Starting phenix.real_space_refine on Sat Apr 13 20:27:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/04_2024/7bv8_30215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/04_2024/7bv8_30215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/04_2024/7bv8_30215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/04_2024/7bv8_30215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/04_2024/7bv8_30215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/04_2024/7bv8_30215.pdb" } resolution = 3.14 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= 0.040 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 3019 5.49 5 S 82 5.16 5 C 45643 2.51 5 N 17048 2.21 5 O 25713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K ARG 37": "NH1" <-> "NH2" Residue "K ARG 96": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 33": "NH1" <-> "NH2" Residue "M ARG 41": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M GLU 86": "OE1" <-> "OE2" Residue "M ARG 126": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "N ARG 44": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "O ARG 46": "NH1" <-> "NH2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P ARG 25": "NH1" <-> "NH2" Residue "P GLU 80": "OE1" <-> "OE2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 94": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 111": "NH1" <-> "NH2" Residue "Q GLU 9": "OE1" <-> "OE2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 39": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q ARG 89": "NH1" <-> "NH2" Residue "Q ARG 101": "NH1" <-> "NH2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "S GLU 16": "OE1" <-> "OE2" Residue "S ARG 21": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S GLU 70": "OE1" <-> "OE2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "S ARG 79": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 95": "NH1" <-> "NH2" Residue "T ARG 110": "NH1" <-> "NH2" Residue "U GLU 4": "OE1" <-> "OE2" Residue "U ARG 73": "NH1" <-> "NH2" Residue "V ARG 6": "NH1" <-> "NH2" Residue "V ARG 7": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V GLU 60": "OE1" <-> "OE2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ARG 86": "NH1" <-> "NH2" Residue "V ARG 94": "NH1" <-> "NH2" Residue "V GLU 101": "OE1" <-> "OE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 37": "NH1" <-> "NH2" Residue "Y ARG 50": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 74": "NH1" <-> "NH2" Residue "Z GLU 5": "OE1" <-> "OE2" Residue "Z GLU 12": "OE1" <-> "OE2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 47": "NH1" <-> "NH2" Residue "Z ARG 52": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a GLU 39": "OE1" <-> "OE2" Residue "a ARG 45": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 12": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 91505 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 62240 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 287, 'rna2p_pyr': 149, 'rna3p_pur': 1385, 'rna3p_pyr': 1076} Link IDs: {'rna2p': 436, 'rna3p': 2460} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 287, 'rna2p_pyr': 149, 'rna3p_pur': 1385, 'rna3p_pyr': 1076} Link IDs: {'rna2p': 436, 'rna3p': 2460} Chain breaks: 1 bond proxies already assigned to first conformer: 69606 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 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: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" 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: "H" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1101 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 3, 'TRANS': 144} Chain: "I" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1023 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "J" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 509 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "K" 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: "L" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "M" 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: "N" Number of atoms: 1082 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} bond proxies already assigned to first conformer: 1084 Chain: "O" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" Number of atoms: 591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 575 Chain: "Y" 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: "Z" 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: "a" Number of atoms: 463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Conformer: "B" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} bond proxies already assigned to first conformer: 439 Chain: "b" 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: "c" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "d" 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: "e" 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: "f" 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} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P A A A 404 " occ=0.60 ... (42 atoms not shown) pdb=" C4 B A A 404 " occ=0.40 residue: pdb=" N AARG X 41 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG X 41 " occ=0.49 residue: pdb=" N AALA a 2 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA a 2 " occ=0.50 residue: pdb=" N ALYS a 3 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS a 3 " occ=0.50 Time building chain proxies: 57.45, per 1000 atoms: 0.63 Number of scatterers: 91505 At special positions: 0 Unit cell: (212.76, 204.12, 246.24, 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 82 16.00 P 3019 15.00 O 25713 8.00 N 17048 7.00 C 45643 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=0, symmetry=0 Time building additional restraints: 37.54 Conformation dependent library (CDL) restraints added in 4.7 seconds 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6282 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 46 sheets defined 27.7% alpha, 18.7% beta 949 base pairs and 1490 stacking pairs defined. Time for finding SS restraints: 34.27 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.646A pdb=" N PHE C 266 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.710A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.853A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.799A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.826A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 17 removed outlier: 4.980A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 46 through 61 removed outlier: 4.143A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 4.094A pdb=" N ARG F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.586A pdb=" N VAL F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'G' and resid 3 through 7 removed outlier: 3.672A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 3 through 7' Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.794A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 76 removed outlier: 3.667A pdb=" N GLU H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'I' and resid 4 through 21 removed outlier: 4.584A pdb=" N GLY I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 49 removed outlier: 