Starting phenix.real_space_refine (version: dev) on Thu May 19 12:23:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzb_10657/05_2022/6xzb_10657_updated.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.014 sd= 0.750 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G2 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H2 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X2 TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 145650 Number of models: 1 Model: "" Number of chains: 55 Chain: "A1" Number of atoms: 32681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 32681 Classifications: {'RNA': 1523} Modifications used: {'rna3p_pyr': 568, 'rna2p_pur': 117, 'rna3p_pur': 752, 'rna2p_pyr': 86} Link IDs: {'rna3p': 1319, 'rna2p': 203} Chain breaks: 9 Chain: "B1" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C1" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D1" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E1" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "F1" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G1" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H1" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I1" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J1" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 796 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93, 'PCIS': 1} Chain: "K1" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L1" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain breaks: 1 Chain: "M1" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N1" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O1" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P1" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q1" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R1" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "S1" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U1" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "A2" Number of atoms: 62252 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1387, 'rna3p_pyr': 1063, 'rna2p_pur': 277, 'rna2p_pyr': 146} Link IDs: {'rna3p': 2467, 'rna2p': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Conformer: "B" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna3p': 17, 'rna2p': 7, 'rna3p_pur': 1387, 'rna3p_pyr': 1063, 'rna2p_pur': 277, 'rna2p_pyr': 146} Link IDs: {'rna3p': 2467, 'rna2p': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 bond proxies already assigned to first conformer: 69623 Chain: "B2" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 50, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "C2" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D2" Number of atoms: 1566 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E2" 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: "F2" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G2" 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: "H2" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1023 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 128, 'PCIS': 1} Chain: "I2" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "J2" 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: "K2" 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: "L2" 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: "M2" Number of atoms: 1075 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N2" 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: "O2" 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: "P2" 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: "Q2" 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: "R2" 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: "S2" 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: "T2" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U2" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V2" 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: "W2" Number of atoms: 580 Number of conformers: 1 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 Chain: "X2" 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: "Y2" 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: "Z2" Number of atoms: 449 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a2" 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: "b2" 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: "c2" 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: "d2" 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: "e2" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "f2" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 29, 'rna2p_pur': 6, 'rna3p_pur': 33, 'rna2p_pyr': 4, 'rna3p': 4} Link IDs: {'rna3p': 66, 'rna2p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "g2" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1667 Classifications: {'RNA': 75, 'peptide': 1} Modifications used: {'5*END': 1, 'rna3p': 12, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna2p': 2, 'rna3p_pyr': 23, 'rna2p_pur': 4} Link IDs: {None: 1, 'rna3p': 64, 'rna2p': 10} Not linked: pdbres=" Cg2 75 " pdbres="31Mg2 76 " Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Chain: "A2" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'DI0': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" P A CA22888 " occ=0.53 ... (38 atoms not shown) pdb=" C6 B CA22888 " occ=0.47 residue: pdb=" N AMEQD2 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2AMEQD2 150 " occ=0.49 residue: pdb=" N AARGW2 41 " occ=0.51 ... (9 atoms not shown) pdb=" NH2AARGW2 41 " occ=0.51 residue: pdb=" N AALAZ2 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB AALAZ2 2 " occ=0.50 residue: pdb=" N ALYSZ2 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYSZ2 3 " occ=0.50 Time building chain proxies: 82.06, per 1000 atoms: 0.56 Number of scatterers: 145650 At special positions: 0 Unit cell: (251.12, 253.7, 270.9, 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 151 16.00 P 4693 15.00 O 40609 8.00 N 27115 7.00 C 73082 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 Atom "ATOM 23116 O5' AA11081 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23094 O5' AA11080 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23116 O5' AA11081 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23116 O5' AA11081 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 54.64 Conformation dependent library (CDL) restraints added in 5.7 seconds 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10536 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 180 helices and 67 sheets defined 39.9% alpha, 18.8% beta 1556 base pairs and 2534 stacking pairs defined. Time for finding SS restraints: 66.03 Creating SS restraints... Processing helix chain 'B1' and resid 5 through 13 Processing helix chain 'B1' and resid 24 through 32 removed outlier: 4.095A pdb=" N LYSB1 28 " --> pdb=" O ASNB1 24 " (cutoff:3.500A) Proline residue: B1 29 - end of helix removed outlier: 5.762A pdb=" N PHEB1 32 " --> pdb=" O LYSB1 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 24 through 32' Processing helix chain 'B1' and resid 42 through 64 Proline residue: B1 48 - end of helix removed outlier: 3.789A pdb=" N LYSB1 64 " --> pdb=" O ILEB1 60 " (cutoff:3.500A) Processing helix chain 'B1' and resid 76 through 88 removed outlier: 3.794A pdb=" N CYSB1 87 " --> pdb=" O ALAB1 83 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASPB1 88 " --> pdb=" O ALAB1 84 " (cutoff:3.500A) Processing helix chain 'B1' and resid 103 through 123 removed outlier: 4.560A pdb=" N GLNB1 109 " --> pdb=" O LYSB1 105 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SERB1 110 " --> pdb=" O THRB1 106 " (cutoff:3.500A) Processing helix chain 'B1' and resid 130 through 148 removed outlier: 5.984A pdb=" N ALAB1 134 " --> pdb=" O THRB1 130 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEUB1 135 " --> pdb=" O LYSB1 131 " (cutoff:3.500A) Processing helix chain 'B1' and resid 165 through 170 removed outlier: 3.611A pdb=" N HISB1 170 " --> pdb=" O ALAB1 166 " (cutoff:3.500A) Processing helix chain 'B1' and resid 171 through 180 Processing helix chain 'B1' and resid 206 through 227 Processing helix chain 'C1' and resid 6 through 12 removed outlier: 3.884A pdb=" N ARGC1 11 " --> pdb=" O PROC1 7 " (cutoff:3.500A) Processing helix chain 'C1' and resid 28 through 48 removed outlier: 3.616A pdb=" N ALAC1 48 " --> pdb=" O THRC1 44 " (cutoff:3.500A) Processing helix chain 'C1' and resid 72 through 78 Processing helix chain 'C1' and resid 81 through 96 removed outlier: 3.730A pdb=" N ASPC1 93 " --> pdb=" O LYSC1 89 " (cutoff:3.500A) Processing helix chain 'C1' and resid 108 through 113 removed outlier: 3.946A pdb=" N ASPC1 112 " --> pdb=" O LYSC1 108 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALAC1 113 " --> pdb=" O PROC1 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C1' and resid 108 through 113' Processing helix chain 'C1' and resid 114 through 127 Processing helix chain 'C1' and resid 129 through 145 removed outlier: 3.807A pdb=" N GLYC1 145 " --> pdb=" O ALAC1 141 " (cutoff:3.500A) Processing helix chain 'D1' and resid 7 through 16 removed outlier: 4.576A pdb=" N LEUD1 11 " --> pdb=" O PROD1 7 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SERD1 12 " --> pdb=" O LYSD1 8 " (cutoff:3.500A) Processing helix chain 'D1' and resid 27 through 32 removed outlier: 3.655A pdb=" N LYSD1 31 " --> pdb=" O ALAD1 27 " (cutoff:3.500A) Processing helix chain 'D1' and resid 49 through 66 Processing helix chain 'D1' and resid 68 through 83 removed outlier: 5.103A pdb=" N LYSD1 83 " --> pdb=" O ALAD1 79 " (cutoff:3.500A) Processing helix chain 'D1' and resid 85 through 97 removed outlier: 4.040A pdb=" N ARGD1 97 " --> pdb=" O LEUD1 93 " (cutoff:3.500A) Processing helix chain 'D1' and resid 98 through 106 Processing helix chain 'D1' and resid 110 through 121 removed outlier: 3.873A pdb=" N LYSD1 121 " --> pdb=" O LEUD1 117 " (cutoff:3.500A) Processing helix chain 'D1' and resid 146 through 151 removed outlier: 4.790A pdb=" N LYSD1 151 " --> pdb=" O GLUD1 147 " (cutoff:3.500A) Processing helix chain 'D1' and resid 152 through 166 removed