Starting phenix.real_space_refine on Tue Mar 19 02:06:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u48_20638/03_2024/6u48_20638_neut_updated.pdb" } resolution = 2.87 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 ------------------------------------------------------------------------------- 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3016 5.49 5 S 83 5.16 5 C 45306 2.51 5 N 16939 2.21 5 O 25606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CC ARG 52": "NH1" <-> "NH2" Residue "CC ARG 63": "NH1" <-> "NH2" Residue "CC ARG 80": "NH1" <-> "NH2" Residue "CC ARG 133": "NH1" <-> "NH2" Residue "CC ARG 167": "NH1" <-> "NH2" Residue "CC ARG 177": "NH1" <-> "NH2" Residue "CC ARG 182": "NH1" <-> "NH2" Residue "CC ARG 189": "NH1" <-> "NH2" Residue "CC ARG 203": "NH1" <-> "NH2" Residue "CC ARG 212": "NH1" <-> "NH2" Residue "CD ARG 13": "NH1" <-> "NH2" Residue "CD ARG 33": "NH1" <-> "NH2" Residue "CD ARG 59": "NH1" <-> "NH2" Residue "CD ARG 77": "NH1" <-> "NH2" Residue "CD ARG 83": "NH1" <-> "NH2" Residue "CD ARG 169": "NH1" <-> "NH2" Residue "CD ARG 184": "NH1" <-> "NH2" Residue "CE ARG 21": "NH1" <-> "NH2" Residue "CE ARG 44": "NH1" <-> "NH2" Residue "CE ARG 49": "NH1" <-> "NH2" Residue "CE ARG 61": "NH1" <-> "NH2" Residue "CE ARG 88": "NH1" <-> "NH2" Residue "CE ARG 102": "NH1" <-> "NH2" Residue "CE ARG 162": "NH1" <-> "NH2" Residue "CE ARG 170": "NH1" <-> "NH2" Residue "CF ARG 71": "NH1" <-> "NH2" Residue "CF ARG 80": "NH1" <-> "NH2" Residue "CF ARG 92": "NH1" <-> "NH2" Residue "CF ARG 102": "NH1" <-> "NH2" Residue "CF ARG 110": "NH1" <-> "NH2" Residue "CF ARG 112": "NH1" <-> "NH2" Residue "CF ARG 115": "NH1" <-> "NH2" Residue "CF ARG 133": "NH1" <-> "NH2" Residue "CG ARG 3": "NH1" <-> "NH2" Residue "CG ARG 153": "NH1" <-> "NH2" Residue "CG ARG 163": "NH1" <-> "NH2" Residue "CG ARG 170": "NH1" <-> "NH2" Residue "CH ARG 27": "NH1" <-> "NH2" Residue "CJ PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK ARG 13": "NH1" <-> "NH2" Residue "CK ARG 37": "NH1" <-> "NH2" Residue "CK ARG 96": "NH1" <-> "NH2" Residue "CK ARG 120": "NH1" <-> "NH2" Residue "CM ARG 21": "NH1" <-> "NH2" Residue "CM ARG 33": "NH1" <-> "NH2" Residue "CM ARG 41": "NH1" <-> "NH2" Residue "CM ARG 47": "NH1" <-> "NH2" Residue "CM ARG 60": "NH1" <-> "NH2" Residue "CM ARG 78": "NH1" <-> "NH2" Residue "CM ARG 126": "NH1" <-> "NH2" Residue "CN ARG 10": "NH1" <-> "NH2" Residue "CN ARG 18": "NH1" <-> "NH2" Residue "CN ARG 40": "NH1" <-> "NH2" Residue "CN ARG 44": "NH1" <-> "NH2" Residue "CN ARG 50": "NH1" <-> "NH2" Residue "CN ARG 55": "NH1" <-> "NH2" Residue "CN ARG 59": "NH1" <-> "NH2" Residue "CN ARG 114": "NH1" <-> "NH2" Residue "CO ARG 8": "NH1" <-> "NH2" Residue "CO ARG 12": "NH1" <-> "NH2" Residue "CO ARG 17": "NH1" <-> "NH2" Residue "CO ARG 22": "NH1" <-> "NH2" Residue "CO ARG 46": "NH1" <-> "NH2" Residue "CO ARG 63": "NH1" <-> "NH2" Residue "CO ARG 64": "NH1" <-> "NH2" Residue "CO ARG 69": "NH1" <-> "NH2" Residue "CO ARG 71": "NH1" <-> "NH2" Residue "CO PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CO ARG 96": "NH1" <-> "NH2" Residue "CO ARG 118": "NH1" <-> "NH2" Residue "CP ARG 10": "NH1" <-> "NH2" Residue "CP ARG 16": "NH1" <-> "NH2" Residue "CP ARG 25": "NH1" <-> "NH2" Residue "CP ARG 81": "NH1" <-> "NH2" Residue "CP ARG 94": "NH1" <-> "NH2" Residue "CP ARG 102": "NH1" <-> "NH2" Residue "CP ARG 111": "NH1" <-> "NH2" Residue "CQ ARG 21": "NH1" <-> "NH2" Residue "CQ ARG 39": "NH1" <-> "NH2" Residue "CQ ARG 62": "NH1" <-> "NH2" Residue "CQ ARG 89": "NH1" <-> "NH2" Residue "CQ TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ ARG 101": "NH1" <-> "NH2" Residue "CQ ARG 109": "NH1" <-> "NH2" Residue "CR ARG 3": "NH1" <-> "NH2" Residue "CR ARG 6": "NH1" <-> "NH2" Residue "CR ARG 13": "NH1" <-> "NH2" Residue "CR ARG 33": "NH1" <-> "NH2" Residue "CR ARG 48": "NH1" <-> "NH2" Residue "CR ARG 70": "NH1" <-> "NH2" Residue "CS TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CS ARG 21": "NH1" <-> "NH2" Residue "CS ARG 68": "NH1" <-> "NH2" Residue "CS ARG 78": "NH1" <-> "NH2" Residue "CS ARG 79": "NH1" <-> "NH2" Residue "CS ARG 84": "NH1" <-> "NH2" Residue "CT PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT ARG 84": "NH1" <-> "NH2" Residue "CT ARG 88": "NH1" <-> "NH2" Residue "CT ARG 95": "NH1" <-> "NH2" Residue "CT ARG 110": "NH1" <-> "NH2" Residue "CU ARG 73": "NH1" <-> "NH2" Residue "CV ARG 6": "NH1" <-> "NH2" Residue "CV ARG 7": "NH1" <-> "NH2" Residue "CV ARG 82": "NH1" <-> "NH2" Residue "CV ARG 86": "NH1" <-> "NH2" Residue "CV ARG 94": "NH1" <-> "NH2" Residue "CV PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CW TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY ARG 3": "NH1" <-> "NH2" Residue "CY ARG 11": "NH1" <-> "NH2" Residue "CY ARG 18": "NH1" <-> "NH2" Residue "CY ARG 37": "NH1" <-> "NH2" Residue "CY ARG 50": "NH1" <-> "NH2" Residue "CY ARG 57": "NH1" <-> "NH2" Residue "CY ARG 74": "NH1" <-> "NH2" Residue "CY TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CZ ARG 29": "NH1" <-> "NH2" Residue "CZ ARG 47": "NH1" <-> "NH2" Residue "CZ ARG 52": "NH1" <-> "NH2" Residue "C0 ARG 11": "NH1" <-> "NH2" Residue "C0 ARG 30": "NH1" <-> "NH2" Residue "C0 ARG 45": "NH1" <-> "NH2" Residue "C1 ARG 10": "NH1" <-> "NH2" Residue "C1 ARG 16": "NH1" <-> "NH2" Residue "C1 ARG 52": "NH1" <-> "NH2" Residue "C2 ARG 44": "NH1" <-> "NH2" Residue "C3 ARG 3": "NH1" <-> "NH2" Residue "C3 ARG 12": "NH1" <-> "NH2" Residue "C3 ARG 14": "NH1" <-> "NH2" Residue "C3 ARG 19": "NH1" <-> "NH2" Residue "C3 ARG 21": "NH1" <-> "NH2" Residue "C3 ARG 33": "NH1" <-> "NH2" Residue "C3 ARG 41": "NH1" <-> "NH2" Residue "C4 ARG 13": "NH1" <-> "NH2" Residue "C4 ARG 30": "NH1" <-> "NH2" Residue "C4 ARG 40": "NH1" <-> "NH2" Residue "C4 ARG 42": "NH1" <-> "NH2" Residue "C5 ARG 24": "NH1" <-> "NH2" Residue "A ARG 11": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90950 Number of models: 1 Model: "" Number of chains: 32 Chain: "CA" Number of atoms: 62229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 62229 Classifications: {'RNA': 2898} Modifications used: {'rna2p': 7, 'rna2p_pur': 277, 'rna2p_pyr': 146, 'rna3p': 16, 'rna3p_pur': 1387, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 430, 'rna3p': 2467} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "CB" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "CC" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "CD" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} 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: "CE" 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: "CF" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "CG" 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: "CH" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "CJ" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "CK" 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: "CL" 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: "CM" 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: "CN" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} 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: "CO" 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: "CP" 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: "CQ" 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: "CR" 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: "CS" 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: "CT" 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: "CU" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "CV" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "CW" 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: "CX" 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: "CY" 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: "CZ" 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: "C0" 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: "C1" 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: "C2" 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: "C3" 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: "C4" 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: "C5" 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 132 Unusual residues: {'A0G': 4} Classifications: {'peptide': 18, 'undetermined': 4} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'TRANS': 13, None: 8} Not linked: pdbres="SER A 8 " pdbres="A0G A 9 " Not linked: pdbres="A0G A 9 " pdbres="SER A 10 " Not linked: pdbres="ALA A 14 " pdbres="A0G A 15 " Not linked: pdbres="A0G A 15 " pdbres="GLY A 16 " Not linked: pdbres="LYS A 17 " pdbres="A0G A 18 " ... (remaining 3 not shown) Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Planarities with less than four sites: {'A0G:plan-1': 4, 'BB9:plan-1': 3} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 36.21, per 1000 atoms: 0.40 Number of scatterers: 90950 At special positions: 0 Unit cell: (232.742, 213.811, 201.