4.200A pdb=" N LEU I 41 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLY I 45 " --> pdb=" O LEU I 41 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG I 46 " --> pdb=" O ARG I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 64 Processing helix chain 'I' and resid 92 through 104 Processing helix chain 'I' and resid 123 through 128 removed outlier: 4.146A pdb=" N ALA I 127 " --> pdb=" O ILE I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 106 removed outlier: 3.521A pdb=" N GLN J 105 " --> pdb=" O SER J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 137 removed outlier: 3.613A pdb=" N SER J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET J 136 " --> pdb=" O THR J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 38 removed outlier: 4.055A pdb=" N GLU K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 62 removed outlier: 3.832A pdb=" N VAL K 62 " --> pdb=" O ALA K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 Processing helix chain 'K' and resid 89 through 95 Processing helix chain 'K' and resid 97 through 107 removed outlier: 4.298A pdb=" N ILE K 101 " --> pdb=" O PRO K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 Processing helix chain 'L' and resid 112 through 117 removed outlier: 3.546A pdb=" N ILE L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 61 removed outlier: 3.739A pdb=" N LEU M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 Processing helix chain 'M' and resid 91 through 96 Processing helix chain 'M' and resid 128 through 137 removed outlier: 3.577A pdb=" N ALA M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE M 135 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 58 Processing helix chain 'N' and resid 109 through 122 removed outlier: 3.606A pdb=" N ALA N 122 " --> pdb=" O LYS N 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 32 Processing helix chain 'O' and resid 38 through 55 removed outlier: 4.495A pdb=" N ARG O 46 " --> pdb=" O LYS O 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL O 47 " --> pdb=" O GLU O 43 " (cutoff:3.500A) Proline residue: O 50 - end of helix Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 72 through 82 removed outlier: 3.698A pdb=" N LYS O 78 " --> pdb=" O GLU O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 removed outlier: 3.802A pdb=" N PHE O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 22 removed outlier: 4.382A pdb=" N ARG P 13 " --> pdb=" O ARG P 9 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 62 removed outlier: 4.021A pdb=" N GLN P 61 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU P 62 " --> pdb=" O ILE P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 86 Processing helix chain 'P' and resid 101 through 113 Processing helix chain 'Q' and resid 3 through 10 Processing helix chain 'Q' and resid 97 through 102 removed outlier: 3.630A pdb=" N GLU Q 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 removed outlier: 3.998A pdb=" N ALA R 12 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.509A pdb=" N ARG R 28 " --> pdb=" O TYR R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 70 removed outlier: 3.946A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG R 51 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS R 54 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG R 55 " --> pdb=" O ARG R 51 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA R 68 " --> pdb=" O ARG R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 91 through 102 Processing helix chain 'R' and resid 102 through 118 Processing helix chain 'T' and resid 13 through 22 removed outlier: 3.519A pdb=" N VAL T 17 " --> pdb=" O SER T 13 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU T 19 " --> pdb=" O GLN T 15 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP T 22 " --> pdb=" O ARG T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 35 removed outlier: 3.868A pdb=" N ASP T 34 " --> pdb=" O SER T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 61 removed outlier: 3.916A pdb=" N VAL T 45 " --> pdb=" O LYS T 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU T 46 " --> pdb=" O LYS T 42 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA T 56 " --> pdb=" O GLU T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 10 Processing helix chain 'U' and resid 17 through 27 Processing helix chain 'U' and resid 39 through 52 removed outlier: 3.527A pdb=" N GLU U 52 " --> pdb=" O GLN U 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 23 Processing helix chain 'W' and resid 44 through 51 Processing helix chain 'W' and resid 53 through 58 Processing helix chain 'Y' and resid 53 through 63 Processing helix chain 'Y' and resid 63 through 74 removed outlier: 4.082A pdb=" N ALA Y 69 " --> pdb=" O ASP Y 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 35 Processing helix chain 'Z' and resid 41 through 63 removed outlier: 3.535A pdb=" N ASP Z 49 " --> pdb=" O GLN Z 45 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 28 Processing helix chain 'a' and resid 41 through 51 removed outlier: 3.950A pdb=" N MET a 47 " --> pdb=" O ALA a 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 17 Processing helix chain 'b' and resid 18 through 20 No H-bonds generated for 'chain 'b' and resid 18 through 20' Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 22 Processing helix chain 'd' and resid 24 through 38 removed outlier: 3.690A pdb=" N ARG d 28 " --> pdb=" O THR d 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 12 Processing helix chain 'e' and resid 37 through 43 Processing helix chain 'e' and resid 51 through 60 removed outlier: 4.402A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 33 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.362A pdb=" N ASN C 37 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLN C 60 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 82 removed outlier: 6.642A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 91 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 131 removed outlier: 5.837A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.675A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 79 through 83 removed outlier: 6.289A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.758A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.484A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 68 removed outlier: 3.565A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 16 through 20 Processing sheet with id=AB3, first strand: chain 'G' and resid 41 through 44 Processing sheet with id=AB4, first strand: chain 'G' and resid 122 through 124 Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AB6, first strand: chain 'H' and resid 19 through 20 Processing sheet with id=AB7, first strand: chain 'H' and resid 128 through 131 Processing sheet with id=AB8, first strand: chain 'I' and resid 50 through 52 removed outlier: 3.657A pdb=" N SER I 85 " --> pdb=" O SER I 24 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER I 24 " --> pdb=" O SER I 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 122 through 124 removed outlier: 6.374A pdb=" N ILE K 54 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP K 15 " --> pdb=" O GLN K 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'L' and resid 7 through 10 removed outlier: 6.714A pdb=" N LYS L 40 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL L 24 " --> pdb=" O ILE L 38 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ILE L 38 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N CYS L 84 " --> pdb=" O MET L 7 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN L 9 " --> pdb=" O CYS L 84 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 69 through 70 removed outlier: 6.600A pdb=" N ALA Q 58 " --> pdb=" O ILE Q 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE Q 50 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR Q 60 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ILE Q 64 " --> pdb=" O GLU Q 44 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLU Q 44 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR Q 25 " --> pdb=" O VAL Q 86 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL Q 86 " --> pdb=" O THR Q 25 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU Q 27 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE Q 84 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS Q 29 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 77 through 78 removed outlier: 3.645A pdb=" N ILE M 111 " --> pdb=" O ILE M 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 89 through 90 Processing sheet with id=AC6, first strand: chain 'N' and resid 62 through 65 removed outlier: 6.057A pdb=" N VAL N 101 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA N 35 " --> pdb=" O VAL N 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR N 103 " --> pdb=" O LEU N 33 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 39 through 42 removed outlier: 5.911A pdb=" N VAL N 89 " --> pdb=" O GLU N 75 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU N 75 " --> pdb=" O VAL N 89 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 33 through 37 Processing sheet with id=AC9, first strand: chain 'P' and resid 47 through 52 Processing sheet with id=AD1, first strand: chain 'S' and resid 10 through 14 removed outlier: 6.591A pdb=" N TYR S 2 " --> pdb=" O ILE S 41 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE S 41 " --> pdb=" O TYR S 2 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL S 4 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.650A pdb=" N GLN S 18 " --> pdb=" O ILE S 98 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE S 93 " --> pdb=" O HIS S 66 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N HIS S 66 " --> pdb=" O PHE S 93 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP S 95 " --> pdb=" O VAL S 64 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS S 60 " --> pdb=" O THR S 99 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE S 101 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 58 " --> pdb=" O ILE S 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 72 through 78 removed outlier: 3.963A pdb=" N TYR S 83 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 3 through 10 removed outlier: 5.407A pdb=" N ILE T 4 " --> pdb=" O VAL T 107 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL T 107 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYS T 6 " --> pdb=" O VAL T 105 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL T 105 " --> pdb=" O LYS T 6 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG T 8 " --> pdb=" O ILE T 103 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE T 103 " --> pdb=" O ARG T 8 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER T 101 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N THR T 100 " --> pdb=" O GLY T 79 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER T 108 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL T 71 " --> pdb=" O SER T 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 83 through 88 removed outlier: 4.011A pdb=" N ARG T 92 " --> pdb=" O ARG T 88 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.964A pdb=" N LYS U 81 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TRP U 80 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL U 62 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS U 82 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR U 60 " --> pdb=" O LYS U 82 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR U 84 " --> pdb=" O VAL U 58 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL U 58 " --> pdb=" O TYR U 84 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR U 86 " --> pdb=" O GLU U 56 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 67 through 70 removed outlier: 3.563A pdb=" N GLY U 75 " --> pdb=" O LYS U 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 65 through 66 removed outlier: 6.653A pdb=" N LYS V 33 " --> pdb=" O VAL V 28 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL V 28 " --> pdb=" O LYS V 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE V 35 " --> pdb=" O LYS V 26 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU V 10 " --> pdb=" O PHE V 73 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE V 72 " --> pdb=" O ASP V 81 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V' and resid 83 through 87 Processing sheet with id=AE1, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.632A pdb=" N ILE W 4 " --> pdb=" O VAL W 64 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N PHE W 91 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE W 29 " --> pdb=" O PHE W 91 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG W 93 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N TYR W 31 " --> pdb=" O ARG W 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 22 through 23 removed outlier: 6.934A pdb=" N LEU X 59 " --> pdb=" O ILE X 37 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 30 through 31 removed outlier: 3.567A pdb=" N GLY X 65 " --> pdb=" O VAL X 31 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS X 46 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE X 82 " --> pdb=" O HIS X 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 13 through 14 Processing sheet with id=AE5, first strand: chain 'Y' and resid 33 through 40 Processing sheet with id=AE6, first strand: chain 'a' and resid 35 through 39 Processing sheet with id=AE7, first strand: chain 'b' and resid 28 through 30 Processing sheet with id=AE8, first strand: chain 'c' and resid 20 through 25 Processing sheet with id=AE9, first strand: chain 'e' and resid 15 through 16 Processing sheet with id=AF1, first strand: chain 'f' and resid 2 through 3 removed outlier: 5.806A pdb=" N LYS f 2 " --> pdb=" O ARG f 36 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2416 hydrogen bonds 3848 hydrogen bond angles 0 basepair planarities 949 basepair parallelities 1490 stacking parallelities Total time for adding SS restraints: 131.51 Time building geometry restraints manager: 40.94 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: 10909 1.32 - 1.45: 43592 1.45 - 1.57: 38948 1.57 - 1.69: 6036 1.69 - 1.82: 150 Bond restraints: 99635 Sorted by residual: bond pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 1.469 