outlier: 3.715A pdb=" N LYSD1 156 " --> pdb=" O GLND1 152 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLUD1 166 " --> pdb=" O ALAD1 162 " (cutoff:3.500A) Processing helix chain 'D1' and resid 187 through 192 removed outlier: 3.867A pdb=" N LEUD1 191 " --> pdb=" O GLUD1 187 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SERD1 192 " --> pdb=" O ARGD1 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D1' and resid 187 through 192' Processing helix chain 'D1' and resid 196 through 206 removed outlier: 3.784A pdb=" N ILED1 200 " --> pdb=" O ASND1 196 " (cutoff:3.500A) Processing helix chain 'E1' and resid 55 through 71 removed outlier: 4.302A pdb=" N ASNE1 70 " --> pdb=" O LYSE1 66 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N METE1 71 " --> pdb=" O ALAE1 67 " (cutoff:3.500A) Processing helix chain 'E1' and resid 108 through 119 removed outlier: 3.623A pdb=" N GLYE1 119 " --> pdb=" O LEUE1 115 " (cutoff:3.500A) Processing helix chain 'E1' and resid 132 through 148 removed outlier: 5.801A pdb=" N ASNE1 148 " --> pdb=" O LEUE1 144 " (cutoff:3.500A) Processing helix chain 'E1' and resid 149 through 158 Processing helix chain 'F1' and resid 15 through 33 Proline residue: F1 19 - end of helix removed outlier: 3.751A pdb=" N ALAF1 32 " --> pdb=" O ALAF1 28 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLUF1 33 " --> pdb=" O ILEF1 29 " (cutoff:3.500A) Processing helix chain 'F1' and resid 67 through 81 removed outlier: 3.530A pdb=" N ILEF1 71 " --> pdb=" O PROF1 67 " (cutoff:3.500A) Processing helix chain 'F1' and resid 100 through 105 Processing helix chain 'G1' and resid 20 through 31 Processing helix chain 'G1' and resid 35 through 55 removed outlier: 3.559A pdb=" N GLNG1 52 " --> pdb=" O GLUG1 48 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARGG1 53 " --> pdb=" O THRG1 49 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SERG1 54 " --> pdb=" O LEUG1 50 " (cutoff:3.500A) Processing helix chain 'G1' and resid 57 through 70 removed outlier: 4.815A pdb=" N ALAG1 61 " --> pdb=" O SERG1 57 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASNG1 68 " --> pdb=" O VALG1 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALG1 69 " --> pdb=" O ALAG1 65 " (cutoff:3.500A) Processing helix chain 'G1' and resid 92 through 112 removed outlier: 3.965A pdb=" N ARGG1 111 " --> pdb=" O ALAG1 107 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLYG1 112 " --> pdb=" O ALAG1 108 " (cutoff:3.500A) Processing helix chain 'G1' and resid 115 through 130 Processing helix chain 'G1' and resid 132 through 149 Processing helix chain 'H1' and resid 5 through 21 Processing helix chain 'H1' and resid 30 through 44 Processing helix chain 'H1' and resid 112 through 120 Processing helix chain 'I1' and resid 34 through 40 removed outlier: 4.144A pdb=" N GLYI1 40 " --> pdb=" O GLUI1 36 " (cutoff:3.500A) Processing helix chain 'I1' and resid 41 through 56 Proline residue: I1 51 - end of helix removed outlier: 3.927A pdb=" N LEUI1 54 " --> pdb=" O GLNI1 50 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VALI1 55 " --> pdb=" O PROI1 51 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASPI1 56 " --> pdb=" O LEUI1 52 " (cutoff:3.500A) Processing helix chain 'I1' and resid 71 through 92 Processing helix chain 'I1' and resid 94 through 102 Processing helix chain 'J1' and resid 14 through 33 Processing helix chain 'J1' and resid 80 through 90 removed outlier: 3.987A pdb=" N ARGJ1 89 " --> pdb=" O ASPJ1 85 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEUJ1 90 " --> pdb=" O ALAJ1 86 " (cutoff:3.500A) Processing helix chain 'K1' and resid 46 through 51 removed outlier: 4.197A pdb=" N GLYK1 51 " --> pdb=" O ALAK1 47 " (cutoff:3.500A) Processing helix chain 'K1' and resid 54 through 59 removed outlier: 4.169A pdb=" N SERK1 58 " --> pdb=" O GLYK1 54 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THRK1 59 " --> pdb=" O SERK1 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K1' and resid 54 through 59' Processing helix chain 'K1' and resid 60 through 76 removed outlier: 3.621A pdb=" N VALK1 74 " --> pdb=" O CYSK1 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYSK1 75 " --> pdb=" O ALAK1 71 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLUK1 76 " --> pdb=" O ASPK1 72 " (cutoff:3.500A) Processing helix chain 'K1' and resid 92 through 104 removed outlier: 3.562A pdb=" N THRK1 96 " --> pdb=" O GLYK1 92 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILEK1 97 " --> pdb=" O ARGK1 93 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLYK1 104 " --> pdb=" O LEUK1 100 " (cutoff:3.500A) Processing helix chain 'L1' and resid 3 through 11 Proline residue: L1 11 - end of helix Processing helix chain 'L1' and resid 113 through 118 removed outlier: 3.934A pdb=" N TYRL1 117 " --> pdb=" O ALAL1 113 " (cutoff:3.500A) Processing helix chain 'M1' and resid 14 through 22 removed outlier: 4.096A pdb=" N THRM1 20 " --> pdb=" O VALM1 16 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SERM1 21 " --> pdb=" O ILEM1 17 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILEM1 22 " --> pdb=" O ALAM1 18 " (cutoff:3.500A) Processing helix chain 'M1' and resid 26 through 38 Processing helix chain 'M1' and resid 49 through 64 removed outlier: 4.287A pdb=" N LYSM1 62 " --> pdb=" O ASPM1 58 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHEM1 63 " --> pdb=" O GLUM1 59 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VALM1 64 " --> pdb=" O VALM1 60 " (cutoff:3.500A) Processing helix chain 'M1' and resid 66 through 84 removed outlier: 3.933A pdb=" N ARGM1 70 " --> pdb=" O GLUM1 66 " (cutoff:3.500A) Processing helix chain 'M1' and resid 85 through 94 Processing helix chain 'M1' and resid 106 through 111 Processing helix chain 'N1' and resid 3 through 24 removed outlier: 4.172A pdb=" N ALAN1 22 " --> pdb=" O ASPN1 18 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYSN1 23 " --> pdb=" O LYSN1 19 " (cutoff:3.500A) Processing helix chain 'N1' and resid 25 through 34 Processing helix chain 'N1' and resid 43 through 51 removed outlier: 3.720A pdb=" N GLNN1 49 " --> pdb=" O VALN1 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THRN1 50 " --> pdb=" O LEUN1 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEUN1 51 " --> pdb=" O LYSN1 47 " (cutoff:3.500A) Processing helix chain 'N1' and resid 80 through 91 Processing helix chain 'N1' and resid 52 through 57 Proline residue: N1 57 - end of helix Processing helix chain 'O1' and resid 4 through 16 Processing helix chain 'O1' and resid 24 through 44 removed outlier: 4.018A pdb=" N GLYO1 41 " --> pdb=" O ASNO1 37 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HISO1 42 " --> pdb=" O HISO1 38 " (cutoff:3.500A) Processing helix chain 'O1' and resid 49 through 74 removed outlier: 3.887A pdb=" N GLYO1 55 " --> pdb=" O HISO1 51 " (cutoff:3.500A) Processing helix chain 'O1' and resid 75 through 86 Processing helix chain 'P1' and resid 53 through 64 removed outlier: 3.526A pdb=" N ILEP1 57 " --> pdb=" O ASPP1 53 " (cutoff:3.500A) Processing helix chain 'P1' and resid 68 through 82 Processing helix chain 'R1' and resid 25 through 34 removed outlier: 4.201A pdb=" N ASNR1 31 " --> pdb=" O ALAR1 27 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYRR1 32 " --> pdb=" O THRR1 28 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILER1 33 " --> pdb=" O LEUR1 29 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THRR1 34 " --> pdb=" O LYSR1 30 " (cutoff:3.500A) Processing helix chain 'R1' and resid 41 through 46 Processing helix chain 'R1' and resid 48 through 66 Processing helix chain 'S1' and resid 12 through 26 removed outlier: 3.507A pdb=" N GLYS1 26 " --> pdb=" O ALAS1 22 " (cutoff:3.500A) Processing helix chain 'S1' and resid 70 through 76 removed outlier: 4.537A pdb=" N PHES1 74 " --> pdb=" O LYSS1 70 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALAS1 75 " --> pdb=" O LEUS1 71 " (cutoff:3.500A) Proline residue: S1 76 - end of helix No H-bonds generated for 'chain 'S1' and resid 70 through 76' Processing helix chain 'T1' and resid 4 through 41 removed outlier: 3.715A pdb=" N VALT1 35 " --> pdb=" O PHET1 31 " (cutoff:3.500A) Processing helix chain 'T1' and resid 44 through 65 Proline residue: T1 56 - end of helix Processing helix chain 'T1' and resid 68 through 87 removed outlier: 4.088A pdb=" N LEUT1 86 " --> pdb=" O GLNT1 82 " (cutoff:3.500A) Processing helix chain 'U1' and resid 11 through 27 removed outlier: 3.515A pdb=" N ALAU1 15 " --> pdb=" O PROU1 11 " (cutoff:3.500A) Processing helix chain 'U1' and resid 28 through 37 removed outlier: 3.800A pdb=" N GLUU1 36 " --> pdb=" O VALU1 32 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N PHEU1 37 " --> pdb=" O ARGU1 33 " (cutoff:3.500A) Processing helix chain 'U1' and resid 40 through 56 removed outlier: 4.448A pdb=" N HISU1 56 " --> pdb=" O ALAU1 52 " (cutoff:3.500A) Processing helix chain 'C2' and resid 10 through 15 removed outlier: 5.027A pdb=" N HISC2 15 " --> pdb=" O PROC2 11 " (cutoff:3.500A) Processing helix chain 'C2' and resid 30 through 35 removed outlier: 3.953A pdb=" N LEUC2 34 " --> pdb=" O PHEC2 30 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLUC2 35 " --> pdb=" O ALAC2 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 30 through 35' Processing helix chain 'C2' and resid 131 through 136 removed outlier: 3.683A pdb=" N ILEC2 135 " --> pdb=" O PROC2 131 " (cutoff:3.500A) Proline residue: C2 136 - end of helix No H-bonds generated for 'chain 'C2' and resid 131 through 136' Processing helix chain 'C2' and resid 207 through 215 removed outlier: 3.898A pdb=" N ALAC2 211 " --> pdb=" O LYSC2 207 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARGC2 214 " --> pdb=" O ALAC2 210 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLYC2 215 " --> pdb=" O ALAC2 211 " (cutoff:3.500A) Processing helix chain 'C2' and resid 221 through 226 removed outlier: 3.912A pdb=" N METC2 225 " --> pdb=" O ARGC2 221 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASNC2 226 " --> pdb=" O GLYC2 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 221 through 226' Processing helix