Starting phenix.real_space_refine on Thu Feb 22 10:11:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw3_24061/02_2024/7mw3_24061.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw3_24061/02_2024/7mw3_24061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw3_24061/02_2024/7mw3_24061.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw3_24061/02_2024/7mw3_24061.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw3_24061/02_2024/7mw3_24061.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mw3_24061/02_2024/7mw3_24061.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21463 2.51 5 N 5539 2.21 5 O 6676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 78": "OE1" <-> "OE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33825 Number of models: 1 Model: "" Number of chains: 33 Chain: "L" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7760 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7743 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7743 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7900 Chain: "B" Number of atoms: 7788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1006, 7771 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 55 Conformer: "B" Number of residues, atoms: 1006, 7771 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 55 bond proxies already assigned to first conformer: 7927 Chain: "G" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 7756 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1004, 7739 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 Conformer: "B" Number of residues, atoms: 1004, 7739 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 50, 'TRANS': 953} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 bond proxies already assigned to first conformer: 7896 Chain: "E" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1595 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AGLN C1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C1010 " occ=0.50 residue: pdb=" N AGLN B1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B1010 " occ=0.50 residue: pdb=" N AGLN A1010 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1010 " occ=0.50 Time building chain proxies: 27.13, per 1000 atoms: 0.80 Number of scatterers: 33825 At special positions: 0 Unit cell: (131.364, 167.676, 242.436, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 147 16.00 O 6676 8.00 N 5539 7.00 C 21463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.03 Simple disulfide: pdb=" SG CYS L 158 " - pdb=" SG CYS L 218 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 164 " - pdb=" SG CYS H 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 158 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS F 164 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 220 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG W 1 " - " NAG W 2 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 122 " " NAG A1308 " - " ASN A 331 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1074 " " NAG B1311 " - " ASN B 234 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 125 " " NAG C1309 " - " ASN C1074 " " NAG I 1 " - " ASN C 331 " " NAG J 1 " - " ASN C1134 " " NAG K 1 " - " ASN C1098 " " NAG M 1 " - " ASN C 801 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 709 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 343 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 343 " " NAG X 1 " - " ASN A1134 " " NAG Y 1 " - " ASN A1098 " " NAG Z 1 " - " ASN A 801 " " NAG a 1 " - " ASN A 717 " " NAG b 1 " - " ASN A 709 " " NAG c 1 " - " ASN A 234 " " NAG d 1 " - " ASN A 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.79 Conformation dependent library (CDL) restraints added in 10.7 seconds 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8030 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 76 sheets defined 20.7% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'L' and resid 103 through 107 removed outlier: 3.530A pdb=" N THR L 107 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'L' and resid 207 through 211 Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.665A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.554A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.822A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.172A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.525A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.575A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.576A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.994A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.537A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.974A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 4.109A pdb=" N GLY B 199 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.571A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.283A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.786A pdb=" N GLY B 545 