1.430 0.038 1.28e-02 6.10e+03 9.03e+00 bond pdb=" CA VAL S 51 " pdb=" C VAL S 51 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.05e-02 9.07e+03 7.73e+00 bond pdb=" C PRO D 152 " pdb=" O PRO D 152 " ideal model delta sigma weight residual 1.235 1.203 0.033 1.30e-02 5.92e+03 6.26e+00 bond pdb=" CA PRO S 52 " pdb=" C PRO S 52 " ideal model delta sigma weight residual 1.520 1.552 -0.033 1.42e-02 4.96e+03 5.34e+00 bond pdb=" N PRO S 52 " pdb=" CA PRO S 52 " ideal model delta sigma weight residual 1.469 1.439 0.029 1.28e-02 6.10e+03 5.29e+00 ... (remaining 99630 not shown) Histogram of bond angle deviations from ideal: 87.76 - 99.78: 12 99.78 - 111.80: 67624 111.80 - 123.82: 67689 123.82 - 135.83: 14173 135.83 - 147.85: 1 Bond angle restraints: 149499 Sorted by residual: angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.84 147.85 -28.01 1.25e+00 6.40e-01 5.02e+02 angle pdb=" C THR I 67 " pdb=" N PRO I 68 " pdb=" CA PRO I 68 " ideal model delta sigma weight residual 119.84 132.08 -12.24 1.25e+00 6.40e-01 9.59e+01 angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CD PRO D 152 " ideal model delta sigma weight residual 125.00 87.76 37.24 4.10e+00 5.95e-02 8.25e+01 angle pdb=" N ASN D 149 " pdb=" CA ASN D 149 " pdb=" C ASN D 149 " ideal model delta sigma weight residual 110.91 118.14 -7.23 1.17e+00 7.31e-01 3.82e+01 angle pdb=" N PRO D 152 " pdb=" CA PRO D 152 " pdb=" C PRO D 152 " ideal model delta sigma weight residual 112.47 100.13 12.34 2.06e+00 2.36e-01 3.59e+01 ... (remaining 149494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 56230 35.95 - 71.91: 6830 71.91 - 107.86: 738 107.86 - 143.81: 17 143.81 - 179.77: 15 Dihedral angle restraints: 63830 sinusoidal: 54076 harmonic: 9754 Sorted by residual: dihedral pdb=" CA HIS e 31 " pdb=" C HIS e 31 " pdb=" N ILE e 32 " pdb=" CA ILE e 32 " ideal model delta harmonic sigma weight residual -180.00 -123.61 -56.39 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA J 77 " pdb=" C ALA J 77 " pdb=" N VAL J 78 " pdb=" CA VAL J 78 " ideal model delta harmonic sigma weight residual 180.00 129.07 50.93 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" O4' U A1779 " pdb=" C1' U A1779 " pdb=" N1 U A1779 " pdb=" C2 U A1779 " ideal model delta sinusoidal sigma weight residual 200.00 41.83 158.17 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 63827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 16976 0.065 - 0.131: 1960 0.131 - 0.196: 207 0.196 - 0.261: 30 0.261 - 0.326: 9 Chirality restraints: 19182 Sorted by residual: chirality pdb=" C1' A A 727 " pdb=" O4' A A 727 " pdb=" C2' A A 727 " pdb=" N9 A A 727 " both_signs ideal model delta sigma weight residual False 2.46 2.13 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C1' A A1652 " pdb=" O4' A A1652 " pdb=" C2' A A1652 " pdb=" N9 A A1652 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C1' G A 738 " pdb=" O4' G A 738 " pdb=" C2' G A 738 " pdb=" N9 G A 738 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 19179 not shown) Planarity restraints: 7697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 51 " 0.080 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO S 52 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO S 52 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO S 52 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 67 " -0.080 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO I 68 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO I 68 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO I 68 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.083 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO D 152 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.031 5.00e-02 4.00e+02 ... (remaining 7694 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 1432 2.59 - 3.16: 71134 3.16 - 3.74: 169012 3.74 - 4.32: 246794 4.32 - 4.90: 342407 Nonbonded interactions: 830779 Sorted by model distance: nonbonded pdb=" O6 G A 881 " pdb=" O2 U A 895 " model vdw 2.007 2.432 nonbonded pdb=" O2' A A2191 " pdb=" O5' U A2192 " model vdw 2.007 2.440 nonbonded pdb=" O2' G A1964 " pdb=" OP2 C A1967 " model vdw 2.011 2.440 nonbonded pdb=" O PRO D 152 " pdb=" N LYS D 154 " model vdw 2.043 2.520 nonbonded pdb=" O2 C A2683 " pdb=" NH2 ARG L 70 " model vdw 2.047 2.520 ... (remaining 830774 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=0.40 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: 1.590 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: 0.090 Extract box with map and model: 10.550 Check model and map are aligned: 0.990 Set scattering table: 0.610 Process input model: 326.830 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.270 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 344.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 0.048 99635 Z= 0.404 Angle : 0.747 37.238 149499 Z= 0.396 Chirality : 0.043 0.326 19182 Planarity : 0.006 0.125 7697 Dihedral : 23.235 179.768 57548 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.26 % Favored : 91.47 % Rotamer: Outliers : 0.29 % Allowed : 8.34 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.23 (0.12), residues: 3382 helix: -2.58 (0.14), residues: 894 sheet: -2.58 (0.17), residues: 688 loop : -3.07 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 248 HIS 0.009 0.001 HIS C 142 PHE 0.022 0.002 PHE Q 59 TYR 0.013 0.002 TYR C 83 ARG 0.013 0.001 ARG R 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 630 time to evaluate : 3.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 174 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8575 (pp) REVERT: C 185 GLU cc_start: 0.7499 (pt0) cc_final: 0.7107 (tt0) REVERT: D 128 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6742 (mtp-110) REVERT: D 169 ARG cc_start: 0.8391 (ttt90) cc_final: 0.7992 (ttp80) REVERT: E 102 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7347 (mtm-85) REVERT: E 163 ASN cc_start: 0.8232 (t0) cc_final: 0.7719 (t0) REVERT: F 64 LYS cc_start: 0.8222 (tttt) cc_final: 0.7841 (mptt) REVERT: F 130 MET cc_start: 0.6805 (ptm) cc_final: 0.6291 (ptt) REVERT: G 30 ASN cc_start: 0.7031 (t0) cc_final: 0.6675 (t0) REVERT: J 117 MET cc_start: 0.1592 (tmm) cc_final: -0.1112 (mmt) REVERT: K 125 TYR cc_start: 0.8779 (m-80) cc_final: 0.8424 (m-80) REVERT: L 22 ILE cc_start: 0.8444 (pt) cc_final: 0.8189 (pt) REVERT: M 55 MET cc_start: 0.7911 (tpp) cc_final: 0.7691 (tpt) REVERT: N 103 TYR cc_start: 0.8953 (m-80) cc_final: 0.8662 (m-80) REVERT: N 127 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8208 (ttmt) REVERT: O 58 ASP cc_start: 0.7572 (t70) cc_final: 0.7181 (t0) REVERT: Q 82 ASP cc_start: 0.8371 (t70) cc_final: 0.8121 (t0) REVERT: W 35 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8009 (mt-10) REVERT: Y 19 SER cc_start: 0.8963 (p) cc_final: 0.8736 (t) REVERT: b 7 LYS cc_start: 0.8501 (tttt) cc_final: 0.8212 (ttpt) outliers start: 6 outliers final: 5 residues processed: 635 average time/residue: 0.9423 time to fit residues: 983.5755 Evaluate side-chains 545 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 539 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain e residue 32 