chain 'C2' and resid 260 through 268 removed outlier: 3.698A pdb=" N ASPC2 264 " --> pdb=" O ASNC2 260 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYSC2 265 " --> pdb=" O LYSC2 261 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHEC2 266 " --> pdb=" O ARGC2 262 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILEC2 267 " --> pdb=" O THRC2 263 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VALC2 268 " --> pdb=" O ASPC2 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 260 through 268' Processing helix chain 'C2' and resid 197 through 202 removed outlier: 3.920A pdb=" N METC2 201 " --> pdb=" O ALAC2 198 " (cutoff:3.500A) Processing helix chain 'D2' and resid 56 through 61 removed outlier: 3.552A pdb=" N VALD2 60 " --> pdb=" O LYSD2 56 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THRD2 61 " --> pdb=" O ALAD2 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D2' and resid 56 through 61' Processing helix chain 'D2' and resid 62 through 72 removed outlier: 3.525A pdb=" N ALAD2 71 " --> pdb=" O HISD2 67 " (cutoff:3.500A) Processing helix chain 'D2' and resid 98 through 103 removed outlier: 4.507A pdb=" N ALAD2 102 " --> pdb=" O VALD2 98 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASPD2 103 " --> pdb=" O GLUD2 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D2' and resid 98 through 103' Processing helix chain 'D2' and resid 120 through 125 Processing helix chain 'D2' and resid 39 through 44 Processing helix chain 'E2' and resid 15 through 20 Processing helix chain 'E2' and resid 24 through 41 removed outlier: 3.562A pdb=" N ARGE2 40 " --> pdb=" O ALAE2 36 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLNE2 41 " --> pdb=" O ALAE2 37 " (cutoff:3.500A) Processing helix chain 'E2' and resid 48 through 53 removed outlier: 6.717A pdb=" N THRE2 53 " --> pdb=" O ARGE2 49 " (cutoff:3.500A) Processing helix chain 'E2' and resid 97 through 116 Processing helix chain 'E2' and resid 130 through 142 removed outlier: 3.527A pdb=" N LEUE2 134 " --> pdb=" O LYSE2 130 " (cutoff:3.500A) Processing helix chain 'E2' and resid 154 through 163 removed outlier: 4.562A pdb=" N ASNE2 163 " --> pdb=" O LEUE2 159 " (cutoff:3.500A) Processing helix chain 'E2' and resid 176 through 183 removed outlier: 3.575A pdb=" N ILEE2 181 " --> pdb=" O PROE2 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHEE2 183 " --> pdb=" O SERE2 179 " (cutoff:3.500A) Processing helix chain 'E2' and resid 189 through 201 Processing helix chain 'F2' and resid 2 through 11 removed outlier: 3.550A pdb=" N ASPF2 10 " --> pdb=" O ASPF2 6 " (cutoff:3.500A) Processing helix chain 'F2' and resid 12 through 21 removed outlier: 3.576A pdb=" N THRF2 18 " --> pdb=" O LYSF2 14 " (cutoff:3.500A) Processing helix chain 'F2' and resid 42 through 47 removed outlier: 4.104A pdb=" N ASPF2 46 " --> pdb=" O GLUF2 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYSF2 47 " --> pdb=" O ALAF2 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F2' and resid 42 through 47' Processing helix chain 'F2' and resid 48 through 62 removed outlier: 3.874A pdb=" N ASNF2 52 " --> pdb=" O LYSF2 48 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SERF2 61 " --> pdb=" O LEUF2 57 " (cutoff:3.500A) Processing helix chain 'F2' and resid 93 through 111 removed outlier: 3.708A pdb=" N ARGF2 102 " --> pdb=" O GLUF2 98 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILEF2 104 " --> pdb=" O PHEF2 100 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VALF2 108 " --> pdb=" O ILEF2 104 " (cutoff:3.500A) Proline residue: F2 109 - end of helix Processing helix chain 'F2' and resid 162 through 174 Processing helix chain 'G2' and resid 2 through 8 removed outlier: 4.034A pdb=" N ALAG2 7 " --> pdb=" O ARGG2 3 " (cutoff:3.500A) Proline residue: G2 8 - end of helix Processing helix chain 'G2' and resid 60 through 81 removed outlier: 3.663A pdb=" N THRG2 67 " --> pdb=" O ALAG2 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THRG2 80 " --> pdb=" O VALG2 76 " (cutoff:3.500A) Processing helix chain 'G2' and resid 137 through 153 removed outlier: 4.277A pdb=" N ARGG2 152 " --> pdb=" O LEUG2 148 " (cutoff:3.500A) Processing helix chain 'H2' and resid 4 through 22 removed outlier: 3.571A pdb=" N GLYH2 21 " --> pdb=" O GLUH2 17 " (cutoff:3.500A) Processing helix chain 'H2' and resid 34 through 49 Processing helix chain 'H2' and resid 56 through 68 removed outlier: 3.553A pdb=" N ARGH2 62 " --> pdb=" O THRH2 58 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLYH2 66 " --> pdb=" O ARGH2 62 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THRH2 67 " --> pdb=" O ALAH2 63 " (cutoff:3.500A) Proline residue: H2 68 - end of helix Processing helix chain 'H2' and resid 69 through 77 removed outlier: 4.013A pdb=" N LYSH2 73 " --> pdb=" O PHEH2 69 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASPH2 74 " --> pdb=" O GLUH2 70 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALAH2 75 " --> pdb=" O CYSH2 71 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHEH2 76 " --> pdb=" O LEUH2 72 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VALH2 77 " --> pdb=" O LYSH2 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H2' and resid 69 through 77' Processing helix chain 'H2' and resid 90 through 104 removed outlier: 5.845A pdb=" N ARGH2 94 " --> pdb=" O GLYH2 90 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYSH2 97 " --> pdb=" O ALAH2 93 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLUH2 98 " --> pdb=" O ARGH2 94 " (cutoff:3.500A) Processing helix chain 'H2' and resid 123 through 129 Processing helix chain 'I2' and resid 24 through 32 removed outlier: 3.580A pdb=" N LEUI2 28 " --> pdb=" O VALI2 24 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLNI2 31 " --> pdb=" O ALAI2 27 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLYI2 32 " --> pdb=" O LEUI2 28 " (cutoff:3.500A) Processing helix chain 'I2' and resid 34 through 47 Processing helix chain 'I2' and resid 75 through 85 Processing helix chain 'I2' and resid 102 through 115 Processing helix chain 'I2' and resid 121 through 137 Processing helix chain 'J2' and resid 24 through 38 removed outlier: 4.034A pdb=" N GLUJ2 31 " --> pdb=" O ARGJ2 27 " (cutoff:3.500A) Processing helix chain 'J2' and resid 88 through 96 Processing helix chain 'J2' and resid 97 through 110 removed outlier: 4.234A pdb=" N ILEJ2 101 " --> pdb=" O PROJ2 97 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N METJ2 108 " --> pdb=" O ALAJ2 104 " (cutoff:3.500A) Proline residue: J2 110 - end of helix Processing helix chain 'J2' and resid 112 through 122 removed outlier: 3.917A pdb=" N LYSJ2 121 " --> pdb=" O ALAJ2 117 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEUJ2 122 " --> pdb=" O METJ2 118 " (cutoff:3.500A) Processing helix chain 'K2' and resid 104 through 109 removed outlier: 4.814A pdb=" N ARGK2 108 " --> pdb=" O THRK2 104 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N SERK2 109 " --> pdb=" O ARGK2 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K2' and resid 104 through 109' Processing helix chain 'K2' and resid 112 through 119 Processing helix chain 'L2' and resid 37 through 42 removed outlier: 3.740A pdb=" N ARGL2 41 " --> pdb=" O GLYL2 37 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SERL2 42 " --> pdb=" O GLNL2 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 37 through 42' Processing helix chain 'L2' and resid 56 through 62 removed outlier: 3.510A pdb=" N LEUL2 61 " --> pdb=" O LEUL2 57 " (cutoff:3.500A) Proline residue: L2 62 - end of helix Processing helix chain 'L2' and resid 68 through 75 removed outlier: 4.126A pdb=" N ALAL2 72 " --> pdb=" O SERL2 68 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILEL2 73 " --> pdb=" O ARGL2 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THRL2 74 " --> pdb=" O LYSL2 70 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ALAL2 75 " --> pdb=" O ALAL2 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 68 through 75' Processing helix chain 'L2' and resid 78 through 85 removed outlier: 3.811A pdb=" N LEUL2 82 " --> pdb=" O ARGL2 78 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALAL2 83 " --> pdb=" O LEUL2 79 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYSL2 84 " --> pdb=" O SERL2 80 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VALL2 85 " --> pdb=" O ASPL2 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L2' and resid 78 through 85' Processing helix chain 'L2' and resid 91 through 99 Processing helix chain 'L2' and resid 128 through 139 removed outlier: 3.647A pdb=" N GLYL2 139 " --> pdb=" O ILEL2 135 " (cutoff:3.500A) Processing helix chain 'M2' and resid 42 through 58 removed outlier: 3.508A pdb=" N LYSM2 58 " --> pdb=" O THRM2 54 " (cutoff:3.500A) Processing helix chain 'M2' and resid 109 through 125 removed outlier: 3.603A pdb=" N GLUM2 115 " --> pdb=" O GLUM2 111 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYSM2 123 " --> pdb=" O LEUM2 119 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEUM2 124 " --> pdb=" O ALAM2 120 " (cutoff:3.500A) Proline residue: M2 125 - end of helix Processing helix chain 'N2' and resid 13 through 32 Processing helix chain 'N2' and resid 38 through 57 removed outlier: 4.270A pdb=" N ARGN2 46 " --> pdb=" O LYSN2 42 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VALN2 47 " --> pdb=" O GLUN2 43 " (cutoff:3.500A) Proline residue: N2 50 - end of helix removed outlier: 4.653A pdb=" N THRN2 57 " --> pdb=" O THRN2 53 " (cutoff:3.500A) Processing helix chain 'N2' and resid 59 through 71 Processing helix chain 'N2' and resid 72 through 88 removed outlier: 4.831A pdb=" N GLYN2 84 " --> pdb=" O PHEN2 80 " (cutoff:3.500A) Proline residue: N2 85 - end of helix Processing helix chain 'N2' and resid 119 through 124 removed outlier: 4.281A pdb=" N GLUN2 123 " --> pdb=" O GLUN2 120 " (cutoff:3.500A) Processing helix chain 'O2' and resid 2 through 22 removed outlier: 3.537A pdb=" N ARGO2 10 " --> pdb=" O ALAO2 6 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARGO2 13 " --> pdb=" O ARGO2 9 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALAO2 