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 83 16.00 P 3016 15.00 O 25606 8.00 N 16939 7.00 C 45306 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 37.68 Conformation dependent library (CDL) restraints added in 4.0 seconds 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BB9 A 6 " Number of C-beta restraints generated: 6148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 49 sheets defined 24.4% alpha, 18.1% beta 974 base pairs and 1629 stacking pairs defined. Time for finding SS restraints: 43.86 Creating SS restraints... Processing helix chain 'CC' and resid 31 through 33 No H-bonds generated for 'chain 'CC' and resid 31 through 33' Processing helix chain 'CC' and resid 200 through 202 No H-bonds generated for 'chain 'CC' and resid 200 through 202' Processing helix chain 'CC' and resid 208 through 214 removed outlier: 4.019A pdb=" N ARGCC 214 " --> pdb=" O ALACC 210 " (cutoff:3.500A) Processing helix chain 'CC' and resid 222 through 224 No H-bonds generated for 'chain 'CC' and resid 222 through 224' Processing helix chain 'CC' and resid 264 through 266 No H-bonds generated for 'chain 'CC' and resid 264 through 266' Processing helix chain 'CD' and resid 62 through 70 Processing helix chain 'CD' and resid 98 through 103 removed outlier: 4.285A pdb=" N ASPCD 103 " --> pdb=" O LEUCD 100 " (cutoff:3.500A) Processing helix chain 'CD' and resid 121 through 125 Processing helix chain 'CE' and resid 25 through 38 Processing helix chain 'CE' and resid 98 through 114 Processing helix chain 'CE' and resid 131 through 140 Processing helix chain 'CE' and resid 156 through 160 Processing helix chain 'CE' and resid 177 through 182 removed outlier: 3.714A pdb=" N ILECE 181 " --> pdb=" O PROCE 177 " (cutoff:3.500A) Processing helix chain 'CE' and resid 190 through 200 Processing helix chain 'CF' and resid 3 through 18 removed outlier: 4.712A pdb=" N VALCF 13 " --> pdb=" O LYSCF 9 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYSCF 14 " --> pdb=" O ASPCF 10 " (cutoff:3.500A) Processing helix chain 'CF' and resid 25 through 27 No H-bonds generated for 'chain 'CF' and resid 25 through 27' Processing helix chain 'CF' and resid 48 through 60 removed outlier: 4.370A pdb=" N ALACF 55 " --> pdb=" O ASPCF 51 " (cutoff:3.500A) Processing helix chain 'CF' and resid 94 through 106 removed outlier: 4.220A pdb=" N ILECF 106 " --> pdb=" O ARGCF 102 " (cutoff:3.500A) Processing helix chain 'CF' and resid 108 through 110 No H-bonds generated for 'chain 'CF' and resid 108 through 110' Processing helix chain 'CF' and resid 163 through 173 removed outlier: 3.850A pdb=" N PHECF 173 " --> pdb=" O LEUCF 169 " (cutoff:3.500A) Processing helix chain 'CG' and resid 62 through 78 Processing helix chain 'CG' and resid 139 through 151 Processing helix chain 'CH' and resid 23 through 28 Processing helix chain 'CH' and resid 31 through 33 No H-bonds generated for 'chain 'CH' and resid 31 through 33' Processing helix chain 'CH' and resid 43 through 68 removed outlier: 4.680A pdb=" N VALCH 61 " --> pdb=" O LYSCH 57 " (cutoff:3.500A) Processing helix chain 'CH' and resid 97 through 103 Processing helix chain 'CJ' and resid 25 through 31 removed outlier: 4.363A pdb=" N GLNCJ 31 " --> pdb=" O ALACJ 27 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 36 through 46 Processing helix chain 'CJ' and resid 76 through 83 Processing helix chain 'CJ' and resid 103 through 115 Processing helix chain 'CJ' and resid 122 through 136 Processing helix chain 'CK' and resid 25 through 37 removed outlier: 4.328A pdb=" N GLUCK 31 " --> pdb=" O ARGCK 27 " (cutoff:3.500A) Processing helix chain 'CK' and resid 89 through 96 Processing helix chain 'CK' and resid 98 through 107 Processing helix chain 'CK' and resid 113 through 121 removed outlier: 4.265A pdb=" N LYSCK 121 " --> pdb=" O ALACK 117 " (cutoff:3.500A) Processing helix chain 'CK' and resid 133 through 135 No H-bonds generated for 'chain 'CK' and resid 133 through 135' Processing helix chain 'CL' and resid 105 through 107 No H-bonds generated for 'chain 'CL' and resid 105 through 107' Processing helix chain 'CL' and resid 113 through 118 Processing helix chain 'CM' and resid 57 through 60 No H-bonds generated for 'chain 'CM' and resid 57 through 60' Processing helix chain 'CM' and resid 94 through 97 No H-bonds generated for 'chain 'CM' and resid 94 through 97' Processing helix chain 'CM' and resid 129 through 136 Processing helix chain 'CN' and resid 43 through 56 Processing helix chain 'CN' and resid 110 through 122 removed outlier: 3.896A pdb=" N ALACN 122 " --> pdb=" O LYSCN 118 " (cutoff:3.500A) Processing helix chain 'CO' and resid 14 through 31 Processing helix chain 'CO' and resid 38 through 43 Processing helix chain 'CO' and resid 45 through 56 Proline residue: CO 50 - end of helix Processing helix chain 'CO' and resid 60 through 68 Processing helix chain 'CO' and resid 73 through 81 Processing helix chain 'CO' and resid 83 through 86 No H-bonds generated for 'chain 'CO' and resid 83 through 86' Processing helix chain 'CP' and resid 3 through 21 removed outlier: 4.744A pdb=" N ARGCP 13 " --> pdb=" O ARGCP 9 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALACP 14 " --> pdb=" O ARGCP 10 " (cutoff:3.500A) Processing helix chain 'CP' and resid 57 through 59 No H-bonds generated for 'chain 'CP' and resid 57 through 59' Processing helix chain 'CP' and resid 68 through 85 Processing helix chain 'CP' and resid 102 through 112 Processing helix chain 'CQ' and resid 3 through 9 Processing helix chain 'CQ' and resid 54 through 56 No H-bonds generated for 'chain 'CQ' and resid 54 through 56' Processing helix chain 'CQ' and resid 98 through 101 Processing helix chain 'CQ' and resid 105 through 108 Processing helix chain 'CR' and resid 7 through 21 removed outlier: 3.810A pdb=" N ILECR 17 " --> pdb=" O ARGCR 13 " (cutoff:3.500A) Processing helix chain 'CR' and resid 26 through 28 No H-bonds generated for 'chain 'CR' and resid 26 through 28' Processing helix chain 'CR' and resid 32 through 72 removed outlier: 3.720A pdb=" N GLNCR 37 " --> pdb=" O ARGCR 33 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARGCR 51 " --> pdb=" O TYRCR 47 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYSCR 54 " --> pdb=" O ARGCR 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARGCR 55 " --> pdb=" O ARGCR 51 " (cutoff:3.500A) Processing helix chain 'CR' and resid 76 through 84 Processing helix chain 'CR' and resid 92 through 101 Processing helix chain 'CR' and resid 103 through 117 Processing helix chain 'CT' and resid 14 through 21 removed outlier: 3.590A pdb=" N LEUCT 19 " --> pdb=" O GLNCT 15 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VALCT 20 " --> pdb=" O LYSCT 16 " (cutoff:3.500A) Processing helix chain 'CT' and resid 29 through 37 removed