 pdb=" N9 1MG I 745 " -0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.049 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' OMC I2498 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.609 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.603 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.619 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.178 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.962 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.230 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.881 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.027 2.00e-02 2.50e+03 5.84e-01 7.66e+03 pdb=" C4' 2MG I2445 " -0.445 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.572 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.220 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.901 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.895 2.00e-02 2.50e+03 ... (remaining 6984 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 210 2.45 - 3.06: 49733 3.06 - 3.67: 158884 3.67 - 4.29: 265924 4.29 - 4.90: 338539 Nonbonded interactions: 813290 Sorted by model distance: nonbonded pdb=" OP1 C I1774 " pdb="MG MG I3043 " model vdw 1.832 2.170 nonbonded pdb=" OP1 U I1782 " pdb="MG MG I3082 " model vdw 1.832 2.170 nonbonded pdb=" OP1 U I 120 " pdb="MG MG I3004 " model vdw 1.874 2.170 nonbonded pdb=" OP2 G I1333 " pdb="MG MG I3032 " model vdw 1.878 2.170 nonbonded pdb=" OP2 G I 15 " pdb="MG MG I3058 " model vdw 1.881 2.170 ... (remaining 813285 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=0.50 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: 2.470 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: 0.080 Extract box with map and model: 12.530 Check model and map are aligned: 0.960 Set scattering table: 0.590 Process input model: 340.070 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.190 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:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 367.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 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 : 0.008 0.365 95484 Z= 0.460 Angle : 0.764 45.554 143882 Z= 0.426 Chirality : 0.047 0.440 18466 Planarity : 0.021 0.597 6987 Dihedral : 14.941 178.207 45105 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.55 % Favored : 96.03 % Rotamer: Outliers : 4.22 % Allowed : 7.68 % Favored : 88.10 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 2843 helix: 1.30 (0.18), residues: 750 sheet: -0.39 (0.19), residues: 662 loop : -0.91 (0.14), residues: 1431 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 412 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 26 residues processed: 488 average time/residue: 2.0511 time to fit residues: 1293.8954 Evaluate side-chains 348 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 322 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 1.6484 time to fit residues: 12.4444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 489 optimal weight: 9.9990 chunk 439 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 454 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 338 optimal weight: 3.9990 chunk 526 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 GLN M 92 HIS O 38 ASN R 67 ASN R 76 HIS W 29 HIS X 75 GLN Y 56 GLN a 9 HIS b 28 ASN j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 95484 Z= 0.440 Angle : 1.337 38.482 143882 Z= 0.637 Chirality : 0.058 0.358 18466 Planarity : 0.011 0.163 6987 Dihedral : 14.558 178.108 39427 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 4.09 % Allowed : 12.67 % Favored : 83.24 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 2843 helix: 0.53 (0.18), residues: 765 sheet: -0.20 (0.19), residues: 680 loop : -0.84 (0.15), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 331 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 52 residues processed: 393 average time/residue: 2.0630 time to fit residues: 1052.3635 Evaluate side-chains 382 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 330 time to evaluate : 3.314 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 37 residues processed: 15 average time/residue: 1.3675 time to fit residues: 32.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 292 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 438 optimal weight: 4.9990 chunk 358 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 527 optimal weight: 5.9990 chunk 570 optimal weight: 5.9990 chunk 469 optimal weight: 1.9990 chunk 523 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 423 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 ASN R 67 ASN R 76 HIS Y 59 GLN a 9 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 95484 Z= 0.440 Angle : 1.337 38.482 143882 Z= 0.637 Chirality : 0.058 0.358 18466 Planarity : 0.011 0.163 6987 Dihedral : 14.558 178.108 39427 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 1.62 % Allowed : 15.82 % Favored : 82.56 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 2843 helix: 0.53 (0.18), residues: 765 sheet: -0.20 (0.19), residues: 680 loop : -0.84 (0.15), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 330 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 37 residues processed: 