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 532 optimal weight: 0.7980 chunk 478 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 322 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 494 optimal weight: 5.9990 chunk 191 optimal weight: 40.0000 chunk 300 optimal weight: 20.0000 chunk 368 optimal weight: 20.0000 chunk 573 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN D 140 HIS E 41 GLN G 22 GLN G 45 HIS G 104 ASN G 111 HIS G 116 GLN K 132 HIS L 3 GLN M 35 HIS M 54 GLN M 93 ASN O 31 HIS P 38 GLN ** P 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 GLN R 37 GLN R 56 GLN R 72 ASN T 7 HIS V 27 ASN V 69 ASN Z 39 GLN a 9 GLN b 19 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 99635 Z= 0.247 Angle : 0.595 13.808 149499 Z= 0.311 Chirality : 0.037 0.290 19182 Planarity : 0.005 0.089 7697 Dihedral : 23.488 178.848 50878 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 2.38 % Allowed : 15.20 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.18 % 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: -3.06 (0.13), residues: 3382 helix: -1.32 (0.16), residues: 890 sheet: -2.13 (0.18), residues: 701 loop : -2.38 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 64 HIS 0.008 0.001 HIS e 31 PHE 0.023 0.002 PHE F 99 TYR 0.019 0.002 TYR F 8 ARG 0.006 0.000 ARG R 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 561 time to evaluate : 3.741 Fit side-chains revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8320 (pp) REVERT: D 128 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6783 (mtp180) REVERT: D 169 ARG cc_start: 0.8296 (ttt90) cc_final: 0.7952 (ttp80) REVERT: E 18 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7609 (t) REVERT: E 102 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7174 (mtm-85) REVERT: E 141 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6537 (ttm) REVERT: E 163 ASN cc_start: 0.8266 (t0) cc_final: 0.7774 (t0) REVERT: F 64 LYS cc_start: 0.8247 (tttt) cc_final: 0.7858 (mttp) REVERT: F 83 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.6137 (t80) REVERT: F 130 MET cc_start: 0.6351 (ptm) cc_final: 0.5855 (ptt) REVERT: G 81 GLU cc_start: 0.7478 (mp0) cc_final: 0.6996 (mp0) REVERT: J 117 MET cc_start: 0.1636 (tmm) cc_final: -0.1162 (mmt) REVERT: J 136 MET cc_start: 0.1307 (mtp) cc_final: 0.0704 (mtp) REVERT: K 125 TYR cc_start: 0.8703 (m-80) cc_final: 0.8433 (m-80) REVERT: L 22 ILE cc_start: 0.8372 (pt) cc_final: 0.8115 (pt) REVERT: M 55 MET cc_start: 0.7849 (tpp) cc_final: 0.7595 (tpt) REVERT: N 127 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8134 (ttmt) REVERT: Q 82 ASP cc_start: 0.8333 (t70) cc_final: 0.8006 (t0) REVERT: S 40 MET cc_start: 0.7848 (ttt) cc_final: 0.7647 (ttt) REVERT: W 35 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7975 (mt-10) REVERT: b 7 LYS cc_start: 0.8419 (tttt) cc_final: 0.8126 (ttpt) outliers start: 64 outliers final: 46 residues processed: 590 average time/residue: 0.8824 time to fit residues: 872.0276 Evaluate side-chains 586 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 536 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Z residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 318 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 0.0770 chunk 390 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 574 optimal weight: 20.0000 chunk 620 optimal weight: 0.6980 chunk 511 optimal weight: 9.9990 chunk 569 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 460 optimal weight: 9.9990 overall best weight: 3.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS G 104 ASN K 135 GLN L 3 GLN M 93 ASN P 100 HIS Q 12 GLN U 70 HIS X 76 ASN a 20 HIS b 5 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 99635 Z= 0.222 Angle : 0.553 12.026 149499 Z= 0.290 Chirality : 0.035 0.278 19182 Planarity : 0.005 0.081 7697 Dihedral : 23.335 177.936 50874 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 3.57 % Allowed : 17.11 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.18 % 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: -2.36 (0.13), residues: 3382 helix: -0.65 (0.17), residues: 904 sheet: -1.82 (0.18), residues: 713 loop : -1.93 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 64 HIS 0.006 0.001 HIS C 142 PHE 0.016 0.001 PHE X 69 TYR 0.020 0.001 TYR F 8 ARG 0.007 0.000 ARG U 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 543 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8337 (pp) REVERT: D 11 MET cc_start: 0.7867 (mtp) cc_final: 0.7585 (ttm) REVERT: D 128 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6711 (mtp180) REVERT: D 169 ARG cc_start: 0.8259 (ttt90) cc_final: 0.7954 (ttp80) REVERT: E 141 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6592 (ttm) REVERT: E 163 ASN cc_start: 0.8292 (t0) cc_final: 0.7791 (t0) REVERT: F 64 LYS cc_start: 0.8221 (tttt) cc_final: 0.7846 (mttp) REVERT: F 83 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6334 (t80) REVERT: F 130 MET cc_start: 0.6210 (ptm) cc_final: 0.5816 (ptt) REVERT: G 81 GLU cc_start: 0.7519 (mp0) cc_final: 0.7081 (mp0) REVERT: J 117 MET cc_start: 0.1491 (tmm) cc_final: -0.0949 (mmt) REVERT: K 125 TYR cc_start: 0.8783 (m-80) cc_final: 0.8185 (m-80) REVERT: N 127 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8060 (ttmt) REVERT: O 32 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7358 (mt-10) REVERT: O 65 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8563 (tt) REVERT: R 57 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: W 35 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7971 (mt-10) REVERT: e 49 MET cc_start: 0.7945 (mtp) cc_final: 0.7717 (mtt) outliers start: 97 outliers final: 66 residues processed: 599 average time/residue: 0.9004 time to fit residues: 908.3185 Evaluate side-chains 580 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 509 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 100 HIS Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 567 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 576 optimal weight: 1.9990 chunk 609 optimal weight: 9.9990 chunk 300 optimal weight: 20.0000 chunk 546 optimal weight: 0.5980 chunk 164 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS G 104 ASN L 3 GLN M 93 ASN ** P 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 99635 Z= 0.241 Angle : 0.564 12.868 149499 Z= 0.294 Chirality : 0.036 0.278 19182 Planarity : 0.005 0.075 7697 Dihedral : 23.311 177.844 50874 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.69 % Favored : 94.25 % Rotamer: Outliers : 4.12 % Allowed : 18.05 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.18 % 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: -2.12 (0.14), residues: 3382 helix: -0.46 (0.17), residues: 909 sheet: -1.68 (0.18), residues: 718 loop : -1.78 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 64 HIS 0.012 0.001 HIS C 53 PHE 0.023 0.002 PHE H 46 TYR 0.019 0.002 TYR F 8 ARG 0.006 0.000 ARG U 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 523 time to evaluate : 3.693 Fit side-chains revert: symmetry clash REVERT: C 167 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7129 (ttp-170) REVERT: C 174 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8243 (pp) REVERT: D 128 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6701 (mtp180) REVERT: D 169 ARG cc_start: 0.8267 (ttt90) cc_final: 0.7970 (ttp80) REVERT: E 163 ASN cc_start: 0.8284 (t0) cc_final: 0.7771 (t0) REVERT: F 64 LYS cc_start: 0.8236 (tttt) cc_final: 0.7865 (mttp) REVERT: F 83 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.6176 (t80) REVERT: F 130 MET cc_start: 0.6258 (ptm) cc_final: 0.5799 (ptt) REVERT: G 81 GLU cc_start: 0.7618 (mp0) cc_final: 0.7230 (mp0) REVERT: J 117 MET cc_start: 0.1260 (tmm) cc_final: -0.0947 (mmt) REVERT: J 136 MET cc_start: 0.1305 (mtp) cc_final: 0.0865 (mtp) REVERT: K 125 TYR cc_start: 0.8810 (m-80) cc_final: 0.8251 (m-80) REVERT: N 127 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8062 (ttmt) REVERT: O 32 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7367 (mt-10) REVERT: O 65 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8540 (tt) REVERT: P 100 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.8046 (t70) REVERT: R 57 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: S 40 MET cc_start: 0.7710 (ttt) cc_final: 0.7481 (ttt) REVERT: Y 19 SER cc_start: 0.8908 (p) cc_final: 0.8687 (t) REVERT: a 37 GLU cc_start: 0.7316 (tt0) cc_final: 0.7060 (tt0) REVERT: e 49 MET cc_start: 0.7951 (mtp) cc_final: 0.7719 (mtt) REVERT: f 4 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7075 (ptp-110) outliers start: 112 outliers final: 87 residues processed: 590 average time/residue: 0.8935 time to fit residues: 888.5556 Evaluate side-chains 593 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 500 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain P residue 4 LYS Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 100 HIS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 507 optimal weight: 1.9990 chunk 346 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 454 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 520 optimal weight: 6.9990 chunk 421 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 0.8980 chunk 547 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN L 90 ASN M 93 ASN N 45 GLN P 38 GLN P 100 HIS b 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 99635 Z= 0.212 Angle : 0.539 12.082 149499 Z= 0.282 Chirality : 0.034 0.269 19182 Planarity : 0.004 0.074 7697 Dihedral : 23.259 177.847 50874 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.64 % Rotamer: Outliers : 4.51 % Allowed : 19.13 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3382 helix: -0.28 (0.17), residues: 912 sheet: -1.59 (0.18), residues: 726 loop : -1.61 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 64 HIS 0.006 0.001 HIS e 31 PHE 0.016 0.001 PHE X 69 TYR 0.022 0.001 TYR F 8 ARG 0.007 0.000 ARG U 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 519 time to evaluate : 3.746 Fit side-chains revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8226 (pp) REVERT: D 11 MET cc_start: 0.7867 (mtp) cc_final: 0.7567 (ttm) REVERT: D 128 ARG cc_start: 0.7072 (mtp85) cc_final: 0.6683 (mtp180) REVERT: D 169 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7927 (ttp80) REVERT: E 163 ASN cc_start: 0.8279 (t0) cc_final: 0.7767 (t0) REVERT: F 64 LYS cc_start: 0.8229 (tttt) cc_final: 0.7849 (mttp) REVERT: F 83 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.6242 (t80) REVERT: F 130 MET cc_start: 0.6204 (ptm) cc_final: 0.5748 (ptt) REVERT: G 81 GLU cc_start: 0.7620 (mp0) cc_final: 0.7251 (mp0) REVERT: J 117 MET cc_start: 0.1300 (tmm) cc_final: -0.0659 (mmt) REVERT: J 136 MET cc_start: 0.1202 (mtp) cc_final: 0.0729 (mtp) REVERT: K 125 TYR cc_start: 0.8810 (m-80) cc_final: 0.8297 (m-80) REVERT: N 127 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8038 (ttmt) REVERT: O 32 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7355 (mt-10) REVERT: O 65 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8521 (tt) REVERT: P 93 ASP cc_start: 0.7245 (t0) cc_final: 0.6699 (t0) REVERT: Q 10 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7954 (tp40) REVERT: R 57 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: S 40 MET cc_start: 0.7681 (ttt) cc_final: 0.7451 (ttt) REVERT: a 37 GLU cc_start: 0.7302 (tt0) cc_final: 0.7065 (tt0) REVERT: e 49 MET cc_start: 0.7921 (mtp) cc_final: 0.7671 (mtt) outliers start: 123 outliers final: 97 residues processed: 599 average time/residue: 0.8956 time to fit residues: 908.5034 Evaluate side-chains 607 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 506 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 98 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 100 HIS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 205 optimal weight: 10.0000 chunk 549 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 358 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 610 optimal weight: 0.3980 chunk 506 optimal weight: 10.0000 chunk 282 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 320 optimal weight: 8.9990 overall best weight: 7.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 ASN L 90 ASN M 93 ASN N 45 GLN P 100 HIS b 5 GLN e 26 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 99635 Z= 0.433 Angle : 0.728 12.780 149499 Z= 0.370 Chirality : 0.043 0.320 19182 Planarity : 0.006 0.077 7697 Dihedral : 23.382 179.392 50873 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.46 % Favored : 92.48 % Rotamer: Outliers : 5.45 % Allowed : 19.53 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.15 % 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: -2.21 (0.14), residues: 3382 helix: -0.64 (0.17), residues: 912 sheet: -1.70 (0.18), residues: 733 loop : -1.78 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 64 HIS 0.010 0.001 HIS C 142 PHE 0.024 0.002 PHE H 46 TYR 0.024 0.002 TYR C 96 ARG 0.009 0.001 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 515 time to evaluate : 5.674 Fit side-chains revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8371 (pp) REVERT: D 169 ARG cc_start: 0.8429 (ttt90) cc_final: 0.8110 (ttp80) REVERT: E 163 ASN cc_start: 0.8352 (t0) cc_final: 0.7755 (t0) REVERT: E 168 ASP cc_start: 0.6106 (OUTLIER) cc_final: 0.5891 (m-30) REVERT: F 64 LYS cc_start: 0.8249 (tttt) cc_final: 0.7839 (mptt) REVERT: F 83 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6187 (t80) REVERT: G 81 GLU cc_start: 0.7614 (mp0) cc_final: 0.7286 (mp0) REVERT: J 117 MET cc_start: 0.1306 (tmm) cc_final: -0.1067 (mmt) REVERT: K 125 TYR cc_start: 0.8828 (m-80) cc_final: 0.8267 (m-80) REVERT: M 18 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8210 (mtp180) REVERT: N 127 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8175 (ttmt) REVERT: O 65 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8490 (tt) REVERT: P 93 ASP cc_start: 0.7302 (t0) cc_final: 0.6781 (t0) REVERT: R 57 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: S 40 MET cc_start: 0.7764 (ttt) cc_final: 0.7523 (ttt) REVERT: e 49 MET cc_start: 0.7879 (mtp) cc_final: 0.7663 (mtt) REVERT: f 4 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7144 (ptp-110) outliers start: 149 outliers final: 118 residues processed: 617 average time/residue: 0.9076 time to fit residues: 946.4295 Evaluate