outlier: 3.648A pdb=" N ASPCT 34 " --> pdb=" O SERCT 30 " (cutoff:3.500A) Processing helix chain 'CT' and resid 42 through 60 removed outlier: 3.638A pdb=" N LYSCT 49 " --> pdb=" O VALCT 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALCT 50 " --> pdb=" O LEUCT 46 " (cutoff:3.500A) Processing helix chain 'CT' and resid 66 through 68 No H-bonds generated for 'chain 'CT' and resid 66 through 68' Processing helix chain 'CT' and resid 89 through 91 No H-bonds generated for 'chain 'CT' and resid 89 through 91' Processing helix chain 'CU' and resid 4 through 10 Processing helix chain 'CU' and resid 20 through 27 Processing helix chain 'CU' and resid 40 through 50 Processing helix chain 'CW' and resid 14 through 22 Processing helix chain 'CW' and resid 44 through 50 Processing helix chain 'CY' and resid 53 through 62 Processing helix chain 'CY' and resid 64 through 72 Processing helix chain 'CZ' and resid 11 through 33 Processing helix chain 'CZ' and resid 40 through 59 removed outlier: 3.604A pdb=" N LEUCZ 43 " --> pdb=" O SERCZ 40 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLNCZ 45 " --> pdb=" O LEUCZ 42 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VALCZ 46 " --> pdb=" O LEUCZ 43 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARGCZ 47 " --> pdb=" O LYSCZ 44 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYSCZ 54 " --> pdb=" O ALACZ 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEUCZ 56 " --> pdb=" O VALCZ 53 " (cutoff:3.500A) Processing helix chain 'C0' and resid 18 through 26 Processing helix chain 'C0' and resid 42 through 50 Processing helix chain 'C1' and resid 10 through 19 removed outlier: 5.081A pdb=" N HISC1 19 " --> pdb=" O METC1 15 " (cutoff:3.500A) Processing helix chain 'C3' and resid 9 through 16 Processing helix chain 'C3' and resid 18 through 22 Processing helix chain 'C3' and resid 25 through 36 Processing helix chain 'C4' and resid 33 through 35 No H-bonds generated for 'chain 'C4' and resid 33 through 35' Processing helix chain 'C4' and resid 38 through 45 Processing helix chain 'C4' and resid 52 through 61 removed outlier: 4.600A pdb=" N GLYC4 56 " --> pdb=" O LYSC4 52 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEUC4 57 " --> pdb=" O GLYC4 53 " (cutoff:3.500A) Processing helix chain 'C5' and resid 31 through 33 No H-bonds generated for 'chain 'C5' and resid 31 through 33' Processing sheet with id= A, first strand: chain 'CC' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'CC' and resid 115 through 117 removed outlier: 6.750A pdb=" N LEUCC 93 " --> pdb=" O GLUCC 79 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEUCC 81 " --> pdb=" O ILECC 91 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILECC 91 " --> pdb=" O LEUCC 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'CC' and resid 129 through 131 Processing sheet with id= D, first strand: chain 'CC' and resid 181 through 185 removed outlier: 3.579A pdb=" N ALACC 166 " --> pdb=" O THRCC 173 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARGCC 175 " --> pdb=" O ILECC 164 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILECC 164 " --> pdb=" O ARGCC 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'CD' and resid 169 through 172 removed outlier: 4.559A pdb=" N THRCD 112 " --> pdb=" O ASPCD 200 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ASPCD 200 " --> pdb=" O THRCD 112 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VALCD 26 " --> pdb=" O VALCD 9 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N METCD 11 " --> pdb=" O VALCD 24 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VALCD 24 " --> pdb=" O METCD 11 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARGCD 13 " --> pdb=" O ILECD 22 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILECD 22 " --> pdb=" O ARGCD 13 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LYSCD 190 " --> pdb=" O VALCD 177 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VALCD 177 " --> pdb=" O LYSCD 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'CD' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLNCD 36 " --> pdb=" O GLNCD 49 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THRCD 51 " --> pdb=" O VALCD 34 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VALCD 34 " --> pdb=" O THRCD 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'CD' and resid 117 through 119 removed outlier: 3.730A pdb=" N GLYCD 117 " --> pdb=" O METCD 165 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'CE' and resid 118 through 121 removed outlier: 6.194A pdb=" N VALCE 186 " --> pdb=" O ILECE 119 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VALCE 121 " --> pdb=" O VALCE 186 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N METCE 188 " --> pdb=" O VALCE 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'CF' and resid 128 through 132 removed outlier: 6.920A pdb=" N THRCF 68 " --> pdb=" O ILECF 85 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYSCF 87 " --> pdb=" O LEUCF 66 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEUCF 66 " --> pdb=" O CYSCF 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'CG' and resid 16 through 20 Processing sheet with id= K, first strand: chain 'CG' and resid 161 through 163 removed outlier: 3.532A pdb=" N VALCG 90 " --> pdb=" O GLYCG 161 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHECG 83 " --> pdb=" O GLYCG 135 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLYCG 135 " --> pdb=" O PHECG 83 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'CG' and resid 95 through 99 Processing sheet with id= M, first strand: chain 'CH' and resid 2 through 4 removed outlier: 3.501A pdb=" N VALCH 19 " --> pdb=" O VALCH 3 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'CH' and resid 126 through 131 Processing sheet with id= O, first strand: chain 'CJ' and resid 9 through 14 Processing sheet with id= P, first strand: chain 'CJ' and resid 99 through 102 removed outlier: 4.223A pdb=" N VALCJ 139 " --> pdb=" O GLYCJ 99 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'CK' and resid 15 through 19 removed outlier: 7.075A pdb=" N TYRCK 53 " --> pdb=" O TYRCK 16 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VALCK 18 " --> pdb=" O TYRCK 53 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILECK 55 " --> pdb=" O VALCK 18 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'CK' and resid 73 through 77 Processing sheet with id= S, first strand: chain 'CL' and resid 7 through 9 removed outlier: 6.714A pdb=" N LYSCL 40 " --> pdb=" O ILECL 22 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VALCL 24 " --> pdb=" O ILECL 38 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILECL 38 " --> pdb=" O VALCL 24 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALACL 83 " --> pdb=" O VALCL 63 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'CN' and resid 128 through 132 removed outlier: 6.312A pdb=" N ALACN 35 " --> pdb=" O VALCN 101 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VALCN 101 " --> pdb=" O ALACN 35 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'CN' and resid 39 through 42 Processing sheet with id= V, first strand: chain 'CN' and resid 72 through 75 removed outlier: 6.322A pdb=" N GLUCN 75 " --> pdb=" O VALCN 89 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VALCN 89 " --> pdb=" O GLUCN 75 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'CO' and resid 33 through 37 Processing sheet with id= X, first strand: chain 'CP' and resid 91 through 93 Processing sheet with id= Y, first strand: chain 'CQ' and resid 83 through 88 removed outlier: 3.673A pdb=" N SERCQ 83 " --> pdb=" O LYSCQ 29 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THRCQ 25 " --> pdb=" O LYSCQ 87 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N GLUCQ 44 " --> pdb=" O ILECQ 64 