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.527A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.730A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.688A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.980A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.682A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.509A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.829A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.811A pdb=" N THR G 107 " --> pdb=" O GLU G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 207 through 211 Processing helix chain 'F' and resid 106 through 110 Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.745A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.532A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.912A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.216A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.792A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.702A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.670A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.658A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.591A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.322A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.526A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.753A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.829A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.109A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.609A pdb=" N THR E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.514A pdb=" N SER D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 removed outlier: 4.461A pdb=" N THR D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AA2, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.702A pdb=" N LEU L 31 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP L 59 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 138 through 142 removed outlier: 5.223A pdb=" N SER L 155 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU L 205 " --> pdb=" O SER L 155 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL L 157 " --> pdb=" O LEU L 203 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU L 203 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU L 159 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER L 201 " --> pdb=" O LEU L 159 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN L 161 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU L 199 " --> pdb=" O ASN L 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 178 through 179 removed outlier: 4.650A pdb=" N TRP L 172 " --> pdb=" O GLN L 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.658A pdb=" N GLN H 58 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET H 53 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.304A pdb=" N GLY H 119 " --> pdb=" O PRO H 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.076A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 144 through 148 removed outlier: 6.076A pdb=" N TYR H 200 " --> pdb=" O ASP H 168 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 201 " --> pdb=" O VAL H 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 175 through 178 removed outlier: 4.107A pdb=" N TYR H 218 " --> pdb=" O VAL H 235 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.667A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.286A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.542A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.728A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 132 through 140 removed outlier: 6.495A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.461A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.643A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC3, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.768A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 702 through 704 removed outlier: 7.084A pdb=" N ASN C 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.169A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'C' and resid 788 through 789 removed outlier: 5.636A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.762A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.890A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.838A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 134 through 140 removed outlier: 8.606A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.869A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.541A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.219A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AE5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.607A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.432A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'G' and resid 24 through 27 Processing sheet with id=AF1, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.244A pdb=" N LEU G 31 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP G 59 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 138 through 142 removed outlier: 6.194A pdb=" N TYR G 197 " --> pdb=" O ASN G 162 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 168 through 174 Processing sheet with id=AF4, first strand: chain 'F' and resid 29 through 31 removed outlier: 