Starting phenix.real_space_refine on Fri Nov 17 12:47:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/11_2023/6mar_9062_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/11_2023/6mar_9062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/11_2023/6mar_9062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/11_2023/6mar_9062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/11_2023/6mar_9062_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mar_9062/11_2023/6mar_9062_updated.pdb" } resolution = 4.5 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= 0.005 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 116 5.16 5 C 12000 2.51 5 N 3158 2.21 5 O 3937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 19211 Number of models: 1 Model: "" Number of chains: 47 Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1050 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "D" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1149 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 1, 'TRANS': 144} Chain breaks: 1 Chain: "C" Number of atoms: 3493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3493 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3448 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 415} Chain breaks: 3 Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "G" 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 chiralities: 2 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 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 chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 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 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "T" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "U" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 124 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "f" 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 chiralities: 2 Chain: "g" 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 chiralities: 2 Chain: "h" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 2 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "l" 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 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 chiralities: 2 Chain: "n" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 121 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 124 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 1, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.51, per 1000 atoms: 0.55 Number of scatterers: 19211 At special positions: 0 Unit cell: (158.4, 142.8, 128.4, 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 116 16.00 O 3937 8.00 N 3158 7.00 C 12000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN K 4 " - " MAN K 5 " " MAN h 4 " - " MAN h 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA T 3 " - " MAN T 9 " " BMA U 3 " - " MAN U 4 " " BMA e 3 " - " MAN e 4 " " BMA h 3 " - " MAN h 4 " " MAN h 6 " - " MAN h 7 " " BMA n 3 " - " MAN n 9 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA K 3 " - " MAN K 6 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " BMA h 3 " - " MAN h 6 " " BMA n 3 " - " MAN n 4 " " BMA o 3 " - " MAN o 8 " BETA1-2 " MAN T 4 " - " NAG T 5 " " MAN T 9 " - " NAG T 10 " " MAN U 4 " - " NAG U 5 " " MAN U 8 " - " NAG U 9 " " MAN n 4 " - " NAG n 5 " " MAN o 4 " - " NAG o 5 " " MAN o 8 " - " NAG o 9 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG T 5 " - " GAL T 6 " " NAG T 7 " - " GAL T 8 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " MAN U 4 " - " NAG U 7 " " NAG U 5 " - " GAL U 6 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 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 e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG n 5 " - " GAL n 6 " " NAG n 7 " - " GAL n 8 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " MAN o 4 " - " NAG o 7 " " NAG o 5 " - " GAL o 6 " BETA1-6 " NAG T 1 " - " FUC T 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN T 4 " - " NAG T 7 " " NAG U 1 " - " FUC U 10 " " NAG n 1 " - " FUC n 10 " " MAN n 4 " - " NAG n 7 " " NAG o 1 " - " FUC o 10 " NAG-ASN " NAG A1000 " - " ASN A 295 " " NAG A1015 " - " ASN A 355 " " NAG A1018 " - " ASN A 392 " " NAG A1022 " - " ASN A 234 " " NAG A1023 " - " ASN A 276 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG C 601 " - " ASN C 295 " " NAG C 610 " - " ASN C 355 " " NAG C 611 " - " ASN C 88 " " NAG C 612 " - " ASN C 392 " " NAG C 615 " - " ASN C 234 " " NAG D1000 " - " ASN D 625 " " NAG D1001 " - " ASN D 618 " " NAG D1004 " - " ASN D 637 " " NAG E1000 " - " ASN E 295 " " NAG E1001 " - " ASN E 301 " " NAG E1015 " - " ASN E 355 " " NAG E1016 " - " ASN E 88 " " NAG E1017 " - " ASN E 392 " " NAG E1021 " - " ASN E 234 " " NAG F1000 " - " ASN F 618 " " NAG G 1 " - " ASN A 301 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 197 " " NAG K 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 448 " " NAG P 1 " - " ASN A 88 " " NAG Q 1 " - " ASN A 386 " " NAG R 1 " - " ASN A 160 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN B 611 " " NAG U 1 " - " ASN B 637 " " NAG V 1 " - " ASN D 611 " " NAG W 1 " - " ASN C 301 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 448 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 276 " " NAG c 1 " - " ASN C 160 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN C 262 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 197 " " NAG h 1 " - " ASN E 262 " " NAG i 1 " - " ASN E 448 " " NAG j 1 " - " ASN E 386 " " NAG k 1 " - " ASN E 276 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 363 " " NAG n 1 " - " ASN F 611 " " NAG o 1 " - " ASN F 637 " Time building additional restraints: 9.69 Conformation dependent library (CDL) restraints added in 3.6 seconds 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 39 sheets defined 17.