14 " --> pdb=" O ARGO2 10 " (cutoff:3.500A) Processing helix chain 'O2' and resid 55 through 63 removed outlier: 5.846A pdb=" N GLNO2 61 " --> pdb=" O ALAO2 57 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEUO2 62 " --> pdb=" O ILEO2 58 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYSO2 63 " --> pdb=" O ALAO2 59 " (cutoff:3.500A) Processing helix chain 'O2' and resid 67 through 86 removed outlier: 3.569A pdb=" N GLUO2 84 " --> pdb=" O GLUO2 80 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYSO2 85 " --> pdb=" O ARGO2 81 " (cutoff:3.500A) Processing helix chain 'O2' and resid 101 through 114 Processing helix chain 'P2' and resid 2 through 14 removed outlier: 3.748A pdb=" N GLUP2 11 " --> pdb=" O GLNP2 7 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLNP2 12 " --> pdb=" O LEUP2 8 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYSP2 14 " --> pdb=" O GLNP2 10 " (cutoff:3.500A) Processing helix chain 'P2' and resid 97 through 104 removed outlier: 4.680A pdb=" N ARGP2 101 " --> pdb=" O LEUP2 97 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLUP2 102 " --> pdb=" O TYRP2 98 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARGP2 103 " --> pdb=" O TYRP2 99 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THRP2 104 " --> pdb=" O LEUP2 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P2' and resid 97 through 104' Processing helix chain 'Q2' and resid 6 through 22 removed outlier: 3.568A pdb=" N GLNQ2 20 " --> pdb=" O LYSQ2 16 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYSQ2 22 " --> pdb=" O LEUQ2 18 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 26 through 31 removed outlier: 3.806A pdb=" N ARGQ2 30 " --> pdb=" O GLYQ2 26 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 32 through 37 removed outlier: 3.651A pdb=" N GLNQ2 37 " --> pdb=" O ARGQ2 33 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 39 through 73 removed outlier: 3.856A pdb=" N ARGQ2 51 " --> pdb=" O TYRQ2 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYSQ2 54 " --> pdb=" O ARGQ2 50 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARGQ2 55 " --> pdb=" O ARGQ2 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARGQ2 58 " --> pdb=" O LYSQ2 54 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASNQ2 72 " --> pdb=" O ALAQ2 68 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 75 through 87 Processing helix chain 'Q2' and resid 91 through 102 Processing helix chain 'Q2' and resid 103 through 118 Processing helix chain 'S2' and resid 13 through 25 removed outlier: 3.762A pdb=" N LEUS2 19 " --> pdb=" O GLNS2 15 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VALS2 20 " --> pdb=" O LYSS2 16 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEUS2 23 " --> pdb=" O LEUS2 19 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILES2 24 " --> pdb=" O VALS2 20 " (cutoff:3.500A) Processing helix chain 'S2' and resid 28 through 39 removed outlier: 3.574A pdb=" N ASPS2 34 " --> pdb=" O SERS2 30 " (cutoff:3.500A) Processing helix chain 'S2' and resid 41 through 61 removed outlier: 3.752A pdb=" N VALS2 45 " --> pdb=" O LYSS2 41 " (cutoff:3.500A) Processing helix chain 'T2' and resid 3 through 11 removed outlier: 3.980A pdb=" N LYST2 9 " --> pdb=" O GLUT2 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALT2 10 " --> pdb=" O ARGT2 6 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEUT2 11 " --> pdb=" O LEUT2 7 " (cutoff:3.500A) Processing helix chain 'T2' and resid 17 through 27 Processing helix chain 'T2' and resid 39 through 51 Processing helix chain 'U2' and resid 66 through 71 removed outlier: 3.887A pdb=" N VALU2 70 " --> pdb=" O GLNU2 66 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALAU2 71 " --> pdb=" O VALU2 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U2' and resid 66 through 71' Processing helix chain 'V2' and resid 13 through 24 Processing helix chain 'V2' and resid 43 through 53 removed outlier: 3.533A pdb=" N METV2 50 " --> pdb=" O LYSV2 46 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALAV2 52 " --> pdb=" O METV2 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYSV2 53 " --> pdb=" O ASNV2 49 " (cutoff:3.500A) Processing helix chain 'V2' and resid 54 through 59 removed outlier: 4.117A pdb=" N SERV2 58 " --> pdb=" O ALAV2 54 " (cutoff:3.500A) Processing helix chain 'X2' and resid 52 through 63 Processing helix chain 'X2' and resid 64 through 75 Processing helix chain 'Y2' and resid 2 through 10 removed outlier: 6.030A pdb=" N LEUY2 6 " --> pdb=" O LYSY2 2 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARGY2 7 " --> pdb=" O ALAY2 3 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLUY2 8 " --> pdb=" O LYSY2 4 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYSY2 9 " --> pdb=" O GLUY2 5 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SERY2 10 " --> pdb=" O LEUY2 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y2' and resid 2 through 10' Processing helix chain 'Y2' and resid 11 through 35 Processing helix chain 'Y2' and resid 39 through 63 removed outlier: 4.661A pdb=" N LEUY2 43 " --> pdb=" O GLNY2 39 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYSY2 44 " --> pdb=" O SERY2 40 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLYY2 62 " --> pdb=" O ASNY2 58 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 17 through 28 Processing helix chain 'Z2' and resid 41 through 52 Processing helix chain 'a2' and resid 9 through 19 removed outlier: 4.811A pdb=" N HISa2 19 " --> pdb=" O METa2 15 " (cutoff:3.500A) Processing helix chain 'c2' and resid 8 through 16 Processing helix chain 'c2' and resid 17 through 24 removed outlier: 4.311A pdb=" N THRc2 24 " --> pdb=" O ALAc2 20 " (cutoff:3.500A) Processing helix chain 'c2' and resid 25 through 38 Processing helix chain 'd2' and resid 7 through 14 removed outlier: 3.885A pdb=" N ARGd2 13 " --> pdb=" O GLYd2 9 " (cutoff:3.500A) Processing helix chain 'd2' and resid 32 through 37 removed outlier: 5.124A pdb=" N LYSd2 36 " --> pdb=" O ILEd2 32 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALAd2 37 " --> pdb=" O LEUd2 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd2' and resid 32 through 37' Processing helix chain 'd2' and resid 38 through 46 Proline residue: d2 46 - end of helix Processing helix chain 'd2' and resid 51 through 63 removed outlier: 4.838A pdb=" N GLYd2 56 " --> pdb=" O LYSd2 52 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LEUd2 57 " --> pdb=" O GLYd2 53 " (cutoff:3.500A) Proline residue: d2 63 - end of helix Processing sheet with id= 1, first strand: chain 'B1' and resid 90 through 93 removed outlier: 3.584A pdb=" N PHEB1 90 " --> pdb=" O ILEB1 67 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C1' and resid 53 through 59 Processing sheet with id= 3, first strand: chain 'C1' and resid 164 through 169 removed outlier: 5.717A pdb=" N ARGC1 164 " --> pdb=" O GLYC1 155 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLYC1 194 " --> pdb=" O THRC1 191 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASPC1 181 " --> pdb=" O LYSC1 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D1' and resid 141 through 145 removed outlier: 3.643A pdb=" N ASPD1 141 " --> pdb=" O PHED1 182 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N METD1 178 " --> pdb=" O ILED1 145 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E1' and resid 12 through 16 removed outlier: 6.705A pdb=" N LEUE1 36 " --> pdb=" O ILEE1 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E1' and resid 84 through 88 removed outlier: 3.661A pdb=" N ALAE1 99 " --> pdb=" O ASNE1 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASNE1 122 " --> pdb=" O ALAE1 99 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E1' and resid 33 through 40 Processing sheet with id= 8, first strand: chain 'F1' and resid 38 through 42 removed outlier: 5.792A pdb=" N TYRF1 59 " --> pdb=" O TRPF1 42 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N HISF1 3 " --> pdb=" O THRF1 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARGF1 86 " --> pdb=" O METF1 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F1' and resid 43 through 47 removed outlier: 5.920A pdb=" N LEUF1 47 " --> pdb=" O HISF1 55 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N HISF1 55 " --> pdb=" O LEUF1 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G1' and resid 73 through 79 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'H1' and resid 23 through 29 removed outlier: 6.558A pdb=" N ALAH1 23 " --> pdb=" O LEUH1 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASPH1 48 " --> pdb=" O THRH1 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H1' and resid 74 through 77 removed outlier: 6.619A pdb=" N VALH1 103 " --> pdb=" O ILEH1 126 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I1' and resid 5 through 11 Processing sheet with id= 14, first strand: chain 'J1' and resid 42 through 52 removed outlier: 4.882A pdb=" N LEUJ1 71 " --> pdb=" O PROJ1 43 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'K1' and resid 42 through 45 removed outlier: 3.731A pdb=" N ASNK1 29 " --> pdb=" O SERK1 26 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'L1' and resid 29 through 32 removed outlier: 5.208A pdb=" N LEUL1 81 " --> pdb=" O VALL1 98 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLYL1 85 " --> pdb=" O ARGL1 94 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ARGL1 94 " --> pdb=" O GLYL1 85 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'L1' and resid 36 through 41 removed outlier: 5.263A pdb=" N LYSL1 51 " --> pdb=" O ILEL1 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'P1' and resid 4 through 10 removed outlier: 3.832A pdb=" N PHEP1 38 " --> pdb=" O ARGP1 51 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARGP1 51 " --> pdb=" O PHEP1 38 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLYP1 49 " --> pdb=" O ASNP1 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Q1' and resid 7 through 11 removed outlier: 6.870A pdb=" N GLUQ1 60 " --> pdb=" O VALQ1 76 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Q1' and resid 19 through 30 