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILECQ 64 " --> pdb=" O GLUCQ 44 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THRCQ 60 " --> pdb=" O ILECQ 48 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILECQ 50 " --> pdb=" O ALACQ 58 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALACQ 58 " --> pdb=" O ILECQ 50 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'CS' and resid 11 through 15 removed outlier: 3.623A pdb=" N METCS 40 " --> pdb=" O VALCS 4 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLNCS 6 " --> pdb=" O VALCS 38 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VALCS 38 " --> pdb=" O GLNCS 6 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'CS' and resid 19 through 22 Processing sheet with id= AB, first strand: chain 'CS' and resid 32 through 35 removed outlier: 6.331A pdb=" N GLUCS 62 " --> pdb=" O ILECS 98 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILECS 98 " --> pdb=" O GLUCS 62 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'CS' and resid 72 through 78 removed outlier: 4.001A pdb=" N TYRCS 83 " --> pdb=" O ARGCS 78 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'CT' and resid 82 through 87 Processing sheet with id= AE, first strand: chain 'CT' and resid 2 through 10 removed outlier: 5.473A pdb=" N SERCT 101 " --> pdb=" O HISCT 9 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYSCT 73 " --> pdb=" O VALCT 106 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N SERCT 108 " --> pdb=" O VALCT 71 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VALCT 71 " --> pdb=" O SERCT 108 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'CU' and resid 11 through 14 removed outlier: 6.670A pdb=" N LYSCU 33 " --> pdb=" O ARGCU 12 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VALCU 31 " --> pdb=" O PROCU 14 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYSCU 81 " --> pdb=" O VALCU 34 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VALCU 57 " --> pdb=" O THRCU 86 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'CU' and resid 67 through 70 Processing sheet with id= AH, first strand: chain 'CV' and resid 22 through 24 Processing sheet with id= AI, first strand: chain 'CV' and resid 64 through 66 removed outlier: 3.921A pdb=" N ASNCV 27 " --> pdb=" O ILECV 35 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'CV' and resid 41 through 45 Processing sheet with id= AK, first strand: chain 'CV' and resid 83 through 88 Processing sheet with id= AL, first strand: chain 'CW' and resid 73 through 78 removed outlier: 6.426A pdb=" N ASPCW 90 " --> pdb=" O GLNCW 75 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VALCW 77 " --> pdb=" O HISCW 88 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HISCW 88 " --> pdb=" O VALCW 77 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N ILECW 89 " --> pdb=" O LYSCW 25 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N PHECW 91 " --> pdb=" O PROCW 27 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILECW 29 " --> pdb=" O PHECW 91 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASPCW 43 " --> pdb=" O ASNCW 5 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASNCW 5 " --> pdb=" O ASPCW 43 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILECW 4 " --> pdb=" O THRCW 62 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'CX' and resid 51 through 53 Processing sheet with id= AN, first strand: chain 'CX' and resid 66 through 72 Processing sheet with id= AO, first strand: chain 'CY' and resid 13 through 18 Processing sheet with id= AP, first strand: chain 'CY' and resid 33 through 40 Processing sheet with id= AQ, first strand: chain 'C0' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'C1' and resid 28 through 30 Processing sheet with id= AS, first strand: chain 'C2' and resid 7 through 12 Processing sheet with id= AT, first strand: chain 'C2' and resid 36 through 40 Processing sheet with id= AU, first strand: chain 'C4' and resid 14 through 16 Processing sheet with id= AV, first strand: chain 'C5' and resid 2 through 4 Processing sheet with id= AW, first strand: chain 'C5' and resid 15 through 18 823 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2465 hydrogen bonds 3872 hydrogen bond angles 0 basepair planarities 974 basepair parallelities 1629 stacking parallelities Total time for adding SS restraints: 165.41 Time building geometry restraints manager: 40.52 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: 9889 1.32 - 1.44: 43322 1.44 - 1.57: 39668 1.57 - 1.69: 6032 1.69 - 1.81: 146 Bond restraints: 99057 Sorted by residual: bond pdb=" C4 5MUCA 747 " pdb=" C5 5MUCA 747 " ideal model delta sigma weight residual 1.802 1.473 0.329 2.00e-02 2.50e+03 2.70e+02 bond pdb=" C4 5MUCA1939 " pdb=" C5 5MUCA1939 " ideal model delta sigma weight residual 1.802 1.476 0.326 2.00e-02 2.50e+03 2.65e+02 bond pdb=" N1 5MUCA 747 " pdb=" C6 5MUCA 747 " ideal model delta sigma weight residual 1.635 1.330 0.305 2.00e-02 2.50e+03 2.33e+02 bond pdb=" N1 5MUCA1939 " pdb=" C6 5MUCA1939 " ideal model delta sigma weight residual 1.635 1.335 0.300 2.00e-02 2.50e+03 2.25e+02 bond pdb=" C5 5MUCA1939 " pdb=" C6 5MUCA1939 " ideal model delta sigma weight residual 1.155 1.386 -0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 99052 not shown) Histogram of bond angle deviations from ideal: 93.11 - 102.02: 2941 102.02 - 110.93: 54679 110.93 - 119.84: 50010 119.84 - 128.75: 37884 128.75 - 137.66: 3171 Bond angle restraints: 148685 Sorted by residual: angle pdb=" N ASPC5 20 " pdb=" CA ASPC5 20 " pdb=" C ASPC5 20 " ideal model delta sigma weight residual 110.80 93.11 17.69 2.13e+00 2.20e-01 6.90e+01 angle pdb=" C SERCV 98 " pdb=" N ASNCV 99 " pdb=" CA ASNCV 99 " ideal model delta sigma weight residual 121.54 137.11 -15.57 1.91e+00 2.74e-01 6.65e+01 angle pdb=" C BB9 A 3 " pdb=" CA BB9 A 3 " pdb=" CB BB9 A 3 " ideal model delta sigma weight residual 110.10 125.14 -15.04 1.90e+00 2.77e-01 6.26e+01 angle pdb=" C BB9 A 12 " pdb=" CA BB9 A 12 " pdb=" CB BB9 A 12 " ideal model delta sigma weight residual 110.10 124.70 -14.60 1.90e+00 2.77e-01 5.90e+01 angle pdb=" C BB9 A 6 " pdb=" CA BB9 A 6 " pdb=" CB BB9 A 6 " ideal model delta sigma weight residual 110.10 124.49 -14.39 1.90e+00 2.77e-01 5.74e+01 ... (remaining 148680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 55860 35.25 - 70.50: 6664 70.50 - 105.76: 835 105.76 - 141.01: 13 141.01 - 176.26: 10 Dihedral angle restraints: 63382 sinusoidal: 53835 harmonic: 9547 Sorted by residual: dihedral pdb=" C BB9 A 3 " pdb=" N BB9 A 3 " pdb=" CA BB9 A 3 " pdb=" CB BB9 A 3 " ideal model delta harmonic sigma weight residual -122.60 -178.95 56.35 0 2.50e+00 1.60e-01 5.08e+02 dihedral pdb=" N BB9 A 3 " pdb=" C BB9 A 3 " pdb=" CA BB9 A 3 " pdb=" CB BB9 A 3 " ideal model delta harmonic sigma weight residual 122.80 178.83 -56.03 0 2.50e+00 1.60e-01 5.02e+02 dihedral pdb=" C BB9 A 12 " pdb=" N BB9 A 12 " pdb=" CA BB9 A 12 " pdb=" CB BB9 A 12 " ideal model delta harmonic sigma weight residual -122.60 -178.61 56.01 0 2.50e+00 1.60e-01 5.02e+02 ... (remaining 63379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 17522 0.083 - 0.165: 1363 0.165 - 0.248: 118 0.248 - 0.331: 14 0.331 - 0.413: 7 Chirality restraints: 19024 Sorted by residual: chirality pdb=" C3' CCA2326 " pdb=" C4' CCA2326 " pdb=" O3' CCA2326 " pdb=" C2' CCA2326 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' UCA2680 " pdb=" C4' UCA2680 " pdb=" O3' UCA2680 " pdb=" C2' UCA2680 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILECK 81 " pdb=" CA ILECK 81 " pdb=" CG1 ILECK 81 " pdb=" CG2 ILECK 81 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 19021 not shown) Planarity restraints: 7614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMCCA2498 " 0.067 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' OMCCA2498 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMCCA2498 " 0.555 2.00e-02 2.50e+03 pdb=" C3' OMCCA2498 " -0.601 2.00e-02 2.50e+03 pdb=" O3' OMCCA2498 " -0.663 2.00e-02 2.50e+03 pdb=" C2' OMCCA2498 " -0.158 2.00e-02 2.50e+03 pdb=" O2' OMCCA2498 " 1.006 2.00e-02 2.50e+03 pdb=" C1' OMCCA2498 " 0.232 2.00e-02 2.50e+03 pdb=" N1 OMCCA2498 " -0.869 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGCA2445 " 0.013 2.00e-02 2.50e+03 5.83e-01 7.66e+03 pdb=" C4' 2MGCA2445 " 0.456 2.00e-02 2.50e+03 pdb=" O4' 2MGCA2445 " 0.705 2.00e-02 2.50e+03 pdb=" C3' 2MGCA2445 " -0.577 2.00e-02 2.50e+03 pdb=" O3' 2MGCA2445 " -0.568 2.00e-02 2.50e+03 pdb=" C2' 2MGCA2445 " -0.224 2.00e-02 2.50e+03 pdb=" O2' 2MGCA2445 " 0.885 2.00e-02 2.50e+03 pdb=" C1' 2MGCA2445 " 0.216 2.00e-02 2.50e+03 pdb=" N9 2MGCA2445 " -0.906 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGCA2251 " 0.008 2.00e-02 2.50e+03 5.64e-01 7.16e+03 pdb=" C4' OMGCA2251 " 0.436 2.00e-02 2.50e+03 pdb=" O4' OMGCA2251 " 0.683 2.00e-02 2.50e+03 pdb=" C3' OMGCA2251 " -0.589 2.00e-02 2.50e+03 pdb=" O3' OMGCA2251 " -0.523 2.00e-02 2.50e+03 pdb=" C2' OMGCA2251 " -0.238 2.00e-02 2.50e+03 pdb=" O2' OMGCA2251 " 0.860 2.00e-02 2.50e+03 pdb=" C1' OMGCA2251 " 0.224 2.00e-02 2.50e+03 pdb=" N9 OMGCA2251 " -0.860 2.00e-02 2.50e+03 ... (remaining 7611 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 7 2.04 - 2.76: 14061 2.76 - 3.47: 109334 3.47 - 4.19: 305969 4.19 - 4.90: 398708 Nonbonded interactions: 828079 Sorted by model distance: nonbonded pdb=" C GLY A 20 " pdb=" OEV A0G A 21 " model vdw 1.331 3.270 nonbonded pdb=" C LYS A 17 " pdb=" OEV A0G A 18 " model vdw 1.331 3.270 nonbonded pdb=" C SER A 8 " pdb=" OEV A0G A 9 " model vdw 1.333 3.270 nonbonded pdb=" C ALA A 14 " pdb=" OEV A0G A 15 " model vdw 1.334 3.270 nonbonded pdb=" C ARG A 11 " pdb=" SG BB9 A 12 " model vdw 1.701 3.630 ... (remaining 828074 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: 1.450 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: 0.060 Extract box with map and model: 10.610 Check model and map are aligned: 1.050 Set scattering table: 0.630 Process input model: 342.980 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.240 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:10.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 369.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.329 99057 Z= 0.413 Angle : 0.930 18.796 148685 Z= 0.460 Chirality : 0.047 0.413 19024 Planarity : 0.019 0.591 7614 Dihedral : 22.635 176.259 57234 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.23 % Favored : 93.35 % Rotamer: Outliers : 0.74 % Allowed : 3.64 % Favored : 95.62 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.12), residues: 3292 helix: -2.75 (0.12), residues: 905 sheet: -1.64 (0.18), residues: 648 loop : -2.56 (0.12), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRPCC 213 HIS 0.028 0.003 HISCN 13 PHE 0.027 0.003 PHECD 127 TYR 0.039 0.003 TYRC2 49 ARG 0.023 0.002 ARGC3 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 422 time to evaluate : 3.748 Fit side-chains TARDY: cannot create tardy model for: "THR A 2 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 17 " (corrupted residue). Skipping it. REVERT: CC 189 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7427 (mtp85) REVERT: CC 213 TRP cc_start: 0.7610 (p90) cc_final: 0.7076 (p90) REVERT: CD 40 LEU cc_start: 0.7600 (mp) cc_final: 0.7376 (mp) REVERT: CD 55 LYS cc_start: 0.7046 (tttt) cc_final: 0.6319 (ttmt) REVERT: CD 100 LEU cc_start: 0.6885 (tp) cc_final: 0.6621 (mp) REVERT: CF 26 MET cc_start: 0.4790 (tpt) cc_final: 0.4440 (mmm) REVERT: CJ 117 MET cc_start: 0.1619 (mmp) cc_final: -0.0170 (pp-130) REVERT: CJ 125 MET cc_start: 0.1906 (mtt) cc_final: 0.1172 (mtp) REVERT: CK 138 GLN cc_start: 0.7228 (pt0) cc_final: 0.6911 (mm-40) REVERT: CN 8 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7276 (tttm) REVERT: CN 51 ARG cc_start: 0.6887 (mtt180) cc_final: 0.6144 (mtp180) REVERT: CO 90 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.8021 (ttm110) REVERT: CQ 89 ARG cc_start: 0.6682 (mtm180) cc_final: 0.6304 (mtp180) REVERT: CR 112 LYS cc_start: 0.7217 (tptt) cc_final: 0.6564 (mptt) REVERT: CT 73 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7275 (tttm) REVERT: C0 38 ARG cc_start: 0.7865 (mmt-90) cc_final: 0.7354 (mmt-90) outliers start: 20 outliers final: 8 residues processed: 442 average time/residue: 2.1174 time to fit residues: 1207.8736 Evaluate side-chains 311 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 303 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 195 VAL Chi-restraints excluded: chain CC residue 204 VAL Chi-restraints excluded: chain CO residue 70 THR Chi-restraints excluded: chain CP residue 47 VAL Chi-restraints excluded: chain C4 residue 32 ILE Chi-restraints excluded: chain C5 residue 3 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 17 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 527 optimal weight: 10.0000 chunk 473 optimal weight: 0.8980 chunk 262 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 489 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 364 optimal weight: 9.9990 chunk 567 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CC 60 GLN CC 86 ASN CC 117 GLN CC 153 GLN CC 197 ASN CD 32 ASN CD 36 GLN CD 126 ASN CG 30 ASN CH 2 GLN CH 20 ASN ** CH 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CH 145 ASN CM 99 ASN CM 104 GLN CO 107 ASN CR 37 GLN CR 44 GLN CR 81 ASN ** CS 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CT 15 GLN CT 61 ASN CU 28 ASN CU 48 GLN CW 49 ASN CY 16 ASN CY 17 ASN C0 9 GLN C1 4 GLN C1 6 ASN C1 42 HIS C3 29 GLN C4 28 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 99057 Z= 0.299 Angle : 0.750 17.440 148685 Z= 0.394 Chirality : 0.041 0.368 19024 Planarity : 0.008 0.141 7614 Dihedral : 23.462 177.220 50710 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.56 % Favored : 93.07 % Rotamer: Outliers : 3.35 % Allowed : 9.05 % Favored : 87.60 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.13), residues: 3292 helix: -1.34 (0.16), residues: 903 sheet: -1.28 (0.19), residues: 670 loop : -2.19 (0.13), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRPCC 213 HIS 0.015 0.002 HISCN 13 PHE 0.019 0.002 PHECV 95 TYR 0.024 0.002 TYRC2 49 ARG 0.009 0.001 ARGCM 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 316 time to evaluate : 3.856 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 2 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A 5 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 17 " (corrupted residue). Skipping it. REVERT: CC 189 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7663 (mtt-85) REVERT: CC 201 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7212 (ptp) REVERT: CC 213 TRP cc_start: 0.7805 (p90) cc_final: 0.7426 (p90) REVERT: CD 55 LYS cc_start: 0.6984 (tttt) cc_final: 0.6230 (ttmt) REVERT: CD 100 LEU cc_start: 0.6607 (tp) cc_final: 0.6318 (mp) REVERT: CE 44 ARG cc_start: 0.8152 (ptt90) cc_final: 0.7874 (ptt90) REVERT: CE 69 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7631 (ptt90) REVERT: CE 94 GLN cc_start: 0.8165 (mt0) cc_final: 0.7913 (mt0) REVERT: CF 96 MET cc_start: 0.4888 (tmt) cc_final: 0.4584 (tmm) REVERT: CG 75 MET cc_start: 0.5192 (OUTLIER) cc_final: 0.4836 (tpp) REVERT: CJ 36 MET cc_start: 0.1227 (tpp) cc_final: -0.0617 (pp-130) REVERT: CJ 117 MET cc_start: 0.1515 (mmp) cc_final: -0.0423 (pp-130) REVERT: CJ 125 MET cc_start: 0.1933 (mtt) cc_final: 0.1221 (mtp) REVERT: CK 1 MET cc_start: 0.4291 (OUTLIER) cc_final: 0.3083 (pp-130) REVERT: CK 34 ARG cc_start: 0.7211 (tmm160) cc_final: 0.6678 (ttt90) REVERT: CK 108 MET cc_start: 0.8983 (mtt) cc_final: 0.8099 (mtm) REVERT: CK 138 GLN cc_start: 0.7136 (pt0) cc_final: 0.6816 (mm110) REVERT: CL 20 MET cc_start: 0.7992 (ttp) cc_final: 0.7692 (ttm) REVERT: CL 69 VAL cc_start: 0.8649 (OUTLIER) cc_final: 0.8374 (p) REVERT: CM 77 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7614 (mt) REVERT: CN 51 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6173 (mtp180) REVERT: CN 64 TRP cc_start: 0.8110 (m-90) cc_final: 0.7888 (m-90) REVERT: CN 118 LYS cc_start: 0.7840 (tppt) cc_final: 0.7336 (tptp) REVERT: CO 90 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8056 (ttm110) REVERT: CP 16 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5043 (mmt180) REVERT: CQ 89 ARG cc_start: 0.6869 (mtm180) cc_final: 0.6285 (mmt180) REVERT: CR 52 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: CR 112 LYS cc_start: 0.7146 (tptt) cc_final: 0.6499 (mptt) REVERT: CU 74 ILE cc_start: 0.5669 (OUTLIER) cc_final: 0.5401 (pp) REVERT: CY 56 MET cc_start: 0.7042 (mtp) cc_final: 0.6701 (mtp) REVERT: C0 38 ARG cc_start: 0.7936 (mmt-90) cc_final: 0.7732 (mmt-90) REVERT: C1 10 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8297 (ptp-170) outliers start: 91 outliers final: 47 residues processed: 373 average time/residue: 1.8666 time to fit residues: 929.2450 Evaluate side-chains 351 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 294 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 51 THR Chi-restraints excluded: chain CC residue 71 LYS Chi-restraints excluded: chain CC residue 195 VAL Chi-restraints excluded: chain CC residue 201 MET Chi-restraints excluded: chain CC residue 204 VAL Chi-restraints excluded: chain CD residue 14 ILE Chi-restraints excluded: chain CD residue 73 VAL Chi-restraints excluded: chain CD residue 91 THR Chi-restraints excluded: chain CD residue 157 LYS Chi-restraints excluded: chain CD residue 177 VAL Chi-restraints excluded: chain CD residue 204 LYS Chi-restraints excluded: chain CE residue 69 ARG Chi-restraints excluded: chain CE residue 72 SER Chi-restraints excluded: chain CE residue 77 ILE Chi-restraints excluded: chain CE residue 178 VAL Chi-restraints excluded: chain CF residue 64 LYS Chi-restraints excluded: chain CF residue 177 PHE Chi-restraints excluded: chain CG residue 75 MET Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CK residue 1 MET Chi-restraints excluded: chain CK residue 70 THR Chi-restraints excluded: chain CK residue 139 VAL Chi-restraints excluded: chain CL residue 17 ARG Chi-restraints excluded: chain CL residue 69 VAL Chi-restraints excluded: chain CM residue 77 ILE Chi-restraints excluded: chain CM residue 100 ILE Chi-restraints excluded: chain CN residue 128 THR Chi-restraints excluded: chain CN residue 131 VAL Chi-restraints excluded: chain CO residue 2 ARG Chi-restraints excluded: chain CO residue 51 LEU Chi-restraints excluded: chain CO residue 65 LEU Chi-restraints excluded: chain CO residue 95 THR Chi-restraints excluded: chain CP residue 16 ARG Chi-restraints excluded: chain CP residue 47 VAL Chi-restraints excluded: chain CR residue 52 GLN Chi-restraints excluded: chain CR residue 114 LYS Chi-restraints excluded: chain CS residue 72 VAL Chi-restraints excluded: chain CT residue 100 THR Chi-restraints excluded: chain CT residue 109 ASP Chi-restraints excluded: chain CU residue 24 MET Chi-restraints excluded: chain CU residue 74 ILE Chi-restraints excluded: chain CU residue 86 THR Chi-restraints excluded: chain CV residue 28 VAL Chi-restraints excluded: chain CW residue 77 VAL Chi-restraints excluded: chain CX residue 81 SER Chi-restraints excluded: chain CY residue 22 LEU Chi-restraints excluded: chain CZ residue 42 LEU Chi-restraints excluded: chain C0 residue 36 VAL Chi-restraints excluded: chain C1 residue 10 ARG Chi-restraints excluded: chain C1 residue 25 VAL Chi-restraints excluded: chain C1 residue 46 ASP Chi-restraints excluded: chain C3 residue 4 THR Chi-restraints excluded: chain C3 residue 44 VAL Chi-restraints excluded: chain C4 residue 32 ILE Chi-restraints excluded: chain C4 residue 34 THR Chi-restraints excluded: chain C5 residue 3 VAL Chi-restraints excluded: chain A residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 315 optimal weight: 8.9990 chunk 176 optimal weight: 10.0000 chunk 472 optimal weight: 9.9990 chunk 386 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 568 optimal weight: 1.9990 chunk 614 optimal weight: 10.0000 chunk 506 optimal weight: 7.9990 chunk 563 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 456 optimal weight: 0.0970 overall best weight: 4.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CD 32 ASN CD 126 ASN ** CH 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CO 11 ASN CS 66 HIS C4 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 99057 Z= 0.224 Angle : 0.667 16.594 148685 Z= 0.356 Chirality : 0.038 0.351 19024 Planarity : 0.007 0.138 7614 Dihedral : 23.342 179.651 50705 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.92 % Favored : 93.71 % Rotamer: Outliers : 3.90 % Allowed : 10.49 % Favored : 85.61 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3292 helix: -0.61 (0.17), residues: 903 sheet: -1.08 (0.19), residues: 682 loop : -1.95 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCC 213 HIS 0.010 0.002 HISCT 7 PHE 0.022 0.002 PHECF 175 TYR 0.016 0.002 TYRC2 49 ARG 0.006 0.001 ARGCL 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 296 time to evaluate : 3.811 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 2 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 17 " (corrupted residue). Skipping it. REVERT: CC 189 ARG cc_start: 0.8019 (mtt-85) cc_final: 0.7624 (mtt-85) REVERT: CC 201 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7220 (ptp) REVERT: CC 213 TRP cc_start: 0.7731 (p90) cc_final: 0.7475 (p90) REVERT: CD 55 LYS cc_start: 0.6910 (tttt) cc_final: 0.6218 (ttmt) REVERT: CD 100 LEU cc_start: 0.6767 (tp) cc_final: 0.6231 (mp) REVERT: CE 69 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7793 (ptt90) REVERT: CE 199 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.5066 (mmm) REVERT: CG 75 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4767 (tpp) REVERT: CJ 36 MET cc_start: 0.1331 (tpp) cc_final: -0.0548 (pp-130) REVERT: CJ 117 MET cc_start: 0.2064 (mmp) cc_final: 0.0025 (pp-130) REVERT: CJ 125 MET cc_start: 0.1765 (mtt) cc_final: 0.1006 (mtp) REVERT: CK 1 MET cc_start: 0.4369 (OUTLIER) cc_final: 0.3062 (pp-130) REVERT: CK 28 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (tp) REVERT: CK 34 ARG cc_start: 0.7169 (tmm160) cc_final: 0.6711 (ttt90) REVERT: CK 108 MET cc_start: 0.8953 (mtt) cc_final: 0.8238 (mtm) REVERT: CL 4 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7407 (mt-10) REVERT: CL 20 MET cc_start: 0.7972 (ttp) cc_final: 0.7660 (ttm) REVERT: CL 53 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6733 (mtmm) REVERT: CL 69 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8402 (p) REVERT: CM 69 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.6733 (mtm110) REVERT: CM 77 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7582 (mt) REVERT: CN 51 ARG cc_start: 0.6833 (mtt180) cc_final: 0.6188 (mtm110) REVERT: CN 118 LYS cc_start: 0.8026 (tppt) cc_final: 0.7255 (tttm) REVERT: CO 1 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7291 (mpp) REVERT: CO 90 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8094 (ttm110) REVERT: CP 16 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5021 (mmt180) REVERT: CQ 21 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7318 (mtm180) REVERT: CQ 89 ARG cc_start: 0.6886 (mtm180) cc_final: 0.6304 (mmt180) REVERT: CR 19 LYS cc_start: 0.8418 (tmmt) cc_final: 0.8204 (ttpp) REVERT: CR 52 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7545 (mt0) REVERT: CR 112 LYS cc_start: 0.7180 (tptt) cc_final: 0.6545 (mptt) REVERT: CU 74 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5496 (pp) REVERT: CW 25 LYS cc_start: 0.7285 (mttt) cc_final: 0.6865 (mtmt) REVERT: CY 33 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7375 (mp) REVERT: C0 38 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7693 (mmt-90) REVERT: C1 10 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8274 (ptp-170) outliers start: 106 outliers final: 55 residues processed: 365 average time/residue: 1.8560 time to fit residues: 908.0817 Evaluate side-chains 358 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 286 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 51 THR Chi-restraints excluded: chain CC residue 71 LYS Chi-restraints excluded: chain CC residue 108 LYS Chi-restraints excluded: chain CC residue 195 VAL Chi-restraints excluded: chain CC residue 201 MET Chi-restraints excluded: chain CC residue 204 VAL Chi-restraints excluded: chain CD residue 14 ILE Chi-restraints excluded: chain CD residue 91 THR Chi-restraints excluded: chain CD residue 157 LYS Chi-restraints excluded: chain CD residue 170 VAL Chi-restraints excluded: chain CD residue 177 VAL Chi-restraints excluded: chain CE residue 69 ARG Chi-restraints excluded: chain CE residue 72 SER Chi-restraints excluded: chain CE residue 96 VAL Chi-restraints excluded: chain CE residue 199 MET Chi-restraints excluded: chain CF residue 38 MET Chi-restraints excluded: chain CF residue 64 LYS Chi-restraints excluded: chain CF residue 132 VAL Chi-restraints excluded: chain CF residue 177 PHE Chi-restraints excluded: chain CG residue 75 MET Chi-restraints excluded: chain CG residue 127 THR Chi-restraints excluded: chain CJ residue 17 MET Chi-restraints excluded: chain CK residue 1 MET Chi-restraints excluded: chain CK residue 28 LEU Chi-restraints excluded: chain CK residue 81 ILE Chi-restraints excluded: chain CK residue 139 VAL Chi-restraints excluded: chain CL residue 17 ARG Chi-restraints excluded: chain CL residue 53 LYS Chi-restraints excluded: chain CL residue 69 VAL Chi-restraints excluded: chain CM residue 69 ARG Chi-restraints excluded: chain CM residue 77 ILE Chi-restraints excluded: chain CM residue 92 LEU Chi-restraints excluded: chain CM residue 100 ILE Chi-restraints excluded: chain CM residue 116 VAL Chi-restraints excluded: chain CN residue 5 LYS Chi-restraints excluded: chain CN residue 8 LYS Chi-restraints excluded: chain CN residue 128 THR Chi-restraints excluded: chain CN residue 131 VAL Chi-restraints excluded: chain CO residue 1 MET Chi-restraints excluded: chain CO residue 2 ARG Chi-restraints excluded: chain CO residue 15 SER Chi-restraints excluded: chain CO residue 51 LEU Chi-restraints excluded: chain CO residue 65 LEU Chi-restraints excluded: chain CO residue 95 THR Chi-restraints excluded: chain CP residue 16 ARG Chi-restraints excluded: chain CP residue 28 VAL Chi-restraints excluded: chain CP residue 47 VAL Chi-restraints excluded: chain CQ residue 21 ARG Chi-restraints excluded: chain CQ residue 80 VAL Chi-restraints excluded: chain CR residue 52 GLN Chi-restraints excluded: chain CT residue 62 ASP Chi-restraints excluded: chain CU residue 24 MET Chi-restraints excluded: chain CU residue 56 GLU Chi-restraints excluded: chain CU residue 74 ILE Chi-restraints excluded: chain CU residue 86 THR Chi-restraints excluded: chain CV residue 28 VAL Chi-restraints excluded: chain CW residue 77 VAL Chi-restraints excluded: chain CY residue 2 SER Chi-restraints excluded: chain CY residue 22 LEU Chi-restraints excluded: chain CY residue 33 LEU Chi-restraints excluded: chain CZ residue 42 LEU Chi-restraints excluded: chain C0 residue 36 VAL Chi-restraints excluded: chain C1 residue 10 ARG Chi-restraints excluded: chain C1 residue 25 VAL Chi-restraints excluded: chain C1 residue 46 ASP Chi-restraints excluded: chain C1 residue 55 ILE Chi-restraints excluded: chain C3 residue 4 THR Chi-restraints excluded: chain C3 residue 24 THR Chi-restraints excluded: chain C3 residue 44 VAL Chi-restraints excluded: chain C4 residue 32 ILE Chi-restraints excluded: chain C5 residue 3 VAL Chi-restraints excluded: chain A residue 2 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 561 optimal weight: 7.9990 chunk 427 optimal weight: 30.0000 chunk 295 optimal weight: 40.0000 chunk 62 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 570 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 298 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CC 153 GLN CD 32 ASN ** CH 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CP 100 HIS ** CS 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C0 9 GLN C3 29 GLN C5 13 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 99057 Z= 0.443 Angle : 0.863 17.416 148685 Z= 0.439 Chirality : 0.047 0.387 19024 Planarity : 0.008 0.152 7614 Dihedral : 23.498 177.866 50705 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.53 % Favored : 92.13 % Rotamer: Outliers : 4.97 % Allowed : 10.96 % Favored : 84.07 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.13), residues: 3292 helix: -0.78 (0.17), residues: 901 sheet: -1.06 (0.19), residues: 686 loop : -1.99 (0.13), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRPCN 64 HIS 0.016 0.002 HISCT 7 PHE 0.028 0.003 PHECF 175 TYR 0.018 0.003 TYRCT 38 ARG 0.011 0.001 ARGCM 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6584 Ramachandran restraints generated. 3292 Oldfield, 0 Emsley, 3292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 296 time to evaluate : 3.886 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 2 " (corrupted residue). Skipping it. REVERT: CC 39 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7518 (mtmt) REVERT: CC 105 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8169 (tp) REVERT: CC 108 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6503 (tmtp) REVERT: CC 161 TYR cc_start: 0.7839 (p90) cc_final: 0.7235 (p90) REVERT: CC 189 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7625 (mtt-85) REVERT: CC 201 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7232 (ptp) REVERT: CC 213 TRP cc_start: 0.7817 (p90) cc_final: 0.7594 (p90) REVERT: CD 55 LYS cc_start: 0.7033 (tttt) cc_final: 0.6266 (ttmt) REVERT: CD 100 LEU cc_start: 0.6785 (tp) cc_final: 0.6285 (mp) REVERT: CE 69 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7713 (ptt90) REVERT: CF 64 LYS cc_start: 0.3172 (OUTLIER) cc_final: 0.2818 (pmmt) REVERT: CF 130 MET cc_start: 0.3134 (ptp) cc_final: 0.1927 (ptt) REVERT: CJ 36 MET cc_start: 0.1278 (tpp) cc_final: -0.0741 (pp-130) REVERT: CJ 117 MET cc_start: 0.2027 (OUTLIER) cc_final: -0.0122 (pp-130) REVERT: CJ 125 MET cc_start: 0.1674 (mtt) cc_final: 0.0946 (mtp) REVERT: CK 1 MET cc_start: 0.4605 (OUTLIER) cc_final: 0.3205 (pp-130) REVERT: CK 28 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8024 (tp) REVERT: CK 108 MET cc_start: 0.8964 (mtt) cc_final: 0.8417 (mtm) REVERT: CL 4 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7398 (mt-10) REVERT: CL 53 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6694 (mtmm) REVERT: CL 69 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8321 (p) REVERT: CL 121 GLU cc_start: 0.7220 (tt0) cc_final: 0.6905 (tt0) REVERT: CM 4 ASN cc_start: 0.8969 (p0) cc_final: 0.8742 (p0) REVERT: CM 69 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6791 (mtm110) REVERT: CN 51 ARG cc_start: 0.6805 (mtt180) cc_final: 0.6087 (mtp180) REVERT: CN 64 TRP cc_start: 0.8092 (m-90) cc_final: 0.7887 (m-90) REVERT: CO 1 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7399 (mpp) REVERT: CO 90 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8117 (ttm110) REVERT: CP 16 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5196 (mmt180) REVERT: CQ 21 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7613 (mtm180) REVERT: CQ 26 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7759 (p) REVERT: CQ 89 ARG cc_start: 0.6948 (mtm180) cc_final: 0.6356 (mmt180) REVERT: CR 19 LYS cc_start: 0.8436 (tmmt) cc_final: 0.8191 (ttpp) REVERT: CR 52 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: CR 112 