368 average time/residue: 2.1100 time to fit residues: 1003.8706 Evaluate side-chains 365 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 37 residues processed: 0 time to fit residues: 3.5240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 521 optimal weight: 4.9990 chunk 396 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 529 optimal weight: 0.6980 chunk 560 optimal weight: 4.9990 chunk 276 optimal weight: 10.0000 chunk 501 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS a 9 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 95484 Z= 0.440 Angle : 1.337 38.482 143882 Z= 0.637 Chirality : 0.058 0.358 18466 Planarity : 0.011 0.163 6987 Dihedral : 14.558 178.108 39427 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 1.62 % Allowed : 15.82 % Favored : 82.56 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 2843 helix: 0.53 (0.18), residues: 765 sheet: -0.20 (0.19), residues: 680 loop : -0.84 (0.15), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 328 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 36 residues processed: 366 average time/residue: 2.0923 time to fit residues: 993.1350 Evaluate side-chains 364 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 328 time to evaluate : 3.380 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 36 residues processed: 0 time to fit residues: 3.4919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 466 optimal weight: 0.9990 chunk 318 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 417 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 478 optimal weight: 4.9990 chunk 387 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 503 optimal weight: 7.9990 chunk 141 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: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS a 9 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 95484 Z= 0.440 Angle : 1.337 38.482 143882 Z= 0.637 Chirality : 0.058 0.358 18466 Planarity : 0.011 0.163 6987 Dihedral : 14.558 178.108 39427 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.41 % Favored : 96.24 % Rotamer: Outliers : 1.58 % Allowed : 15.86 % Favored : 82.56 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 2843 helix: 0.53 (0.18), residues: 765 sheet: -0.20 (0.19), residues: 680 loop : -0.84 (0.15), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 36 residues processed: 365 average time/residue: 2.1461 time to fit residues: 1011.9991 Evaluate side-chains 364 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 328 time to evaluate : 3.322 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 36 residues processed: 0 time to fit residues: 3.5189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 188 optimal weight: 9.9990 chunk 504 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 329 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 561 optimal weight: 9.9990 chunk 465 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN L 173 GLN M 90 GLN R 67 ASN R 76 HIS S 88 ASN V 9 GLN a 9 HIS b 28 ASN b 70 HIS ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS d 88 HIS g 58 ASN j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 95484 Z= 0.353 Angle : 1.103 32.421 143882 Z= 0.540 Chirality : 0.050 0.327 18466 Planarity : 0.010 0.154 6987 Dihedral : 14.847 178.388 39427 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.97 % Favored : 95.81 % Rotamer: Outliers : 3.58 % Allowed : 13.99 % Favored : 82.43 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.14), residues: 2843 helix: 0.33 (0.18), residues: 741 sheet: -0.25 (0.20), residues: 650 loop : -0.88 (0.15), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 344 time to evaluate : 3.894 Fit side-chains outliers start: 84 outliers final: 44 residues processed: 402 average time/residue: 2.1721 time to fit residues: 1137.1893 Evaluate side-chains 380 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 336 time to evaluate : 3.384 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 39 residues processed: 5 average time/residue: 0.8354 time to fit residues: 10.6556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 541 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 319 optimal weight: 3.9990 chunk 409 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 472 optimal weight: 7.9990 chunk 313 optimal weight: 0.8980 chunk 559 optimal weight: 10.0000 chunk 349 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS j 45 GLN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 95484 Z= 0.238 Angle : 0.865 27.569 143882 Z= 0.445 Chirality : 0.042 0.336 18466 Planarity : 0.009 0.145 6987 Dihedral : 14.654 177.880 39427 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 3.11 % Allowed : 15.22 % Favored : 81.66 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2843 helix: 0.58 (0.18), residues: 743 sheet: -0.33 (0.20), residues: 650 loop : -0.81 (0.15), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 344 time to evaluate : 3.414 Fit side-chains outliers start: 73 outliers final: 52 residues processed: 400 average time/residue: 2.0700 time to fit residues: 1077.1393 Evaluate side-chains 390 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 338 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 42 