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'S1' and resid 30 through 33 removed outlier: 4.746A pdb=" N LEUS1 47 " --> pdb=" O VALS1 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'C2' and resid 2 through 6 removed outlier: 5.541A pdb=" N VALC2 16 " --> pdb=" O CYSC2 6 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'C2' and resid 80 through 83 removed outlier: 3.641A pdb=" N ARGC2 80 " --> pdb=" O LEUC2 93 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEUC2 93 " --> pdb=" O GLUC2 79 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILEC2 74 " --> pdb=" O SERC2 118 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SERC2 118 " --> pdb=" O ILEC2 74 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASPC2 114 " --> pdb=" O VALC2 78 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLYC2 127 " --> pdb=" O GLNC2 115 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLNC2 117 " --> pdb=" O GLYC2 127 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C2' and resid 162 through 165 removed outlier: 3.734A pdb=" N GLNC2 163 " --> pdb=" O ARGC2 175 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THRC2 173 " --> pdb=" O VALC2 165 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLUC2 180 " --> pdb=" O LEUC2 176 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C2' and resid 90 through 96 removed outlier: 5.378A pdb=" N ASNC2 90 " --> pdb=" O ALAC2 106 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLUC2 100 " --> pdb=" O TYRC2 96 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D2' and resid 3 through 6 removed outlier: 3.993A pdb=" N GLUD2 168 " --> pdb=" O SERD2 113 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D2' and resid 10 through 16 removed outlier: 3.603A pdb=" N GLYD2 10 " --> pdb=" O VALD2 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALD2 20 " --> pdb=" O THRD2 16 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D2' and resid 79 through 84 removed outlier: 5.775A pdb=" N ARGD2 46 " --> pdb=" O LEUD2 84 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLND2 49 " --> pdb=" O THRD2 35 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLND2 94 " --> pdb=" O VALD2 34 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D2' and resid 105 through 108 removed outlier: 6.599A pdb=" N LYSD2 105 " --> pdb=" O VALD2 177 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E2' and resid 1 through 6 removed outlier: 4.695A pdb=" N SERE2 10 " --> pdb=" O LEUE2 5 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E2' and resid 117 through 120 removed outlier: 5.515A pdb=" N ARGE2 117 " --> pdb=" O ASPE2 184 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASPE2 168 " --> pdb=" O VALE2 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F2' and resid 65 through 69 removed outlier: 3.855A pdb=" N LYSF2 33 " --> pdb=" O THRF2 157 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THRF2 35 " --> pdb=" O THRF2 155 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRF2 155 " --> pdb=" O THRF2 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLYF2 39 " --> pdb=" O GLYF2 151 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLYF2 151 " --> pdb=" O GLYF2 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G2' and resid 16 through 19 Processing sheet with id= 34, first strand: chain 'G2' and resid 82 through 89 removed outlier: 5.804A pdb=" N THRG2 129 " --> pdb=" O LEUG2 89 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G2' and resid 94 through 98 removed outlier: 3.615A pdb=" N ARGG2 95 " --> pdb=" O SERG2 106 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VALG2 113 " --> pdb=" O LEUG2 105 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'H2' and resid 50 through 54 removed outlier: 3.907A pdb=" N SERH2 24 " --> pdb=" O VALH2 85 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VALH2 27 " --> pdb=" O LYSH2 109 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASPH2 29 " --> pdb=" O GLUH2 107 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLUH2 107 " --> pdb=" O ASPH2 29 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'I2' and resid 8 through 13 removed outlier: 3.876A pdb=" N SERI2 66 " --> pdb=" O TYRI2 62 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'J2' and resid 52 through 57 removed outlier: 5.268A pdb=" N ASPJ2 19 " --> pdb=" O LEUJ2 140 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J2' and resid 74 through 78 removed outlier: 7.296A pdb=" N GLYJ2 83 " --> pdb=" O THRJ2 78 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'K2' and resid 18 through 21 removed outlier: 4.119A pdb=" N THRK2 6 " --> pdb=" O CYSK2 21 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASNK2 82 " --> pdb=" O METK2 7 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K2' and resid 38 through 41 Processing sheet with id= 42, first strand: chain 'M2' and resid 37 through 40 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'M2' and resid 62 through 65 removed outlier: 3.698A pdb=" N TYRM2 103 " --> pdb=" O LEUM2 33 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEUM2 33 " --> pdb=" O LEUM2 102 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYSM2 100 " --> pdb=" O ALAM2 35 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M2' and resid 30 through 36 removed outlier: 7.538A pdb=" N SERM2 30 " --> pdb=" O LYSM2 133 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYSM2 127 " --> pdb=" O VALM2 36 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'N2' and resid 33 through 37 removed outlier: 4.610A pdb=" N METN2 110 " --> pdb=" O CYSN2 100 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N TYRN2 94 " --> pdb=" O VALN2 116 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'O2' and resid 49 through 53 removed outlier: 3.788A pdb=" N VALO2 49 " --> pdb=" O VALO2 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILEO2 35 " --> pdb=" O THRO2 53 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P2' and resid 38 through 45 removed outlier: 6.800A pdb=" N THRP2 25 " --> pdb=" O LYSP2 87 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P2' and resid 49 through 52 removed outlier: 3.714A pdb=" N ALAP2 49 " --> pdb=" O THRP2 60 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R2' and resid 11 through 15 removed outlier: 6.633A pdb=" N LEUR2 39 " --> pdb=" O GLYR2 50 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R2' and resid 18 through 23 removed outlier: 4.034A pdb=" N GLNR2 18 " --> pdb=" O ILER2 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASPR2 95 " --> pdb=" O VALR2 64 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYSR2 60 " --> pdb=" O THRR2 99 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLUR2 31 " --> pdb=" O VALR2 63 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'R2' and resid 57 through 60 Processing sheet with id= 52, first strand: chain 'R2' and resid 65 through 68 Processing sheet with id= 53, first strand: chain 'R2' and resid 71 through 78 removed outlier: 4.149A pdb=" N TYRR2 83 " --> pdb=" O ARGR2 78 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S2' and resid 2 through 8 removed outlier: 6.927A pdb=" N VALS2 106 " --> pdb=" O THRS2 72 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S2' and resid 81 through 88 removed outlier: 3.829A pdb=" N ARGS2 92 " --> pdb=" O ARGS2 88 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T2' and resid 28 through 33 removed outlier: 6.483A pdb=" N ASNT2 28 " --> pdb=" O LEUT2 87 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYST2 66 " --> pdb=" O ARGT2 77 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASPT2 79 " --> pdb=" O LYST2 64 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYST2 64 " --> pdb=" O ASPT2 79 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYST2 81 " --> pdb=" O VALT2 62 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VALT2 62 " --> pdb=" O LYST2 81 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALAT2 83 " --> pdb=" O THRT2 60 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THRT2 60 " --> pdb=" O ALAT2 83 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VALT2 85 " --> pdb=" O VALT2 58 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VALT2 58 " --> pdb=" O VALT2 85 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'U2' and resid 82 through 86 removed outlier: 6.985A pdb=" N ARGU2 82 " --> pdb=" O LYSU2 97 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARGU2 94 " --> pdb=" O ILEU2 103 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLUU2 101 " --> pdb=" O PHEU2 96 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'V2' and resid 69 through 72 removed outlier: 6.591A pdb=" N ALAV2 39 " --> pdb=" O ARGV2 9 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILEV2 89 " --> pdb=" O PROV2 27 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W2' and resid 51 through 54 removed outlier: 6.439A pdb=" N GLYW2 52 " --> pdb=" O LEUW2 59 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEUW2 59 " --> pdb=" O GLYW2 52 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLYW2 54 " --> pdb=" O HISW2 57 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'W2' and resid 65 through 72 Processing sheet with id= 61, first strand: chain 'X2' and resid 12 through 19 removed outlier: 4.490A pdb=" N ASNX2 23 " --> pdb=" O SERX2 19 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X2' and resid 35 through 41 Processing sheet with id= 63, first strand: chain 'Z2' and resid 33 through 39 removed outlier: 4.423A pdb=" N HISZ2 34 " --> pdb=" O GLNZ2 9 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N METZ2 54 " --> pdb=" O THRZ2 10 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a2' and resid 28 through 31 removed outlier: 6.472A pdb=" N SERa2 29 " --> pdb=" O LYSa2 37 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYSa2 37 " --> pdb=" O SERa2 29 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASPa2 31 " --> pdb=" O GLYa2 35 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'b2' and resid 20 through 25 removed outlier: 7.283A pdb=" N ILEb2 48 " --> pdb=" O SERb2 14 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEUb2 34 " --> pdb=" O GLUb2 51 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'd2' and resid 22 through 25 removed outlier: 5.657A pdb=" N PHEd2 22 " --> pdb=" O VALd2 50 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'e2' and resid 1 through 5 removed outlier: 6.503A pdb=" N HISe2 33 " --> pdb=" O CYSe2 27 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N CYSe2 27 " --> pdb=" O HISe2 33 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILEe2 23 " --> pdb=" O GLNe2 37 " (cutoff:3.500A) 1933 hydrogen bonds defined for protein. 