LYS cc_start: 0.7242 (tptt) cc_final: 0.6616 (mptt) REVERT: CU 18 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: CU 74 ILE cc_start: 0.5915 (OUTLIER) cc_final: 0.5457 (pp) REVERT: CW 25 LYS cc_start: 0.7500 (mttt) cc_final: 0.6996 (mtmt) REVERT: CY 27 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.6930 (ppp80) REVERT: CY 33 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7404 (mp) REVERT: C1 10 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8405 (ptp-170) outliers start: 135 outliers final: 79 residues processed: 382 average time/residue: 1.8245 time to fit residues: 943.2369 Evaluate side-chains 390 residues out of total 2719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 290 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CC residue 51 THR Chi-restraints excluded: chain CC residue 71 LYS Chi-restraints excluded: chain CC residue 105 LEU Chi-restraints excluded: chain CC residue 108 LYS Chi-restraints excluded: chain CC residue 130 LEU Chi-restraints excluded: chain CC residue 195 VAL Chi-restraints excluded: chain CC residue 201 MET Chi-restraints excluded: chain CC residue 204 VAL Chi-restraints excluded: chain CD residue 14 ILE Chi-restraints excluded: chain CD residue 73 VAL Chi-restraints excluded: chain CD residue 91 THR Chi-restraints excluded: chain CD residue 157 LYS Chi-restraints excluded: chain CD residue 170 VAL Chi-restraints excluded: chain CD residue 177 VAL Chi-restraints excluded: chain CE residue 69 ARG Chi-restraints excluded: chain CE residue 72 SER Chi-restraints excluded: chain CE residue 96 VAL Chi-restraints excluded: chain CE residue 178 VAL Chi-restraints excluded: chain CF residue 25 VAL Chi-restraints excluded: chain CF residue 28 VAL Chi-restraints excluded: chain CF residue 38 MET Chi-restraints excluded: chain CF residue 64 LYS Chi-restraints excluded: chain CF residue 108 VAL Chi-restraints excluded: chain CF residue 132 VAL Chi-restraints excluded: chain CG residue 127 THR Chi-restraints excluded: chain CH residue 21 VAL Chi-restraints excluded: chain CH residue 75 LEU Chi-restraints excluded: chain CJ residue 73 THR Chi-restraints excluded: chain CJ residue 117 MET Chi-restraints excluded: chain CK residue 1 MET Chi-restraints excluded: chain CK residue 28 LEU Chi-restraints excluded: chain CK residue 70 THR Chi-restraints excluded: chain CK residue 81 ILE Chi-restraints excluded: chain CK residue 92 MET Chi-restraints excluded: chain CK residue 131 ASN Chi-restraints excluded: chain CK residue 139 VAL Chi-restraints excluded: chain CL residue 17 ARG Chi-restraints excluded: chain CL residue 53 LYS Chi-restraints excluded: chain CL residue 69 VAL Chi-restraints excluded: chain CM residue 69 ARG Chi-restraints excluded: chain CM residue 92 LEU Chi-restraints excluded: chain CM residue 100 ILE Chi-restraints excluded: chain CM residue 117 THR Chi-restraints excluded: chain CN residue 5 LYS Chi-restraints excluded: chain CN residue 88 ASN Chi-restraints excluded: chain CN residue 128 THR Chi-restraints excluded: chain CN residue 131 VAL Chi-restraints excluded: chain CO residue 1 MET Chi-restraints excluded: chain CO residue 2 ARG Chi-restraints excluded: chain CO residue 15 SER Chi-restraints excluded: chain CO residue 32 GLU Chi-restraints excluded: chain CO residue 51 LEU Chi-restraints excluded: chain CO residue 65 LEU Chi-restraints excluded: chain CO residue 95 THR Chi-restraints excluded: chain CP residue 16 ARG Chi-restraints excluded: chain CP residue 28 VAL Chi-restraints excluded: chain CP residue 47 VAL Chi-restraints excluded: chain CQ residue 21 ARG Chi-restraints excluded: chain CQ residue 26 VAL Chi-restraints excluded: chain CQ residue 80 VAL Chi-restraints excluded: chain CR residue 9 ILE Chi-restraints excluded: chain CR residue 52 GLN Chi-restraints excluded: chain CR residue 100 VAL Chi-restraints excluded: chain CS residue 20 VAL Chi-restraints excluded: chain CS residue 72 VAL Chi-restraints excluded: chain CT residue 62 ASP Chi-restraints excluded: chain CT residue 97 LEU Chi-restraints excluded: chain CT residue 100 THR Chi-restraints excluded: chain CT residue 109 ASP Chi-restraints excluded: chain CU residue 18 GLU Chi-restraints excluded: chain CU residue 24 MET Chi-restraints excluded: chain CU residue 56 GLU Chi-restraints excluded: chain CU residue 74 ILE Chi-restraints excluded: chain CU residue 76 ARG Chi-restraints excluded: chain CU residue 86 THR Chi-restraints excluded: chain CV residue 28 VAL Chi-restraints excluded: chain CW residue 65 VAL Chi-restraints excluded: chain CW residue 77 VAL Chi-restraints excluded: chain CY residue 2 SER Chi-restraints excluded: chain CY residue 22 LEU Chi-restraints excluded: chain CY residue 27 ARG Chi-restraints excluded: chain CY residue 33 LEU Chi-restraints excluded: chain CY residue 35 SER Chi-restraints excluded: chain CY residue 48 THR Chi-restraints excluded: chain CZ residue 42 LEU Chi-restraints excluded: chain C0 residue 36 VAL Chi-restraints excluded: chain C1 residue 10 ARG Chi-restraints excluded: chain C1 residue 25 VAL Chi-restraints excluded: chain C1 residue 30 VAL Chi-restraints excluded: chain C1 residue 46 ASP Chi-restraints excluded: chain C1 residue 55 ILE Chi-restraints excluded: chain C2 residue 47 VAL Chi-restraints excluded: chain C3 residue 4 THR Chi-restraints excluded: chain C3 residue 24 THR Chi-restraints excluded: chain C3 residue 44 VAL Chi-restraints excluded: chain C4 residue 32 ILE Chi-restraints excluded: chain C4 residue 34 THR Chi-restraints excluded: chain C5 residue 3 VAL Chi-restraints excluded: chain C5 residue 6 SER Chi-restraints excluded: chain A residue 2 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.6194 > 50: distance: 79 - 84: 33.695 distance: 84 - 85: 38.657 distance: 85 - 86: 38.845 distance: 86 - 87: 57.132 distance: 86 - 95: 39.307 distance: 89 - 90: 40.220 distance: 90 - 91: 14.992 distance: 91 - 92: 26.588 distance: 92 - 93: 6.723 distance: 92 - 94: 9.758 distance: 96 - 97: 40.466 distance: 96 - 99: 40.543 distance: 97 - 98: 31.941 distance: 97 - 106: 3.985 distance: 99 - 100: 40.168 distance: 100 - 101: 39.620 distance: 101 - 102: 27.180 distance: 102 - 103: 18.953 distance: 103 - 104: 16.151 distance: 103 - 105: 18.736 distance: 106 - 107: 57.942 distance: 106 - 112: 68.699 distance: 107 - 108: 56.659 distance: 107 - 110: 3.004 distance: 108 - 109: 39.720 distance: 110 - 111: 19.029 distance: 111 - 112: 46.410 distance: 113 - 114: 15.640 distance: 114 - 115: 32.733 distance: 114 - 117: 16.428 distance: 115 - 116: 23.066 distance: 115 - 121: 43.093 distance: 117 - 118: 38.758 distance: 118 - 119: 40.301 distance: 118 - 120: 40.045 distance: 123 - 124: 60.457 distance: 123 - 125: 43.680 distance: 125 - 126: 20.506 distance: 126 - 127: 42.459 distance: 126 - 129: 33.352 distance: 127 - 128: 12.294 distance: 127 - 131: 32.831 distance: 129 - 130: 56.252 distance: 131 - 132: 44.529 distance: 132 - 133: 21.982 distance: 133 - 134: 45.911 distance: 133 - 138: 33.346 distance: 135 - 136: 55.489 distance: 135 - 137: 40.508 distance: 138 - 139: 56.594 distance: 139 - 140: 56.103 distance: 139 - 142: 42.095 distance: 140 - 141: 41.043 distance: 142 - 143: 50.825 distance: 142 - 144: 45.762 distance: 143 - 145: 33.041 distance: 146 - 147: 46.375 distance: 147 - 148: 54.788 distance: 147 - 150: 17.774 distance: 148 - 149: 34.418 distance: 148 - 157: 45.687 distance: 150 - 151: 45.800 distance: 151 - 152: 39.503 distance: 152 - 153: 7.739 distance: 153 - 154: 27.778 distance: 154 - 155: 17.413 distance: 154 - 156: 8.245 distance: 158 - 161: 15.650 distance: 159 - 160: 52.375 distance: 159 - 168: 35.638 distance: 161 - 162: 25.697 distance: 162 - 163: 56.581 distance: 162 - 164: 37.200 distance: 163 - 165: 28.640 distance: 164 - 166: 28.765 distance: 165 - 167: 13.429 distance: 166 - 167: 17.624