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 84 through 86 No H-bonds generated for 'chain 'M' and resid 84 through 86' Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 336 through 351 removed outlier: 4.065A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 475 through 482 removed outlier: 4.093A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.133A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 530 through 535 removed outlier: 5.566A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 4.124A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 651 Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'D' and resid 530 through 535 removed outlier: 5.795A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 removed outlier: 4.263A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 639 through 651 Processing helix chain 'D' and resid 656 through 660 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.623A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 3.854A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 336 through 349 Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'E' and resid 100 through 117 removed outlier: 3.847A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.961A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 336 through 351 removed outlier: 3.892A pdb=" N ARG E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 378 through 380 No H-bonds generated for 'chain 'E' and resid 378 through 380' Processing helix chain 'E' and resid 388 through 391 removed outlier: 3.550A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 388 through 391' Processing helix chain 'E' and resid 477 through 485 removed outlier: 4.136A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS E 485 " --> pdb=" O SER E 481 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.724A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 639 through 651 Processing helix chain 'F' and resid 656 through 662 Processing sheet with id= A, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.514A pdb=" N GLY M 10 " --> pdb=" O THR M 108 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG M 91 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL M 37 " --> pdb=" O ARG M 91 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA M 40 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU M 45 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 20 through 23 Processing sheet with id= C, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.508A pdb=" N THR N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 85 through 90 removed outlier: 3.501A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU N 46 " --> pdb=" O ARG N 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 63 through 66 removed outlier: 3.764A pdb=" N VAL N 63 " --> pdb=" O ARG N 74 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARG N 74 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER N 65 " --> pdb=" O THR N 72 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR N 72 " --> pdb=" O SER N 65 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.719A pdb=" N ARG H 91 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA H 93 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.633A pdb=" N MET H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS H 22 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.535A pdb=" N ARG H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 21 through 24 removed outlier: 3.507A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 102 through 104 removed outlier: 3.689A pdb=" N TRP L 35 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 35 through 40 removed outlier: 4.042A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.180A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.792A pdb=" N MET A 161 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= O, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.819A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.380A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 443 through 447 removed outlier: 3.883A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 333 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 359 through 361 removed outlier: 6.175A pdb=" N GLU A 466 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'A' and resid 383 through 385 Processing sheet with id= T, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.702A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 35 through 39 Processing sheet with id= V, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.609A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 53 through 56 removed outlier: 3.843A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.778A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.522A pdb=" N MET C 161 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= AA, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.921A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 444 through 447 removed outlier: 3.532A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 333 " --> pdb=" O ILE C 414 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE C 414 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 383 through 385 Processing sheet with id= AD, first strand: chain 'C' and resid 307 through 312 removed outlier: 6.590A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= AF, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.696A pdb=" N THR E 244 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.780A pdb=" N GLN E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AI, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.629A pdb=" N MET E 271 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 443 through 447 removed outlier: 3.765A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 359 through 361 removed outlier: 5.885A pdb=" N GLU E 466 " --> pdb=" O ARG E 360 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'E' and resid 374 through 376 removed outlier: 3.962A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 383 " --> pdb=" O PHE E 376 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 307 through 312 removed outlier: 6.782A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1158 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: 5.88 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5901 1.34 - 1.46: 4949 1.46 - 1.59: 8558 1.59 - 1.71: 2 1.71 - 1.83: 164 Bond restraints: 19574 Sorted by residual: bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.91e+01 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" C1 BMA o 3 " pdb=" C2 BMA o 3 " ideal model delta sigma weight residual 1.519 1.595 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 19569 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.75: 401 105.75 - 112.85: 11299 112.85 - 119.94: 