5.106A pdb=" N ALA F 125 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY F 119 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N TRP F 127 " --> pdb=" O ARG F 117 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG F 117 " --> pdb=" O TRP F 127 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN F 129 " --> pdb=" O CYS F 115 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS F 115 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N MET F 53 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR F 69 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 37 through 42 Processing sheet with id=AF6, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.110A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 144 through 148 removed outlier: 6.110A pdb=" N TYR F 200 " --> pdb=" O ASP F 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER F 201 " --> pdb=" O VAL F 193 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 175 through 178 removed outlier: 4.133A pdb=" N TYR F 218 " --> pdb=" O VAL F 235 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.766A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.716A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.028A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 132 through 140 removed outlier: 3.875A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 312 through 319 removed outlier: 5.833A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'A' and resid 354 through 358 removed outlier: 7.196A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AG7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AG8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.155A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 714 through 728 removed outlier: 6.200A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.291A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.578A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.848A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 24 through 27 Processing sheet with id=AH5, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.256A pdb=" N LEU E 31 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP E 59 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AH7, first strand: chain 'E' and resid 138 through 142 removed outlier: 5.839A pdb=" N TYR E 197 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 169 through 174 Processing sheet with id=AH9, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AI1, first strand: chain 'D' and resid 29 through 31 removed outlier: 5.083A pdb=" N ALA D 125 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY D 119 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TRP D 127 " --> pdb=" O ARG D 117 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG D 117 " --> pdb=" O TRP D 127 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN D 129 " --> pdb=" O CYS D 115 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS D 115 " --> pdb=" O GLN D 129 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET D 53 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.089A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 144 through 148 removed outlier: 6.089A pdb=" N TYR D 200 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.383A pdb=" N TYR D 218 " --> pdb=" O VAL D 235 " (cutoff:3.500A) 1393 hydrogen bonds defined for protein. 3756 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.89 Time building geometry restraints manager: 13.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7653 1.33 - 1.46: 9701 1.46 - 1.58: 17043 1.58 - 1.71: 0 1.71 - 1.84: 189 Bond restraints: 34586 Sorted by residual: bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 34581 not shown) Histogram of bond angle deviations from ideal: 96.44 - 103.95: 528 103.95 - 111.47: 15930 111.47 - 118.98: 11753 118.98 - 126.49: 18522 126.49 - 134.00: 411 Bond angle restraints: 47144 Sorted by residual: angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.91 104.47 7.44 8.90e-01 1.26e+00 7.00e+01 angle pdb=" N ASN A1074 " pdb=" CA ASN A1074 " pdb=" C ASN A1074 " ideal model delta sigma weight residual 111.30 122.09 -10.79 1.43e+00 4.89e-01 5.69e+01 angle pdb=" N PHE C 559 " pdb=" CA PHE C 559 " pdb=" C PHE C 559 " ideal model delta sigma weight residual 112.92 121.77 -8.85 1.23e+00 6.61e-01 5.17e+01 angle pdb=" N PHE A1075 " pdb=" CA PHE A1075 " pdb=" C PHE A1075 " ideal model delta sigma weight residual 110.50 119.20 -8.70 1.41e+00 5.03e-01 3.81e+01 angle pdb=" N ILE A 233 " pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 109.12 118.13 -9.01 1.58e+00 4.01e-01 3.25e+01 ... (remaining 47139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.65: 20498 25.65 - 51.30: 767 51.30 - 76.95: 126 76.95 - 102.60: 59 102.60 - 128.25: 32 Dihedral angle restraints: 21482 sinusoidal: 8989 harmonic: 12493 Sorted by residual: dihedral pdb=" CA SER L 27 " pdb=" C SER L 27 " pdb=" N PRO L 28 " pdb=" CA PRO L 28 " ideal model delta harmonic sigma weight residual -180.00 -107.92 -72.08 0 5.00e+00 4.00e-02 2.08e+02 dihedral pdb=" CA SER G 27 " pdb=" C SER G 27 " pdb=" N PRO G 28 " pdb=" CA PRO G 28 " ideal model delta harmonic sigma weight residual -180.00 -107.98 -72.02 0 5.00e+00 4.00e-02 2.07e+02 dihedral pdb=" CA SER E 27 " pdb=" C SER E 27 " pdb=" N PRO E 28 " pdb=" CA PRO E 28 " ideal model delta harmonic sigma weight residual -180.00 -108.20 -71.80 0 5.00e+00 4.00e-02 2.06e+02 ... (remaining 21479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.579: 5590 0.579 - 1.159: 3 1.159 - 1.738: 0 1.738 - 2.318: 1 2.318 - 2.897: 1 Chirality restraints: 5595 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 0.50 -2.90 2.00e-01 2.50e+01 2.10e+02 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -0.66 -1.74 2.00e-01 2.50e+01 7.61e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.65e+01 ... (remaining 5592 not shown) Planarity restraints: 6055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.247 2.00e-02 2.50e+03 2.09e-01 5.48e+02 pdb=" C7 NAG B1309 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.164 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.357 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1308 " 0.232 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG C1308 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1308 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C1308 " -0.336 2.00e-02 2.50e+03 pdb=" O7 NAG C1308 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " 0.082 2.00e-02 2.50e+03 6.75e-02 5.69e+01 pdb=" C7 NAG A1309 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " 0.062 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " -0.107 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " -0.015 2.00e-02 2.50e+03 ... (remaining 6052 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 8 2.22 - 2.89: 13083 2.89 - 3.56: 45655 3.56 - 4.23: 79593 4.23 - 4.90: 135953 Nonbonded interactions: 274292 Sorted by model distance: nonbonded pdb=" ND2 ASN C1074 " pdb=" C1 NAG C1308 " model vdw 1.549 3.550 nonbonded pdb=" ND2 ASN A1074 " pdb=" C1 NAG A1309 " model vdw 1.559 3.550 nonbonded pdb=" ND2 ASN B1074 " pdb=" C1 NAG B1310 " model vdw 1.559 3.550 nonbonded pdb=" OE1 GLU G 129 " pdb=" OH TYR G 197 " model vdw 2.134 2.440 nonbonded pdb=" OG SER C 530 " pdb=" OE1 GLN C 580 " model vdw 2.153 2.440 ... (remaining 274287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 172 or resid 187 through 339 or (resid 340 and \ (name N or name CA or name C or name O or name CB )) or resid 341 through 461 or \ (resid 462 and (name N or name CA or name C or name O or name CB )) or resid 46 \ 3 through 465 or resid 467 through 528 or (resid 529 and (name N or name CA or n \ ame C or name O or name CB )) or resid 530 through 1009 or resid 1011 through 11 \ 45 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 128 or (resid 129 and (name N o \ r name CA or name C or name O or name CB )) or resid 130 through 212 or (resid 2 \ 13 through 215 and (name N or name CA or name C or name O or name CB )) or resid \ 216 through 238 or (resid 239 and (name N or name CA or name C or name O or nam \ e CB )) or resid 240 through 244 or (resid 245 and (name N or name CA or name C \ or name O or name CB )) or resid 263 through 465 or resid 467 through 528 or (re \ sid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 th \ rough 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 1009 or resid 1011 through 1145 or resid 1301 through 1309 \ )) selection = (chain 'C' and (resid 27 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 172 or resid 187 through 238 or \ (resid 239 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 0 through 332 or (resid 333 and (name N or name CA or name C or name O or name C \ B )) or resid 334 through 461 or (resid 462 and (name N or name CA or name C or \ name O or name CB )) or resid 463 through 465 or resid 467 through 557 or (resid \ 558 and (name N or name CA or name C or name O or name CB )) or resid 559 throu \ gh 1009 or resid 1011 through 1145 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 13.900 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 106.100 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.098 34586 Z= 0.278 Angle : 0.712 12.673 47144 Z= 0.399 Chirality : 0.071 2.897 5595 Planarity : 0.007 0.209 6007 Dihedral : 15.410 128.247 13299 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.53 % Favored : 96.12 % Rotamer: Outliers : 0.33 % Allowed : 0.28 % Favored : 99.39 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 4235 helix: 1.24 (0.19), residues: 719 sheet: 0.27 (0.14), residues: 1236 loop : -1.04 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 178 HIS 0.004 0.001 HIS D 188 PHE 0.026 0.001 PHE A 220 TYR 0.020 0.001 TYR B 369 ARG 0.008 0.001 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 254 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7072 (ttm-80) REVERT: D 233 LYS cc_start: 0.5764 (mmmt) cc_final: 0.5321 (mmmt) outliers start: 9 outliers final: 5 residues processed: 262 average time/residue: 0.4460 time to fit residues: 193.9422 Evaluate side-chains 203 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.9980 chunk 322 