residues processed: 10 average time/residue: 1.0771 time to fit residues: 20.3549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 345 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 333 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 chunk 355 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 439 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 95484 Z= 0.241 Angle : 0.865 27.674 143882 Z= 0.445 Chirality : 0.042 0.337 18466 Planarity : 0.009 0.145 6987 Dihedral : 14.654 177.885 39427 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 1.88 % Allowed : 16.63 % Favored : 81.49 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 2843 helix: 0.58 (0.18), residues: 743 sheet: -0.33 (0.20), residues: 650 loop : -0.81 (0.15), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 337 time to evaluate : 3.696 Fit side-chains outliers start: 44 outliers final: 42 residues processed: 380 average time/residue: 2.1352 time to fit residues: 1051.3065 Evaluate side-chains 377 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 335 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 42 residues processed: 0 time to fit residues: 3.4981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 508 optimal weight: 7.9990 chunk 535 optimal weight: 5.9990 chunk 488 optimal weight: 4.9990 chunk 520 optimal weight: 8.9990 chunk 313 optimal weight: 0.0970 chunk 226 optimal weight: 10.0000 chunk 409 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 470 optimal weight: 50.0000 chunk 492 optimal weight: 0.0970 chunk 519 optimal weight: 10.0000 overall best weight: 3.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 95484 Z= 0.240 Angle : 0.871 26.950 143882 Z= 0.446 Chirality : 0.043 0.341 18466 Planarity : 0.009 0.146 6987 Dihedral : 14.628 178.099 39427 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 2.39 % Allowed : 16.20 % Favored : 81.41 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2843 helix: 0.58 (0.18), residues: 743 sheet: -0.32 (0.20), residues: 650 loop : -0.80 (0.15), residues: 1450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 337 time to evaluate : 3.383 Fit side-chains outliers start: 56 outliers final: 46 residues processed: 386 average time/residue: 2.1403 time to fit residues: 1070.5019 Evaluate side-chains 381 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 335 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 42 residues processed: 4 average time/residue: 0.9292 time to fit residues: 9.9310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 342 optimal weight: 0.0020 chunk 550 optimal weight: 4.9990 chunk 336 optimal weight: 30.0000 chunk 261 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 577 optimal weight: 0.7980 chunk 531 optimal weight: 5.9990 chunk 460 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 overall best weight: 3.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 95484 Z= 0.240 Angle : 0.871 26.950 143882 Z= 0.446 Chirality : 0.043 0.341 18466 Planarity : 0.009 0.146 6987 Dihedral : 14.628 178.099 39427 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 1.83 % Allowed : 16.67 % Favored : 81.49 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2843 helix: 0.58 (0.18), residues: 743 sheet: -0.32 (0.20), residues: 650 loop : -0.80 (0.15), residues: 1450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5686 Ramachandran restraints generated. 2843 Oldfield, 0 Emsley, 2843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 335 time to evaluate : 3.413 Fit side-chains outliers start: 43 outliers final: 42 residues processed: 378 average time/residue: 2.1848 time to fit residues: 1068.7810 Evaluate side-chains 377 residues out of total 2346 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 335 time to evaluate : 3.521 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 42 residues processed: 0 time to fit residues: 3.6318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 580 random chunks: chunk 365 optimal weight: 20.0000 chunk 490 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 424 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 460 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 473 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 4.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 67 ASN R 76 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 45 HIS ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.211882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.182916 restraints weight = 66883.680| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 0.84 r_work: 0.3628 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 95484 Z= 0.240 Angle : 0.871 26.950 143882 Z= 0.446 Chirality : 0.043 0.341 18466 Planarity : 0.009 0.146 6987 Dihedral : 14.628 178.099 39427 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.83 % Favored : 95.99 % Rotamer: Outliers : 1.83 % Allowed : 16.67 % Favored : 81.49 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2843 helix: 0.58 (0.18), residues: 743 sheet: -0.32 (0.20), residues: 650 loop : -0.80 (0.15), residues: 1450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19057.68 seconds wall clock time: 337 minutes 21.88 seconds (20241.88 seconds total)