6149 119.94 - 127.04: 8475 127.04 - 134.14: 240 Bond angle restraints: 26564 Sorted by residual: angle pdb=" C MET C 426 " pdb=" N TRP C 427 " pdb=" CA TRP C 427 " ideal model delta sigma weight residual 121.19 128.68 -7.49 1.59e+00 3.96e-01 2.22e+01 angle pdb=" C ALA C 70 " pdb=" N THR C 71 " pdb=" CA THR C 71 " ideal model delta sigma weight residual 122.46 128.87 -6.41 1.41e+00 5.03e-01 2.07e+01 angle pdb=" N SER A 199 " pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 110.24 115.31 -5.07 1.30e+00 5.92e-01 1.52e+01 angle pdb=" C THR A 198 " pdb=" N SER A 199 " pdb=" CA SER A 199 " ideal model delta sigma weight residual 120.82 126.54 -5.72 1.47e+00 4.63e-01 1.52e+01 angle pdb=" C ALA A 70 " pdb=" N THR A 71 " pdb=" CA THR A 71 " ideal model delta sigma weight residual 122.41 130.50 -8.09 2.09e+00 2.29e-01 1.50e+01 ... (remaining 26559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 10152 14.98 - 29.96: 455 29.96 - 44.94: 121 44.94 - 59.92: 15 59.92 - 74.90: 7 Dihedral angle restraints: 10750 sinusoidal: 4354 harmonic: 6396 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -155.18 69.18 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -153.59 67.59 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -152.29 66.29 1 1.00e+01 1.00e-02 5.74e+01 ... (remaining 10747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3167 0.115 - 0.230: 173 0.230 - 0.345: 16 0.345 - 0.461: 9 0.461 - 0.576: 3 Chirality restraints: 3368 Sorted by residual: chirality pdb=" C1 NAG E1015 " pdb=" ND2 ASN E 355 " pdb=" C2 NAG E1015 " pdb=" O5 NAG E1015 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 301 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 3365 not shown) Planarity restraints: 3253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 497 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO C 498 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 498 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 498 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR M 32 " 0.050 5.00e-02 4.00e+02 7.52e-02 9.05e+00 pdb=" N PRO M 33 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO M 33 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO M 33 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 469 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.47e+00 pdb=" N PRO E 470 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 470 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 470 " -0.040 5.00e-02 4.00e+02 ... (remaining 3250 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 276 2.60 - 3.18: 15792 3.18 - 3.75: 27591 3.75 - 4.33: 37204 4.33 - 4.90: 58440 Nonbonded interactions: 139303 Sorted by model distance: nonbonded pdb=" OE1 GLU N 50 " pdb=" ND2 ASN N 53 " model vdw 2.031 2.520 nonbonded pdb=" O ILE A 424 " pdb=" O ASN A 425 " model vdw 2.035 3.040 nonbonded pdb=" CE2 TRP H 55 " pdb=" O7 NAG T 5 " model vdw 2.078 3.260 nonbonded pdb=" CZ3 TRP H 55 " pdb=" C6 BMA T 3 " model vdw 2.207 3.740 nonbonded pdb=" CD1 TRP H 55 " pdb=" OH TYR H 100M" model vdw 2.221 3.260 ... (remaining 139298 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 32 through 56 or resid 67 through 396 or resid 412 through \ 505 or resid 1000 through 1023)) selection = (chain 'C' and (resid 32 through 56 or resid 67 through 396 or resid 412 through \ 505 or resid 601 through 615)) selection = (chain 'E' and (resid 32 through 505 or resid 1000 through 1017)) } ncs_group { reference = (chain 'B' and (resid 521 through 664 or resid 801)) selection = (chain 'D' and (resid 521 through 549 or resid 569 through 664 or resid 1000)) selection = (chain 'F' and (resid 521 through 549 or resid 569 through 664 or resid 1000)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' 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' selection = chain 'f' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'K' and (resid 1 or resid 4 through 6)) selection = (chain 'h' and (resid 2 or resid 5 through 7)) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'j' } ncs_group { reference = (chain 'T' and (resid 2 or resid 11)) selection = (chain 'U' and (resid 1 or resid 10)) selection = (chain 'n' and (resid 1 or resid 10)) selection = (chain 'o' and (resid 1 or resid 10)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.010 Extract box with map and model: 7.880 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 53.770 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.300 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: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 19574 Z= 0.455 Angle : 1.040 10.046 26564 Z= 0.511 Chirality : 0.065 0.576 3368 Planarity : 0.007 0.077 3200 Dihedral : 9.477 74.900 6524 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.81 % Favored : 89.96 % Rotamer: Outliers : 0.26 % Allowed : 0.61 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.41 (0.15), residues: 2181 helix: -1.70 (0.21), residues: 387 sheet: -1.66 (0.20), residues: 564 loop : -2.84 (0.15), residues: 1230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 0.3730 time to fit residues: 154.0290 Evaluate side-chains 132 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 2.014 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1600 time to fit residues: 3.0178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 0.2980 chunk 165 optimal weight: 8.9990 chunk 91 optimal weight: 0.0670 chunk 56 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 170 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN H 100KASN L 90 GLN A 293 GLN A 348 GLN A 352 HIS A 440 GLN C 82 GLN C 348 GLN C 440 GLN C 478 ASN F 540 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19574 Z= 0.162 Angle : 0.669 9.792 26564 Z= 0.328 Chirality : 0.047 0.402 3368 Planarity : 0.005 0.063 3200 Dihedral : 5.898 41.941 2387 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.65 (0.17), residues: 2181 helix: -0.49 (0.25), residues: 392 sheet: -1.43 (0.21), residues: 559 loop : -2.42 (0.16), residues: 1230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3475 time to fit residues: 110.3466 Evaluate side-chains 131 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 2.