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B1010 GLN B ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 34586 Z= 0.379 Angle : 0.681 11.173 47144 Z= 0.341 Chirality : 0.050 0.389 5595 Planarity : 0.005 0.117 6007 Dihedral : 12.356 110.850 6105 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.29 % Favored : 95.48 % Rotamer: Outliers : 0.78 % Allowed : 4.58 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4235 helix: 1.44 (0.19), residues: 737 sheet: 0.15 (0.14), residues: 1251 loop : -1.11 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1102 HIS 0.006 0.001 HIS L 100 PHE 0.035 0.002 PHE C 906 TYR 0.026 0.002 TYR B1067 ARG 0.008 0.001 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7712 (tpp) outliers start: 25 outliers final: 17 residues processed: 227 average time/residue: 0.4660 time to fit residues: 176.8403 Evaluate side-chains 209 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 0.0040 chunk 120 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 387 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 345 optimal weight: 0.6980 chunk 384 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 542 ASN ** F 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 907 ASN E 51 ASN E 62 GLN D 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34586 Z= 0.205 Angle : 0.600 10.875 47144 Z= 0.297 Chirality : 0.047 0.378 5595 Planarity : 0.005 0.127 6007 Dihedral : 10.381 108.018 6100 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.26 % Rotamer: Outliers : 0.78 % Allowed : 6.06 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4235 helix: 1.75 (0.20), residues: 728 sheet: 0.16 (0.14), residues: 1244 loop : -1.05 (0.12), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 178 HIS 0.003 0.001 HIS F 188 PHE 0.024 0.001 PHE A 92 TYR 0.031 0.001 TYR B 369 ARG 0.005 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 4.248 Fit side-chains REVERT: H 83 PHE cc_start: 0.8171 (m-80) cc_final: 0.7868 (m-10) REVERT: C 740 MET cc_start: 0.7907 (tmm) cc_final: 0.7540 (ttt) REVERT: G 150 LYS cc_start: 0.7641 (mppt) cc_final: 0.7316 (mtmm) REVERT: A 131 CYS cc_start: 0.5330 (m) cc_final: 0.4859 (m) outliers start: 25 outliers final: 16 residues processed: 225 average time/residue: 0.4865 time to fit residues: 184.2157 Evaluate side-chains 204 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 201 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 260 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 411 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 171 GLN H 25 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 542 ASN A 188 ASN A 540 ASN A 580 GLN E 51 ASN E 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 34586 Z= 0.479 Angle : 0.715 10.230 47144 Z= 0.359 Chirality : 0.051 0.385 5595 Planarity : 0.005 0.115 6007 Dihedral : 9.924 108.095 6099 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.14 % Favored : 94.62 % Rotamer: Outliers : 1.28 % Allowed : 7.92 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4235 helix: 1.48 (0.20), residues: 721 sheet: -0.04 (0.14), residues: 1284 loop : -1.20 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 178 HIS 0.007 0.002 HIS A1058 PHE 0.027 0.002 PHE C 906 TYR 0.025 0.002 TYR B 369 ARG 0.006 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 4.138 Fit side-chains revert: symmetry clash REVERT: C 740 MET cc_start: 0.7816 (tmm) cc_final: 0.7391 (ttt) REVERT: A 131 CYS cc_start: 0.5335 (m) cc_final: 0.4793 (m) REVERT: A 220 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7192 (t80) REVERT: A 699 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8882 (mt) outliers start: 43 outliers final: 29 residues processed: 225 average time/residue: 0.4373 time to fit residues: 165.7657 Evaluate side-chains 217 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 221 ASN Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.8980 chunk 233 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 chunk 306 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 351 optimal weight: 0.2980 chunk 284 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 369 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN B 542 ASN A 188 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34586 Z= 0.175 Angle : 0.588 10.239 47144 Z= 0.291 Chirality : 0.046 0.354 5595 Planarity : 0.005 0.104 6007 Dihedral : 9.066 105.435 6097 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.60 % Favored : 96.16 % Rotamer: Outliers : 1.28 % Allowed : 8.58 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4235 helix: 1.80 (0.20), residues: 730 sheet: 0.08 (0.14), residues: 1261 loop : -1.06 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 178 HIS 0.003 0.001 HIS F 188 PHE 0.023 0.001 PHE A 92 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 4.