side-chains 628 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 503 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 132 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 22 ILE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 100 HIS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 62 ASP Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain X residue 38 VAL Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 26 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 588 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 445 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 513 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 chunk 608 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 370 optimal weight: 0.9980 chunk 280 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 ASN G 104 ASN L 90 ASN M 93 ASN ** P 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN V 45 HIS b 5 GLN e 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 99635 Z= 0.162 Angle : 0.521 12.227 149499 Z= 0.273 Chirality : 0.033 0.271 19182 Planarity : 0.004 0.074 7697 Dihedral : 23.230 178.437 50873 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 4.04 % Allowed : 21.55 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3382 helix: -0.14 (0.17), residues: 900 sheet: -1.52 (0.18), residues: 723 loop : -1.52 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 64 HIS 0.006 0.001 HIS e 31 PHE 0.013 0.001 PHE X 69 TYR 0.021 0.001 TYR F 8 ARG 0.006 0.000 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 542 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8266 (pp) REVERT: D 11 MET cc_start: 0.7825 (mtp) cc_final: 0.7567 (ttm) REVERT: D 128 ARG cc_start: 0.7278 (mtp-110) cc_final: 0.6758 (mtp180) REVERT: D 169 ARG cc_start: 0.8215 (ttt90) cc_final: 0.7933 (ttp80) REVERT: E 163 ASN cc_start: 0.8281 (t0) cc_final: 0.7782 (t0) REVERT: F 64 LYS cc_start: 0.8224 (tttt) cc_final: 0.7842 (mttp) REVERT: F 67 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7802 (mp) REVERT: F 83 TYR cc_start: 0.6531 (OUTLIER) cc_final: 0.6210 (t80) REVERT: G 81 GLU cc_start: 0.7580 (mp0) cc_final: 0.7283 (mp0) REVERT: J 117 MET cc_start: 0.1358 (tmm) cc_final: -0.0755 (mmt) REVERT: K 125 TYR cc_start: 0.8809 (m-80) cc_final: 0.8246 (m-80) REVERT: O 32 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7331 (mt-10) REVERT: O 65 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8525 (tt) REVERT: P 93 ASP cc_start: 0.7127 (t0) cc_final: 0.6662 (t0) REVERT: R 57 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: S 40 MET cc_start: 0.7685 (ttt) cc_final: 0.7463 (ttt) REVERT: e 49 MET cc_start: 0.7874 (mtp) cc_final: 0.7640 (mtt) REVERT: f 4 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7019 (ptp-110) outliers start: 109 outliers final: 89 residues processed: 613 average time/residue: 0.9002 time to fit residues: 929.0039 Evaluate side-chains 617 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 522 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 117 ASP Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 376 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 363 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 386 optimal weight: 4.9990 chunk 414 optimal weight: 0.7980 chunk 300 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 478 optimal weight: 0.0060 overall best weight: 3.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN L 90 ASN M 93 ASN ** P 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 99635 Z= 0.225 Angle : 0.548 12.427 149499 Z= 0.286 Chirality : 0.035 0.273 19182 Planarity : 0.004 0.071 7697 Dihedral : 23.222 178.264 50873 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 4.26 % Allowed : 21.91 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3382 helix: -0.11 (0.17), residues: 908 sheet: -1.42 (0.18), residues: 719 loop : -1.49 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 64 HIS 0.011 0.001 HIS F 5 PHE 0.027 0.001 PHE H 46 TYR 0.019 0.002 TYR C 96 ARG 0.009 0.000 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 523 time to evaluate : 3.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8221 (pp) REVERT: D 11 MET cc_start: 0.7949 (mtp) cc_final: 0.7646 (ttm) REVERT: D 169 ARG cc_start: 0.8246 (ttt90) cc_final: 0.7975 (ttp80) REVERT: E 35 TYR cc_start: 0.8921 (t80) cc_final: 0.8658 (t80) REVERT: E 163 ASN cc_start: 0.8285 (t0) cc_final: 0.7752 (t0) REVERT: F 64 LYS cc_start: 0.8229 (tttt) cc_final: 0.7811 (mptt) REVERT: F 67 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7801 (mp) REVERT: J 117 MET cc_start: 0.1345 (tmm) cc_final: -0.0752 (mmt) REVERT: J 136 MET cc_start: 0.0681 (mtp) cc_final: 0.0339 (mtt) REVERT: K 125 TYR cc_start: 0.8808 (m-80) cc_final: 0.8280 (m-80) REVERT: O 32 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7448 (mt-10) REVERT: O 65 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8528 (tt) REVERT: P 93 ASP cc_start: 0.7222 (t0) cc_final: 0.6785 (t0) REVERT: R 57 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7208 (m-80) REVERT: S 40 MET cc_start: 0.7687 (ttt) cc_final: 0.7450 (ttt) REVERT: d 14 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7661 (mtt180) REVERT: e 49 MET cc_start: 0.7832 (mtp) cc_final: 0.7592 (mtt) REVERT: f 4 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7019 (ptp-110) outliers start: 114 outliers final: 102 residues processed: 602 average time/residue: 0.8962 time to fit residues: 910.6943 Evaluate side-chains 612 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 504 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 108 MET Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain V residue 52 LEU Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 553 optimal weight: 10.0000 chunk 582 optimal weight: 0.0070 chunk 531 optimal weight: 2.9990 chunk 566 optimal weight: 10.0000 chunk 341 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 445 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 512 optimal weight: 10.0000 chunk 536 optimal weight: 20.0000 chunk 564 optimal weight: 10.0000 overall best weight: 3.