Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 16 07:11:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/10_2023/7bv8_30215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/10_2023/7bv8_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_30215/10_2023/7bv8_30215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/10_2023/7bv8_30215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/10_2023/7bv8_30215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bv8_30215/10_2023/7bv8_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-1.21rc1-5097/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: 55.60, per 1000 atoms: 0.61 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: 37.32 Conformation dependent library (CDL) restraints added in 4.0 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: 34.87 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: 132.65 Time building geometry restraints manager: 40.41 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: 50818 35.95 - 71.91: 1995 71.91 - 107.86: 145 107.86 - 143.81: 17 143.81 - 179.77: 15 Dihedral angle restraints: 52990 sinusoidal: 43236 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 52987 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 10.710 Check model and map are aligned: 1.010 Set scattering table: 0.610 Process input model: 323.740 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.320 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 342.850 ------------------------------------------------------------------------------- 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 : 15.529 179.768 46708 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 *********************** 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 : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 635 average time/residue: 1.0382 time to fit residues: 1086.8959 Evaluate side-chains 543 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 538 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6365 time to fit residues: 10.1374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 X 76 ASN Z 39 GLN a 9 GLN b 19 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 99635 Z= 0.246 Angle : 0.589 12.930 149499 Z= 0.309 Chirality : 0.037 0.290 19182 Planarity : 0.005 0.082 7697 Dihedral : 14.794 179.183 40029 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 2.35 % Allowed : 15.42 % Favored : 82.24 % 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: -3.05 (0.13), residues: 3382 helix: -1.31 (0.16), residues: 893 sheet: -2.09 (0.18), residues: 698 loop : -2.38 (0.13), residues: 1791 *********************** 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 618 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 555 time to evaluate : 3.716 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 46 residues processed: 586 average time/residue: 0.9200 time to fit residues: 909.6912 Evaluate side-chains 578 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 532 time to evaluate : 3.671 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.7102 time to fit residues: 64.9869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 318 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 476 optimal weight: 0.0040 chunk 390 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 574 optimal weight: 5.9990 chunk 620 optimal weight: 0.9980 chunk 511 optimal weight: 9.9990 chunk 569 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 460 optimal weight: 9.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 HIS ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN K 135 GLN L 3 GLN M 93 ASN P 100 HIS Q 12 GLN U 70 HIS b 5 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 99635 Z= 0.216 Angle : 0.549 11.998 149499 Z= 0.288 Chirality : 0.035 0.280 19182 Planarity : 0.005 0.078 7697 Dihedral : 14.562 178.127 40029 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 1.99 % Allowed : 17.76 % Favored : 80.25 % 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: -2.36 (0.14), residues: 3382 helix: -0.66 (0.17), residues: 904 sheet: -1.82 (0.18), residues: 701 loop : -1.93 (0.14), residues: 1777 *********************** 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 604 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 551 time to evaluate : 3.839 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 587 average time/residue: 0.9179 time to fit residues: 905.5762 Evaluate side-chains 536 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 509 time to evaluate : 3.751 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.6617 time to fit residues: 38.