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.7796 (tmm) cc_final: 0.7412 (ttt) REVERT: B 277 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8237 (mt) REVERT: B 740 MET cc_start: 0.7976 (tpt) cc_final: 0.7770 (tpt) REVERT: G 102 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6459 (tmm) REVERT: A 131 CYS cc_start: 0.5170 (m) cc_final: 0.4551 (m) outliers start: 43 outliers final: 22 residues processed: 239 average time/residue: 0.4406 time to fit residues: 177.6841 Evaluate side-chains 219 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 1135 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 115 CYS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 0.5980 chunk 370 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 412 optimal weight: 3.9990 chunk 342 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34586 Z= 0.178 Angle : 0.582 17.846 47144 Z= 0.285 Chirality : 0.045 0.298 5595 Planarity : 0.005 0.099 6007 Dihedral : 8.480 103.510 6097 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.14 % Favored : 95.64 % Rotamer: Outliers : 1.25 % Allowed : 9.14 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 4235 helix: 1.94 (0.20), residues: 732 sheet: 0.08 (0.14), residues: 1265 loop : -1.02 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 178 HIS 0.003 0.001 HIS H 224 PHE 0.026 0.001 PHE C 168 TYR 0.024 0.001 TYR C 170 ARG 0.007 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 209 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 740 MET cc_start: 0.7765 (tmm) cc_final: 0.7386 (ttt) REVERT: B 277 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8305 (mt) REVERT: B 740 MET cc_start: 0.7961 (tpt) cc_final: 0.7686 (tpp) REVERT: G 73 TYR cc_start: 0.8151 (p90) cc_final: 0.7897 (p90) REVERT: G 102 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6536 (tmm) REVERT: G 150 LYS cc_start: 0.7560 (mppt) cc_final: 0.7203 (mtmm) REVERT: G 179 GLN cc_start: 0.5876 (mm-40) cc_final: 0.5674 (mm-40) REVERT: A 131 CYS cc_start: 0.5255 (m) cc_final: 0.4644 (m) REVERT: D 39 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6893 (mtp) REVERT: D 233 LYS cc_start: 0.5417 (mmmt) cc_final: 0.5195 (mmmt) outliers start: 42 outliers final: 27 residues processed: 236 average time/residue: 0.4441 time to fit residues: 176.0610 Evaluate side-chains 223 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 346 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 410 optimal weight: 0.5980 chunk 256 optimal weight: 9.9990 chunk 250 optimal weight: 0.4980 chunk 189 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN C 188 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN E 51 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34586 Z= 0.176 Angle : 0.570 13.500 47144 Z= 0.281 Chirality : 0.045 0.292 5595 Planarity : 0.005 0.100 6007 Dihedral : 8.096 101.918 6097 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.72 % Favored : 96.02 % Rotamer: Outliers : 1.36 % Allowed : 9.36 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 4235 helix: 2.00 (0.20), residues: 732 sheet: 0.12 (0.14), residues: 1262 loop : -0.96 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 178 HIS 0.003 0.001 HIS H 224 PHE 0.023 0.001 PHE C 168 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 205 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: L 150 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7505 (mttm) REVERT: C 740 MET cc_start: 0.7775 (tmm) cc_final: 0.7463 (ttt) REVERT: B 277 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8295 (mt) REVERT: G 73 TYR cc_start: 0.8106 (p90) cc_final: 0.7876 (p90) REVERT: G 102 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6522 (tmm) REVERT: G 150 LYS cc_start: 0.7581 (mppt) cc_final: 0.7248 (mtmm) REVERT: G 179 GLN cc_start: 0.5898 (mm-40) cc_final: 0.5680 (mm-40) REVERT: A 131 CYS cc_start: 0.5231 (m) cc_final: 0.4628 (m) REVERT: D 39 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6958 (mtp) outliers start: 46 outliers final: 32 residues processed: 234 average time/residue: 0.4325 time to fit residues: 170.1680 Evaluate side-chains 228 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34586 Z= 0.230 Angle : 0.581 12.887 47144 Z= 0.287 Chirality : 0.046 0.265 5595 Planarity : 0.005 0.104 6007 Dihedral : 8.010 101.033 6097 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.74 % Rotamer: Outliers : 1.25 % Allowed : 9.67 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4235 helix: 1.95 (0.20), residues: 726 sheet: 0.14 (0.14), residues: 1248 loop : -0.97 (0.13), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 178 HIS 0.003 0.001 HIS F 188 PHE 0.024 0.001 PHE C 168 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 4.147 Fit side-chains revert: symmetry clash REVERT: L 103 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: L 150 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7416 (mttm) REVERT: H 77 THR cc_start: 0.7553 (t) cc_final: 0.7303 (t) REVERT: C 740 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7509 (ttt) REVERT: B 277 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8305 (mt) REVERT: G 73 TYR cc_start: 0.8110 (p90) cc_final: 0.7871 (p90) REVERT: G 102 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6492 (tmm) REVERT: G 150 LYS cc_start: 0.7564 (mppt) cc_final: 0.7293 (mtmm) REVERT: A 131 CYS cc_start: 0.5255 (m) cc_final: 0.4640 (m) REVERT: D 233 LYS cc_start: 0.5674 (mmmt) cc_final: 0.5298 (mmmt) outliers start: 42 outliers final: 31 residues processed: 225 average time/residue: 0.4418 time to fit residues: 167.1712 Evaluate side-chains 223 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 3.9990 chunk 393 optimal weight: 0.7980 chunk 358 optimal weight: 2.9990 chunk 382 optimal weight: 5.9990 chunk 230 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 300 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 345 optimal weight: 0.9980 chunk 361 optimal weight: 2.9990 chunk 381 optimal weight: 0.0980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34586 Z= 0.226 Angle : 0.581 12.266 47144 Z= 0.288 Chirality : 0.046 0.271 5595 Planarity : 0.005 0.108 6007 Dihedral : 7.867 100.040 6097 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.95 % Favored : 95.86 % Rotamer: Outliers : 1.14 % Allowed : 9.86 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4235 helix: 1.97 (0.20), residues: 725 sheet: 0.11 (0.14), residues: 1279 loop : -0.98 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 178 HIS 0.003 0.001 HIS F 188 PHE 0.024 0.001 PHE C 168 TYR 0.022 0.001 TYR E 52 ARG 0.008 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 3.775 Fit side-chains revert: symmetry clash REVERT: L 103 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: L 150 LYS cc_start: 0.7643 (mtpp) cc_final: 0.7395 (mttm) REVERT: C 740 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7486 (ttt) REVERT: B 277 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8310 (mt) REVERT: G 73 TYR cc_start: 0.8094 (p90) cc_final: 0.7851 (p90) REVERT: G 102 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6362 (tmm) REVERT: G 150 LYS cc_start: 0.7557 (mppt) cc_final: 0.7288 (mtmm) REVERT: A 131 CYS cc_start: 0.5342 (m) cc_final: 0.4847 (m) REVERT: D 233 LYS cc_start: 0.5308 (mmmt) cc_final: 0.4968 (mmmt) outliers start: 38 outliers final: 34 residues processed: 223 average time/residue: 0.4446 time to fit residues: 167.3337 Evaluate side-chains 232 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 117 GLU Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 0.8980 chunk 404 optimal weight: 6.9990 chunk 246 optimal weight: 0.0030 chunk 191 optimal weight: 6.9990 chunk 281 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 390 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN G 179 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34586 Z= 0.320 Angle : 0.626 11.587 47144 Z= 0.312 Chirality : 0.047 0.288 5595 Planarity : 0.005 0.112 6007 Dihedral : 7.997 101.093 6097 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.66 % Favored : 95.12 % Rotamer: Outliers : 1.11 % Allowed : 9.92 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4235 helix: 1.84 (0.20), residues: 726 sheet: -0.00 (0.14), residues: 1307 loop : -1.05 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 178 HIS 0.005 0.001 HIS F 188 PHE 0.025 0.002 PHE C 168 TYR 0.021 0.002 TYR B1067 ARG 0.007 0.000 ARG L 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8470 Ramachandran restraints generated. 4235 Oldfield, 0 Emsley, 4235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 103 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: L 150 LYS cc_start: 0.7621 (mtpp) cc_final: 0.7406 (mttm) REVERT: C 740 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7481 (ttt) REVERT: B 277 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8325 (mt) REVERT: B 740 MET cc_start: 0.7953 (tpt) cc_final: 0.7637 (tpt) REVERT: G 73 TYR cc_start: 0.8133 (p90) cc_final: 0.7850 (p90) REVERT: G 102 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6300 (tmm) REVERT: A 131 CYS cc_start: 0.5259 (m) cc_final: 0.4737 (m) REVERT: D 233 LYS cc_start: 0.5397 (mmmt) cc_final: 0.4969 (mmmt) outliers start: 37 outliers final: 31 residues processed: 221 average time/residue: 0.4511 time to fit residues: 167.2016 Evaluate side-chains 228 residues out of total 3719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 193 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 182 ASN Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 chunk 311 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.064187 restraints weight = 186178.657| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.86 r_work: 0.2941 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34586 Z= 0.260 Angle : 0.597 11.275 47144 Z= 0.297 Chirality : 0.046 0.280 5595 Planarity : 0.005 0.108 6007 Dihedral : 7.846 100.527 6097 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.17 % Favored : 95.64 % Rotamer: Outliers : 1.17 % Allowed : 9.94 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 1.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4235 helix: 1.86 (0.20), residues: 726 sheet: -0.00 (0.14), residues: 1305 loop : -1.05 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 178 HIS 0.004 0.001 HIS C 66 PHE 0.024 0.001 PHE C 168 TYR 0.028 0.001 TYR H 79 ARG 0.007 0.000 ARG L 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6715.58 seconds wall clock time: 124 minutes 1.78 seconds (7441.78 seconds total)