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN L 90 ASN M 93 ASN P 100 HIS b 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 99635 Z= 0.204 Angle : 0.533 12.137 149499 Z= 0.279 Chirality : 0.034 0.267 19182 Planarity : 0.004 0.070 7697 Dihedral : 23.203 178.457 50873 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 4.48 % Allowed : 21.84 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3382 helix: -0.06 (0.17), residues: 912 sheet: -1.36 (0.19), residues: 706 loop : -1.42 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 64 HIS 0.008 0.001 HIS F 5 PHE 0.016 0.001 PHE X 69 TYR 0.025 0.001 TYR F 8 ARG 0.008 0.000 ARG K 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 520 time to evaluate : 3.828 Fit side-chains revert: symmetry clash REVERT: C 174 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8224 (pp) REVERT: D 11 MET cc_start: 0.7877 (mtp) cc_final: 0.7580 (ttm) REVERT: D 169 ARG cc_start: 0.8226 (ttt90) cc_final: 0.7957 (ttp80) REVERT: E 35 TYR cc_start: 0.8899 (t80) cc_final: 0.8594 (t80) REVERT: E 163 ASN cc_start: 0.8284 (t0) cc_final: 0.7750 (t0) REVERT: F 64 LYS cc_start: 0.8228 (tttt) cc_final: 0.7801 (mptt) REVERT: F 67 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7798 (mp) REVERT: J 117 MET cc_start: 0.1221 (tmm) cc_final: -0.0780 (mmt) REVERT: J 136 MET cc_start: 0.0379 (mtp) cc_final: 0.0121 (mtt) REVERT: K 125 TYR cc_start: 0.8808 (m-80) cc_final: 0.8286 (m-80) REVERT: O 32 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7348 (mt-10) REVERT: O 65 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8543 (tt) REVERT: P 83 LEU cc_start: 0.7407 (mt) cc_final: 0.7125 (mm) REVERT: P 93 ASP cc_start: 0.7154 (t0) cc_final: 0.6777 (t0) REVERT: R 57 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: S 40 MET cc_start: 0.7686 (ttt) cc_final: 0.7445 (ttt) REVERT: d 14 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.7608 (mtt180) REVERT: e 49 MET cc_start: 0.7912 (mtp) cc_final: 0.7655 (mtt) REVERT: f 4 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7078 (ptp-110) outliers start: 120 outliers final: 112 residues processed: 604 average time/residue: 0.8911 time to fit residues: 914.1286 Evaluate side-chains 638 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 520 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 95 ASP Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 16 HIS Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 372 optimal weight: 6.9990 chunk 599 optimal weight: 5.9990 chunk 365 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 416 optimal weight: 20.0000 chunk 628 optimal weight: 6.9990 chunk 578 optimal weight: 8.9990 chunk 500 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 386 optimal weight: 20.0000 chunk 306 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN G 104 ASN H 73 ASN L 90 ASN M 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 99635 Z= 0.304 Angle : 0.611 12.337 149499 Z= 0.315 Chirality : 0.038 0.288 19182 Planarity : 0.005 0.072 7697 Dihedral : 23.239 178.566 50873 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.37 % Favored : 93.57 % Rotamer: Outliers : 4.77 % Allowed : 21.70 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3382 helix: -0.25 (0.17), residues: 911 sheet: -1.42 (0.18), residues: 727 loop : -1.47 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 64 HIS 0.008 0.001 HIS e 31 PHE 0.028 0.002 PHE H 46 TYR 0.028 0.002 TYR F 8 ARG 0.007 0.001 ARG d 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 519 time to evaluate : 3.931 Fit side-chains REVERT: C 174 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8312 (pp) REVERT: D 11 MET cc_start: 0.8028 (mtp) cc_final: 0.7712 (ttm) REVERT: D 169 ARG cc_start: 0.8320 (ttt90) cc_final: 0.8070 (ttp80) REVERT: E 163 ASN cc_start: 0.8347 (t0) cc_final: 0.7762 (t0) REVERT: F 64 LYS cc_start: 0.8244 (tttt) cc_final: 0.7785 (mptt) REVERT: F 67 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7798 (mp) REVERT: F 134 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6499 (pm20) REVERT: J 117 MET cc_start: 0.1273 (tmm) cc_final: -0.0818 (mmt) REVERT: J 136 MET cc_start: 0.0327 (mtp) cc_final: 0.0118 (mtt) REVERT: K 125 TYR cc_start: 0.8828 (m-80) cc_final: 0.8270 (m-80) REVERT: O 32 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7478 (mt-10) REVERT: O 65 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8562 (tt) REVERT: P 83 LEU cc_start: 0.7445 (mt) cc_final: 0.7149 (mm) REVERT: R 57 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: S 40 MET cc_start: 0.7706 (ttt) cc_final: 0.7458 (ttt) REVERT: d 14 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7615 (mtt180) REVERT: e 49 MET cc_start: 0.7967 (mtp) cc_final: 0.7749 (mtt) REVERT: f 4 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7024 (ptp-110) outliers start: 128 outliers final: 114 residues processed: 609 average time/residue: 0.8878 time to fit residues: 916.1824 Evaluate side-chains 625 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 505 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 83 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 99 PHE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 17 VAL Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 60 ASP Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 67 ASN Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 120 VAL Chi-restraints excluded: chain M residue 121 THR Chi-restraints excluded: chain M residue 135 ILE Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain O residue 15 SER Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain P residue 20 GLU Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 35 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 32 VAL Chi-restraints excluded: chain Q residue 66 ASN Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain R residue 57 PHE Chi-restraints excluded: chain S residue 47 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 67 ASP Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 97 LEU Chi-restraints excluded: chain U residue 16 VAL Chi-restraints excluded: chain U residue 53 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain V residue 28 VAL Chi-restraints excluded: chain W residue 4 ILE Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain W residue 62 THR Chi-restraints excluded: chain W residue 65 VAL Chi-restraints excluded: chain W residue 77 VAL Chi-restraints excluded: chain Y residue 2 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 52 SER Chi-restraints excluded: chain Y residue 59 ILE Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 45 GLN Chi-restraints excluded: chain d residue 14 ARG Chi-restraints excluded: chain d residue 16 HIS Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain e residue 6 THR Chi-restraints excluded: chain f residue 4 ARG Chi-restraints excluded: chain f residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 397 optimal weight: 9.9990 chunk 533 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 461 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 501 optimal weight: 10.0000 chunk 209 optimal weight: 30.0000 chunk 514 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN L 90 ASN M 93 ASN b 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.162605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.134670 restraints weight = 178106.714| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.11 r_work: 0.3693 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 99635 Z= 0.408 Angle : 0.706 12.164 149499 Z= 0.360 Chirality : 0.042 0.316 19182 Planarity : 0.005 0.075 7697 Dihedral : 23.329 179.299 50873 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.68 % Rotamer: Outliers : 4.77 % Allowed : 21.95 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.80 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3382 helix: -0.52 (0.17), residues: 911 sheet: -1.56 (0.19), residues: 719 loop : -1.59 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 64 HIS 0.011 0.001 HIS e 31 PHE 0.023 0.002 PHE X 69 TYR 0.028 0.002 TYR C 96 ARG 0.007 0.001 ARG d 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17279.65 seconds wall clock time: 306 minutes 18.85 seconds (18378.85 seconds total)