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 chunk 164 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100KASN A 170 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN F 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19574 Z= 0.170 Angle : 0.632 9.642 26564 Z= 0.307 Chirality : 0.045 0.381 3368 Planarity : 0.004 0.058 3200 Dihedral : 5.466 39.226 2387 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.43 % Favored : 92.53 % Rotamer: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.24 (0.17), residues: 2181 helix: 0.15 (0.27), residues: 386 sheet: -1.25 (0.21), residues: 564 loop : -2.21 (0.16), residues: 1231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.3409 time to fit residues: 87.6945 Evaluate side-chains 120 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN C 130 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN E 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19574 Z= 0.210 Angle : 0.651 9.604 26564 Z= 0.315 Chirality : 0.045 0.381 3368 Planarity : 0.004 0.061 3200 Dihedral : 5.335 37.703 2387 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.30 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.09 (0.18), residues: 2181 helix: 0.45 (0.28), residues: 379 sheet: -1.27 (0.22), residues: 551 loop : -2.10 (0.17), residues: 1251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3363 time to fit residues: 83.0210 Evaluate side-chains 115 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 145 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 189 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 170 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN D 652 GLN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19574 Z= 0.198 Angle : 0.633 9.621 26564 Z= 0.304 Chirality : 0.045 0.378 3368 Planarity : 0.004 0.059 3200 Dihedral : 5.179 35.298 2387 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.93 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.99 (0.18), residues: 2181 helix: 0.51 (0.28), residues: 379 sheet: -1.25 (0.22), residues: 551 loop : -2.00 (0.17), residues: 1251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3285 time to fit residues: 79.1678 Evaluate side-chains 111 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19574 Z= 0.221 Angle : 0.651 9.622 26564 Z= 0.312 Chirality : 0.045 0.380 3368 Planarity : 0.004 0.059 3200 Dihedral : 5.175 33.490 2387 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.62 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.87 (0.18), residues: 2181 helix: 0.62 (0.28), residues: 376 sheet: -1.16 (0.22), residues: 557 loop : -1.93 (0.17), residues: 1248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3702 time to fit residues: 86.7920 Evaluate side-chains 112 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN B 591 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 188 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19574 Z= 0.191 Angle : 0.636 9.654 26564 Z= 0.303 Chirality : 0.045 0.377 3368 Planarity : 0.004 0.056 3200 Dihedral : 5.058 31.239 2387 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.57 % Favored : 92.39 % Rotamer: Outliers : 0.05 % Allowed : 0.82 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.71 (0.18), residues: 2181 helix: 0.83 (0.28), residues: 370 sheet: -1.01 (0.22), residues: 562 loop : -1.86 (0.17), residues: 1249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.3415 time to fit residues: 82.3744 Evaluate side-chains 122 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 10.0000 chunk 83 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN H 39 GLN L 45 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN B 591 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19574 Z= 0.419 Angle : 0.871 9.619 26564 Z= 0.414 Chirality : 0.050 0.430 3368 Planarity : 0.005 0.062 3200 Dihedral : 5.850 32.864 2387 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.65 % Favored : 88.31 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.24 (0.17), residues: 2181 helix: 0.05 (0.27), residues: 374 sheet: -1.41 (0.21), residues: 582 loop : -2.08 (0.17), residues: 1225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.3152 time to fit residues: 66.7664 Evaluate side-chains 103 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.969 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19574 Z= 0.265 Angle : 0.739 9.693 26564 Z= 0.351 Chirality : 0.047 0.402 3368 Planarity : 0.004 0.055 3200 Dihedral : 5.597 30.832 2387 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.30 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.12 (0.17), residues: 2181 helix: 0.32 (0.28), residues: 364 sheet: -1.37 (0.21), residues: 573 loop : -2.02 (0.17), residues: 1244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3129 time to fit residues: 67.8540 Evaluate side-chains 111 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.097 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 0.0050 chunk 126 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 172 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19574 Z= 0.177 Angle : 0.671 12.387 26564 Z= 0.319 Chirality : 0.046 0.382 3368 Planarity : 0.004 0.052 3200 Dihedral : 5.284 28.068 2387 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.86 (0.18), residues: 2181 helix: 0.82 (0.28), residues: 357 sheet: -1.13 (0.21), residues: 578 loop : -1.97 (0.17), residues: 1246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3332 time to fit residues: 73.9114 Evaluate side-chains 112 residues out of total 1953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 159 optimal weight: 10.0000 chunk 25 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 GLN A 170 GLN B 630 GLN B 650 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.039833 restraints weight = 153661.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.040902 restraints weight = 96354.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.041670 restraints weight = 69263.100| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19574 Z= 0.299 Angle : 0.748 9.809 26564 Z= 0.355 Chirality : 0.048 0.406 3368 Planarity : 0.004 0.062 3200 Dihedral : 5.504 27.916 2387 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.02 (0.18), residues: 2181 helix: 0.59 (0.28), residues: 359 sheet: -1.28 (0.21), residues: 565 loop : -2.01 (0.17), residues: 1257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3106.01 seconds wall clock time: 61 minutes 4.00 seconds (3664.00 seconds total)