5688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3902 hydrogen bonds 6056 hydrogen bond angles 0 basepair planarities 1556 basepair parallelities 2536 stacking parallelities Total time for adding SS restraints: 265.33 Time building geometry restraints manager: 60.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 11746 1.27 - 1.40: 49330 1.40 - 1.54: 87308 1.54 - 1.68: 9684 1.68 - 1.82: 271 Bond restraints: 158339 Sorted by residual: bond pdb=" C4 5MUA21939 " pdb=" C5 5MUA21939 " ideal model delta sigma weight residual 1.805 1.422 0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" C4 5MUA2 747 " pdb=" C5 5MUA2 747 " ideal model delta sigma weight residual 1.805 1.424 0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" C4 5MUg2 54 " pdb=" C5 5MUg2 54 " ideal model delta sigma weight residual 1.805 1.463 0.342 2.00e-02 2.50e+03 2.93e+02 bond pdb=" N1 5MUA21939 " pdb=" C6 5MUA21939 " ideal model delta sigma weight residual 1.638 1.297 0.341 2.00e-02 2.50e+03 2.91e+02 bond pdb=" N1 5MUA2 747 " pdb=" C6 5MUA2 747 " ideal model delta sigma weight residual 1.638 1.300 0.338 2.00e-02 2.50e+03 2.86e+02 ... (remaining 158334 not shown) Histogram of bond angle deviations from ideal: 93.98 - 103.68: 12278 103.68 - 113.39: 109909 113.39 - 123.09: 89706 123.09 - 132.80: 25025 132.80 - 142.51: 115 Bond angle restraints: 237033 Sorted by residual: angle pdb=" C1' YYGg2 37 " pdb=" N9 YYGg2 37 " pdb=" C8 YYGg2 37 " ideal model delta sigma weight residual 84.98 123.51 -38.53 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C2' 1MAg2 58 " pdb=" C1' 1MAg2 58 " pdb=" N9 1MAg2 58 " ideal model delta sigma weight residual 114.00 132.26 -18.26 1.50e+00 4.44e-01 1.48e+02 angle pdb=" N2 YYGg2 37 " pdb=" C11 YYGg2 37 " pdb=" C10 YYGg2 37 " ideal model delta sigma weight residual 93.59 126.73 -33.14 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C2' OMCg2 32 " pdb=" C1' OMCg2 32 " pdb=" N1 OMCg2 32 " ideal model delta sigma weight residual 112.00 96.21 15.79 1.50e+00 4.44e-01 1.11e+02 angle pdb=" N TYRH2 132 " pdb=" CA TYRH2 132 " pdb=" C TYRH2 132 " ideal model delta sigma weight residual 111.07 121.05 -9.98 1.07e+00 8.73e-01 8.70e+01 ... (remaining 237028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 81207 35.85 - 71.71: 2925 71.71 - 107.56: 238 107.56 - 143.41: 18 143.41 - 179.26: 17 Dihedral angle restraints: 84405 sinusoidal: 68075 harmonic: 16330 Sorted by residual: dihedral pdb=" C4' AA1 532 " pdb=" C3' AA1 532 " pdb=" C2' AA1 532 " pdb=" C1' AA1 532 " ideal model delta sinusoidal sigma weight residual -35.00 34.81 -69.81 1 8.00e+00 1.56e-02 9.82e+01 dihedral pdb=" CA HISd2 31 " pdb=" C HISd2 31 " pdb=" N ILEd2 32 " pdb=" CA ILEd2 32 " ideal model delta harmonic sigma weight residual 180.00 -131.12 -48.88 0 5.00e+00 4.00e-02 9.56e+01 dihedral pdb=" CA VALR2 51 " pdb=" C VALR2 51 " pdb=" N PROR2 52 " pdb=" CA PROR2 52 " ideal model delta harmonic sigma weight residual 180.00 -131.49 -48.51 0 5.00e+00 4.00e-02 9.41e+01 ... (remaining 84402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 29910 0.133 - 0.265: 257 0.265 - 0.398: 17 0.398 - 0.530: 8 0.530 - 0.663: 1 Chirality restraints: 30193 Sorted by residual: chirality pdb=" C2' Cg2 25 " pdb=" C3' Cg2 25 " pdb=" O2' Cg2 25 " pdb=" C1' Cg2 25 " both_signs ideal model delta sigma weight residual False -2.75 -2.09 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C3' Cg2 13 " pdb=" C4' Cg2 13 " pdb=" O3' Cg2 13 " pdb=" C2' Cg2 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.98 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" C3' GA22193 " pdb=" C4' GA22193 " pdb=" O3' GA22193 " pdb=" C2' GA22193 " both_signs ideal model delta sigma weight residual False -2.48 -1.99 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 30190 not shown) Planarity restraints: 12596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 1MAg2 58 " 0.799 2.00e-02 2.50e+03 6.61e-01 9.83e+03 pdb=" C4' 1MAg2 58 " -0.290 2.00e-02 2.50e+03 pdb=" O4' 1MAg2 58 " -0.359 2.00e-02 2.50e+03 pdb=" C3' 1MAg2 58 " -0.060 2.00e-02 2.50e+03 pdb=" O3' 1MAg2 58 " -1.308 2.00e-02 2.50e+03 pdb=" C2' 1MAg2 58 " 0.739 2.00e-02 2.50e+03 pdb=" O2' 1MAg2 58 " 0.861 2.00e-02 2.50e+03 pdb=" C1' 1MAg2 58 " -0.241 2.00e-02 2.50e+03 pdb=" N9 1MAg2 58 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGg2 10 " -0.001 2.00e-02 2.50e+03 6.54e-01 9.62e+03 pdb=" C4' 2MGg2 10 " 0.476 2.00e-02 2.50e+03 pdb=" O4' 2MGg2 10 " 0.766 2.00e-02 2.50e+03 pdb=" C3' 2MGg2 10 " -0.561 2.00e-02 2.50e+03 pdb=" O3' 2MGg2 10 " -0.686 2.00e-02 2.50e+03 pdb=" C2' 2MGg2 10 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MGg2 10 " 1.063 2.00e-02 2.50e+03 pdb=" C1' 2MGg2 10 " 0.160 2.00e-02 2.50e+03 pdb=" N9 2MGg2 10 " -1.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' YYGg2 37 " 0.072 2.00e-02 2.50e+03 6.35e-01 9.06e+03 pdb=" C4' YYGg2 37 " 0.367 2.00e-02 2.50e+03 pdb=" O4' YYGg2 37 " 0.596 2.00e-02 2.50e+03 pdb=" C3' YYGg2 37 " -0.703 2.00e-02 2.50e+03 pdb=" O3' YYGg2 37 " -0.642 2.00e-02 2.50e+03 pdb=" C2' YYGg2 37 " -0.116 2.00e-02 2.50e+03 pdb=" O2' YYGg2 37 " 1.107 2.00e-02 2.50e+03 pdb=" C1' YYGg2 37 " 0.272 2.00e-02 2.50e+03 pdb=" N9 YYGg2 37 " -0.954 2.00e-02 2.50e+03 ... (remaining 12593 not shown) Histogram of nonbonded interaction distances: 0.18 - 1.12: 12 1.12 - 2.07: 55 2.07 - 3.01: 74734 3.01 - 3.96: 476978 3.96 - 4.90: 816850 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1368629 Sorted by model distance: nonbonded pdb=" NH1 ARGI1 130 " pdb=" C4 Uf2 33 " model vdw 0.178 3.340 nonbonded pdb=" CZ ARGI1 130 " pdb=" C5 Uf2 33 " model vdw 0.331 3.570 nonbonded pdb=" OP1 AA11080 " pdb=" CE LYSE1 52 " model vdw 0.349 3.440 nonbonded pdb=" NH2 ARGI1 130 " pdb=" C6 Uf2 33 " model vdw 0.516 3.420 nonbonded pdb=" P AA11080 " pdb=" NZ LYSE1 52 " model vdw 0.655 3.480 ... (remaining 1368624 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4693 5.49 5 S 151 5.16 5 C 73082 2.51 5 N 27115 2.21 5 O 40609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 8.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 37.850 Check model and map are aligned: 1.690 Convert atoms to be neutral: 0.960 Process input model: 577.390 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 642.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.383 158339 Z= 0.475 Angle : 0.642 38.533 237033 Z= 0.354 Chirality : 0.038 0.663 30193 Planarity : 0.024 0.661 12596 Dihedral : 14.451 179.265 73869 Min Nonbonded Distance : 0.178 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.13 % Favored : 96.45 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.10), residues: 5626 helix: -1.28 (0.10), residues: 1901 sheet: -1.19 (0.14), residues: 1097 loop : -1.22 (0.11), residues: 2628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2406 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 2269 time to evaluate : 6.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 137 outliers final: 41 residues processed: 2342 average time/residue: 2.2826 time to fit residues: 7741.5262 Evaluate side-chains 1756 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1715 time to evaluate : 6.372 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 29 residues processed: 16 average time/residue: 1.2745 time to fit residues: 42.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 858 optimal weight: 1.9990 chunk 770 optimal weight: 0.9980 chunk 427 optimal weight: 7.9990 chunk 263 optimal weight: 4.9990 chunk 519 optimal weight: 10.0000 chunk 411 optimal weight: 10.0000 chunk 797 optimal weight: 20.0000 chunk 308 optimal weight: 3.9990 chunk 484 optimal weight: 20.0000 chunk 593 optimal weight: 50.0000 chunk 923 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 39 HIS B1 58 ASN B1 177 ASN ** C1 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 100 GLN D1 36 GLN D1 74 ASN D1 136 GLN D1 164 GLN E1 70 ASN E1 78 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 146 ASN F1 63 ASN G1 122 ASN H1 67 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1 56 HIS J1 58 ASN K1 101 ASN L1 5 ASN L1 46 ASN M1 14 HIS O1 37 ASN O1 40 GLN P1 26 ASN Q1 9 GLN R1 52 GLN T1 13 GLN T1 20 HIS T1 70 ASN C2 134 ASN D2 36 GLN D2 42 ASN E2 9 GLN E2 41 GLN E2 163 ASN E2 165 HIS E2 195 GLN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2 37 ASN ** G2 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 111 HIS I2 12 GLN J2 58 ASN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 99 ASN M2 3 GLN N2 11 ASN O2 98 GLN P2 12 GLN P2 41 GLN S2 9 HIS T2 70 HIS ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 69 ASN V2 49 ASN ** V2 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN Y2 20 ASN Y2 27 ASN c2 29 GLN d2 43 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 158339 Z= 0.237 Angle : 0.693 24.108 237033 Z= 0.375 Chirality : 0.036 0.425 30193 Planarity : 0.007 0.131 12596 Dihedral : 13.861 179.837 62600 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer Outliers : 7.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.11), residues: 5626 helix: 0.35 (0.12), residues: 1923 sheet: -0.65 (0.15), residues: 1076 loop : -0.80 (0.11), residues: 2627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2117 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1790 time to evaluate : 6.