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 631 random chunks: chunk 567 optimal weight: 20.0000 chunk 431 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 576 optimal weight: 5.9990 chunk 609 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 546 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN ** F 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 93 ASN a 20 HIS b 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 99635 Z= 0.327 Angle : 0.634 12.931 149499 Z= 0.328 Chirality : 0.039 0.295 19182 Planarity : 0.005 0.075 7697 Dihedral : 14.717 178.549 40029 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 2.74 % Allowed : 19.03 % Favored : 78.23 % 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: -2.30 (0.14), residues: 3382 helix: -0.66 (0.17), residues: 909 sheet: -1.77 (0.18), residues: 729 loop : -1.87 (0.14), residues: 1744 *********************** 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 597 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 523 time to evaluate : 3.675 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 52 residues processed: 564 average time/residue: 0.9138 time to fit residues: 872.0536 Evaluate side-chains 547 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 495 time to evaluate : 3.740 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.6731 time to fit residues: 70.9859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 8 optimal weight: 10.0000 chunk 454 optimal weight: 0.4980 chunk 251 optimal weight: 10.0000 chunk 520 optimal weight: 7.9990 chunk 421 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 547 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 HIS F 52 ASN G 104 ASN L 3 GLN L 90 ASN M 93 ASN N 45 GLN ** O 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN P 98 GLN Q 41 GLN V 45 HIS b 42 HIS d 26 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 99635 Z= 0.126 Angle : 0.495 12.526 149499 Z= 0.261 Chirality : 0.032 0.256 19182 Planarity : 0.004 0.076 7697 Dihedral : 14.346 177.880 40029 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 1.84 % Allowed : 20.22 % Favored : 77.94 % 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: -1.82 (0.14), residues: 3382 helix: -0.15 (0.17), residues: 902 sheet: -1.58 (0.18), residues: 723 loop : -1.58 (0.14), residues: 1757 *********************** 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 591 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 542 time to evaluate : 3.710 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 29 residues processed: 577 average time/residue: 0.9648 time to fit residues: 946.3568 Evaluate side-chains 534 residues out of total 2766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 505 time to evaluate : 3.691 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.6850 time to fit residues: 41.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7856 > 50: distance: 45 - 73: 6.745 distance: 48 - 70: 9.101 distance: 60 - 65: 11.189 distance: 65 - 66: 9.069 distance: 66 - 69: 4.747 distance: 67 - 68: 16.128 distance: 67 - 70: 11.122 distance: 70 - 71: 8.384 distance: 71 - 72: 5.387 distance: 71 - 74: 12.081 distance: 72 - 73: 10.164 distance: 72 - 75: 8.770 distance: 75 - 76: 11.765 distance: 76 - 77: 6.063 distance: 76 - 79: 20.393 distance: 77 - 78: 12.781 distance: 77 - 81: 8.647 distance: 79 - 80: 10.036 distance: 81 - 82: 7.038 distance: 82 - 83: 5.216 distance: 82 - 85: 4.881 distance: 83 - 84: 14.480 distance: 83 - 88: 9.649 distance: 85 - 86: 5.654 distance: 85 - 87: 15.020 distance: 88 - 89: 12.591 distance: 89 - 90: 13.191 distance: 89 - 92: 10.798 distance: 90 - 91: 16.362 distance: 90 - 95: 17.487 distance: 92 - 93: 7.324 distance: 92 - 94: 8.814 distance: 95 - 96: 8.155 distance: 96 - 97: 9.480 distance: 96 - 99: 11.089 distance: 97 - 98: 8.866 distance: 97 - 104: 10.838 distance: 98 - 126: 10.245 distance: 99 - 100: 19.231 distance: 100 - 101: 23.157 distance: 101 - 102: 15.747 distance: 101 - 103: 10.586 distance: 104 - 105: 3.347 distance: 105 - 108: 5.972 distance: 106 - 107: 16.950 distance: 106 - 113: 14.488 distance: 107 - 131: 14.815 distance: 108 - 109: 16.872 distance: 109 - 110: 10.258 distance: 110 - 111: 9.224 distance: 111 - 112: 11.865 distance: 113 - 114: 13.645 distance: 114 - 115: 18.066 distance: 114 - 117: 18.342 distance: 115 - 116: 27.282 distance: 115 - 118: 27.701 distance: 118 - 119: 3.988 distance: 119 - 120: 13.126 distance: 119 - 122: 12.024 distance: 120 - 121: 11.694 distance: 120 - 126: 14.172 distance: 122 - 123: 11.618 distance: 122 - 124: 12.907 distance: 123 - 125: 9.395 distance: 126 - 127: 5.151 distance: 127 - 128: 9.780 distance: 127 - 130: 3.011 distance: 128 - 129: 14.303 distance: 128 - 131: 12.946