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 327 outliers final: 161 residues processed: 1918 average time/residue: 2.0378 time to fit residues: 5764.5723 Evaluate side-chains 1839 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1678 time to evaluate : 6.399 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 64 residues processed: 98 average time/residue: 1.1972 time to fit residues: 220.7735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 513 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 768 optimal weight: 20.0000 chunk 628 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 925 optimal weight: 5.9990 chunk 999 optimal weight: 0.9980 chunk 823 optimal weight: 0.9980 chunk 917 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 742 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 78 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1 52 ASN G1 122 ASN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 101 ASN L1 6 GLN M1 14 HIS O1 37 ASN R1 52 GLN D2 36 GLN D2 42 ASN D2 130 GLN E2 41 GLN E2 115 GLN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J2 128 ASN M2 17 ASN ** P2 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P2 12 GLN Q2 20 GLN R2 6 GLN R2 87 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 69 ASN V2 24 ASN V2 49 ASN V2 87 GLN W2 76 ASN X2 6 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 158339 Z= 0.220 Angle : 0.653 23.922 237033 Z= 0.358 Chirality : 0.035 0.405 30193 Planarity : 0.007 0.130 12596 Dihedral : 13.768 179.270 62600 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.87 % Rotamer Outliers : 7.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5626 helix: 0.72 (0.12), residues: 1929 sheet: -0.49 (0.15), residues: 1047 loop : -0.60 (0.12), residues: 2650 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2095 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 1729 time to evaluate : 6.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 366 outliers final: 207 residues processed: 1883 average time/residue: 2.0373 time to fit residues: 5697.8398 Evaluate side-chains 1828 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1621 time to evaluate : 6.429 Switching outliers to nearest non-outliers outliers start: 207 outliers final: 94 residues processed: 115 average time/residue: 1.2608 time to fit residues: 264.5478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 914 optimal weight: 3.9990 chunk 695 optimal weight: 5.9990 chunk 480 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 441 optimal weight: 10.0000 chunk 621 optimal weight: 10.0000 chunk 928 optimal weight: 3.9990 chunk 983 optimal weight: 9.9990 chunk 485 optimal weight: 50.0000 chunk 880 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1 78 ASN ** E1 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1 122 ASN H1 67 GLN I1 32 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1 6 GLN M1 14 HIS O1 37 ASN R1 52 GLN ** T1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2 37 ASN C2 153 GLN C2 239 ASN D2 36 GLN D2 126 ASN D2 130 GLN D2 167 ASN E2 41 GLN E2 92 HIS E2 163 ASN ** E2 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 104 ASN J2 128 ASN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 89 ASN N2 3 HIS P2 12 GLN Q2 20 GLN R2 87 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2 48 GLN ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 69 ASN V2 24 ASN V2 49 ASN V2 87 GLN W2 57 HIS X2 6 GLN ** Y2 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.205 158339 Z= 0.537 Angle : 0.817 23.126 237033 Z= 0.429 Chirality : 0.043 0.477 30193 Planarity : 0.008 0.136 12596 Dihedral : 14.101 178.603 62600 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.98 % Favored : 95.91 % Rotamer Outliers : 9.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5626 helix: 0.78 (0.12), residues: 1929 sheet: -0.47 (0.15), residues: 1094 loop : -0.72 (0.12), residues: 2603 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2163 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 466 poor density : 1697 time to evaluate : 6.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 466 outliers final: 258 residues processed: 1904 average time/residue: 2.0648 time to fit residues: 5830.9919 Evaluate side-chains 1888 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1630 time to evaluate : 6.502 Switching outliers to nearest non-outliers outliers start: 258 outliers final: 122 residues processed: 142 average time/residue: 1.2340 time to fit residues: 324.2037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 818 optimal weight: 2.9990 chunk 558 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 731 optimal weight: 0.8980 chunk 405 optimal weight: 2.9990 chunk 838 optimal weight: 0.8980 chunk 679 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 501 optimal weight: 5.9990 chunk 882 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 18 HIS ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1 3 GLN ** D1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 78 ASN G1 122 ASN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 28 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1 14 HIS O1 37 ASN R1 52 GLN T1 70 ASN C2 153 GLN D2 36 GLN D2 126 ASN D2 130 GLN D2 167 ASN D2 173 GLN E2 163 ASN ** E2 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 104 ASN H2 88 HIS J2 86 GLN K2 5 GLN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M2 17 ASN M2 60 GLN ** O2 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P2 12 GLN Q2 20 GLN R2 87 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 57 ASN T2 48 GLN ** U2 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 66 GLN U2 69 ASN ** V2 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 49 ASN X2 6 GLN Z2 49 ASN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 158339 Z= 0.180 Angle : 0.654 23.169 237033 Z= 0.359 Chirality : 0.034 0.376 30193 Planarity : 0.007 0.127 12596 Dihedral : 13.833 179.413 62600 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer Outliers : 6.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5626 helix: 1.02 (0.12), residues: 1920 sheet: -0.46 (0.15), residues: 1087 loop : -0.56 (0.12), residues: 2619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2023 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1700 time to evaluate : 6.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 323 outliers final: 206 residues processed: 1862 average time/residue: 2.0182 time to fit residues: 5595.3104 Evaluate side-chains 1841 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1635 time to evaluate : 6.470 Switching outliers to nearest non-outliers outliers start: 206 outliers final: 115 residues processed: 94 average time/residue: 1.2518 time to fit residues: 218.0896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 330 optimal weight: 10.0000 chunk 885 optimal weight: 0.0770 chunk 194 optimal weight: 9.9990 chunk 577 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 983 optimal weight: 0.9990 chunk 816 optimal weight: 3.9990 chunk 455 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 325 optimal weight: 8.9990 chunk 516 optimal weight: 7.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 ASN ** D1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 135 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 28 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 6 GLN M1 14 HIS O1 35 GLN O1 37 ASN R1 52 GLN ** C2 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 36 GLN D2 136 ASN D2 167 ASN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 104 ASN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M2 17 ASN P2 12 GLN Q2 20 GLN R2 87 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 59 ASN ** V2 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 49 ASN V2 51 GLN V2 87 GLN ** Y2 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 158339 Z= 0.272 Angle : 0.682 23.009 237033 Z= 0.370 Chirality : 0.036 0.422 30193 Planarity : 0.007 0.128 12596 Dihedral : 13.815 179.290 62600 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.54 % Favored : 96.34 % Rotamer Outliers : 7.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5626 helix: 0.98 (0.12), residues: 1931 sheet: -0.39 (0.15), residues: 1069 loop : -0.57 (0.12), residues: 2626 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2007 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1680 time to evaluate : 6.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 327 outliers final: 232 residues processed: 1826 average time/residue: 1.9866 time to fit residues: 5423.3324 Evaluate side-chains 1868 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1636 time to evaluate : 6.647 Switching outliers to nearest non-outliers outliers start: 232 outliers final: 113 residues processed: 121 average time/residue: 1.2051 time to fit residues: 272.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 948 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 560 optimal weight: 5.9990 chunk 718 optimal weight: 7.9990 chunk 556 optimal weight: 5.9990 chunk 828 optimal weight: 4.9990 chunk 549 optimal weight: 6.9990 chunk 980 optimal weight: 0.9990 chunk 613 optimal weight: 10.0000 chunk 597 optimal weight: 50.0000 chunk 452 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1 75 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1 58 ASN K1 28 ASN K1 101 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 6 GLN M1 14 HIS O1 37 ASN R1 52 GLN ** S1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S1 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 153 GLN D2 36 GLN D2 136 ASN D2 167 ASN D2 173 GLN E2 115 GLN E2 136 GLN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 88 GLN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M2 17 ASN M2 60 GLN P2 12 GLN R2 87 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 24 ASN V2 49 ASN V2 51 GLN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.147 158339 Z= 0.337 Angle : 0.709 23.016 237033 Z= 0.382 Chirality : 0.037 0.409 30193 Planarity : 0.008 0.129 12596 Dihedral : 13.843 179.083 62600 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.86 % Favored : 96.02 % Rotamer Outliers : 6.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.11), residues: 5626 helix: 0.91 (0.12), residues: 1936 sheet: -0.45 (0.15), residues: 1070 loop : -0.61 (0.12), residues: 2620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1973 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1648 time to evaluate : 6.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 325 outliers final: 230 residues processed: 1807 average time/residue: 1.9962 time to fit residues: 5400.6616 Evaluate side-chains 1845 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1615 time to evaluate : 6.085 Switching outliers to nearest non-outliers outliers start: 230 outliers final: 124 residues processed: 108 average time/residue: 1.1902 time to fit residues: 238.9207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 606 optimal weight: 6.9990 chunk 391 optimal weight: 8.9990 chunk 585 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 623 optimal weight: 3.9990 chunk 667 optimal weight: 10.0000 chunk 484 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 770 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 ASN ** D1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 116 GLN G1 122 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1 58 ASN K1 28 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 6 GLN M1 14 HIS O1 37 ASN R1 52 GLN ** S1 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2 36 GLN D2 136 ASN D2 167 ASN E2 115 GLN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 88 GLN K2 5 GLN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 89 ASN M2 17 ASN P2 12 GLN R2 87 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2 59 ASN ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 49 ASN X2 6 GLN ** Y2 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.101 158339 Z= 0.389 Angle : 0.739 22.923 237033 Z= 0.395 Chirality : 0.038 0.474 30193 Planarity : 0.008 0.131 12596 Dihedral : 13.901 179.605 62600 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.03 % Favored : 95.82 % Rotamer Outliers : 6.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 5626 helix: 0.79 (0.12), residues: 1936 sheet: -0.49 (0.16), residues: 1070 loop : -0.63 (0.12), residues: 2620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1948 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1631 time to evaluate : 6.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 317 outliers final: 232 residues processed: 1789 average time/residue: 2.0154 time to fit residues: 5422.3297 Evaluate side-chains 1832 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1600 time to evaluate : 6.427 Switching outliers to nearest non-outliers outliers start: 232 outliers final: 127 residues processed: 107 average time/residue: 1.2013 time to fit residues: 244.0525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 891 optimal weight: 0.9990 chunk 939 optimal weight: 5.9990 chunk 856 optimal weight: 0.9980 chunk 913 optimal weight: 0.7980 chunk 938 optimal weight: 1.9990 chunk 549 optimal weight: 6.9990 chunk 397 optimal weight: 10.0000 chunk 717 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 825 optimal weight: 1.9990 chunk 863 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 40 GLN E1 135 ASN G1 122 ASN H1 18 GLN ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 28 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 6 GLN M1 14 HIS O1 37 ASN R1 52 GLN ** S1 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2 37 ASN C2 153 GLN D2 36 GLN D2 136 ASN D2 167 ASN D2 173 GLN E2 97 ASN E2 136 GLN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 88 GLN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 5 GLN ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M2 17 ASN M2 60 GLN P2 12 GLN R2 87 GLN S2 57 ASN T2 48 GLN ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V2 49 ASN X2 6 GLN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 29 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.125 158339 Z= 0.169 Angle : 0.670 22.903 237033 Z= 0.363 Chirality : 0.033 0.434 30193 Planarity : 0.007 0.123 12596 Dihedral : 13.765 179.884 62600 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.27 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.11), residues: 5626 helix: 0.78 (0.12), residues: 1949 sheet: -0.35 (0.16), residues: 1006 loop : -0.57 (0.12), residues: 2671 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1886 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1679 time to evaluate : 6.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 144 residues processed: 1810 average time/residue: 2.0031 time to fit residues: 5470.3478 Evaluate side-chains 1760 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1616 time to evaluate : 6.427 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 107 residues processed: 38 average time/residue: 1.1775 time to fit residues: 89.9885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 910 optimal weight: 0.5980 chunk 599 optimal weight: 10.0000 chunk 965 optimal weight: 6.9990 chunk 589 optimal weight: 20.0000 chunk 458 optimal weight: 5.9990 chunk 671 optimal weight: 10.0000 chunk 1013 optimal weight: 7.9990 chunk 932 optimal weight: 6.9990 chunk 806 optimal weight: 50.0000 chunk 83 optimal weight: 10.0000 chunk 623 optimal weight: 5.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 36 ASN ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1 177 ASN ** B1 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 70 ASN E1 135 ASN G1 122 ASN ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1 64 GLN K1 28 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1 14 HIS O1 40 GLN C2 37 ASN C2 153 GLN D2 36 GLN D2 167 ASN E2 115 GLN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2 88 GLN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 89 ASN P2 12 GLN ** S2 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S2 61 ASN T2 59 ASN ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 69 ASN V2 5 ASN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 29 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.149 158339 Z= 0.414 Angle : 0.769 22.768 237033 Z= 0.408 Chirality : 0.039 0.417 30193 Planarity : 0.008 0.133 12596 Dihedral : 13.927 179.511 62600 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.41 % Favored : 95.45 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5626 helix: 0.74 (0.12), residues: 1919 sheet: -0.42 (0.16), residues: 1014 loop : -0.61 (0.12), residues: 2693 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11252 Ramachandran restraints generated. 5626 Oldfield, 0 Emsley, 5626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1849 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1666 time to evaluate : 6.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 135 residues processed: 1781 average time/residue: 2.0284 time to fit residues: 5438.9602 Evaluate side-chains 1724 residues out of total 4676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1589 time to evaluate : 6.481 Switching outliers to nearest non-outliers outliers start: 135 outliers final: 104 residues processed: 33 average time/residue: 1.4770 time to fit residues: 89.3415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 494 optimal weight: 7.9990 chunk 640 optimal weight: 3.9990 chunk 859 optimal weight: 3.9990 chunk 247 optimal weight: 20.0000 chunk 743 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 808 optimal weight: 8.9990 chunk 338 optimal weight: 0.0970 chunk 829 optimal weight: 0.5980 chunk 102 optimal weight: 50.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 36 ASN ** B1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 71 GLN ** E1 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1 135 ASN G1 122 ASN ** G1 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 28 ASN ** K1 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1 75 GLN M1 14 HIS O1 80 GLN R1 52 GLN C2 37 ASN C2 153 GLN D2 36 GLN D2 136 ASN D2 167 ASN E2 163 ASN ** F2 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G2 38 ASN G2 64 GLN G2 88 GLN ** J2 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M2 60 GLN R2 87 GLN S2 57 ASN S2 61 ASN ** U2 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U2 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V2 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 6 GLN ** a2 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.129476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.087456 restraints weight = 360858.846| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.89 r_work: 0.3177 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.3162 rms_B_bonded: 1.80 restraints_weight: 0.1250 r_work: 0.3155 rms_B_bonded: 1.83 restraints_weight: 0.0625 r_work: 0.3147 rms_B_bonded: 1.88 restraints_weight: 0.0312 r_work: 0.3140 rms_B_bonded: 1.94 restraints_weight: 0.0156 r_work: 0.3132 rms_B_bonded: 2.01 restraints_weight: 0.0078 r_work: 0.3124 rms_B_bonded: 2.09 restraints_weight: 0.0039 r_work: 0.3116 rms_B_bonded: 2.18 restraints_weight: 0.0020 r_work: 0.3108 rms_B_bonded: 2.28 restraints_weight: 0.0010 r_work: 0.3100 rms_B_bonded: 2.39 restraints_weight: 0.0005 r_work: 0.3091 rms_B_bonded: 2.51 restraints_weight: 0.0002 r_work: 0.3083 rms_B_bonded: 2.64 restraints_weight: 0.0001 r_work: 0.3073 rms_B_bonded: 2.78 restraints_weight: 0.0001 r_work: 0.3064 rms_B_bonded: 2.93 restraints_weight: 0.0000 r_work: 0.3054 rms_B_bonded: 3.09 restraints_weight: 0.0000 r_work: 0.3044 rms_B_bonded: 3.26 restraints_weight: 0.0000 r_work: 0.3034 rms_B_bonded: 3.44 restraints_weight: 0.0000 r_work: 0.3023 rms_B_bonded: 3.63 restraints_weight: 0.0000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.124 158339 Z= 0.194 Angle : 0.693 22.826 237033 Z= 0.373 Chirality : 0.034 0.438 30193 Planarity : 0.007 0.123 12596 Dihedral : 13.796 179.875 62600 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.05 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.52 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5626 helix: 0.74 (0.12), residues: 1940 sheet: -0.31 (0.16), residues: 1028 loop : -0.60 (0.12), residues: 2658 =============================================================================== Job complete usr+sys time: 74113.89 seconds wall clock time: 1258 minutes 38.48 seconds (75518.48 seconds total)