Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 18 00:24:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/08_2023/6uda_20735_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/08_2023/6uda_20735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/08_2023/6uda_20735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/08_2023/6uda_20735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/08_2023/6uda_20735_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uda_20735/08_2023/6uda_20735_neut.pdb" } resolution = 4.2 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= 0.004 sd= 0.075 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 141 5.16 5 C 14913 2.51 5 N 4056 2.21 5 O 4623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "Z PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 205": "OD1" <-> "OD2" Residue "H TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 275": "OE1" <-> "OE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 205": "OD1" <-> "OD2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 23733 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3567 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 428} Chain breaks: 1 Chain: "C" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Z" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 199} Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3567 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 428} Chain breaks: 1 Chain: "F" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 199} Chain: "I" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3567 Classifications: {'peptide': 452} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 21, 'TRANS': 428} Chain breaks: 1 Chain: "J" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1001 Classifications: {'peptide': 126} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1620 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 199} Chain: "B" 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: "M" 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: "N" 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: "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: "E" 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 Time building chain proxies: 11.50, per 1000 atoms: 0.48 Number of scatterers: 23733 At special positions: 0 Unit cell: (184.68, 182.52, 118.8, 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 141 16.00 O 4623 8.00 N 4056 7.00 C 14913 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.07 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS Z 605 " distance=2.13 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 193 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 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=2.07 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=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.05 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.13 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 137 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.07 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.12 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.07 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.04 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.05 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.13 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG CYS K 193 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.07 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 ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 276 " " NAG B 1 " - " ASN A 262 " " NAG E 605 " - " ASN E 448 " " NAG E 606 " - " ASN E 276 " " NAG I 605 " - " ASN I 448 " " NAG I 606 " - " ASN I 276 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN I 262 " Time building additional restraints: 9.57 Conformation dependent library (CDL) restraints added in 3.2 seconds 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 63 sheets defined 19.1% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.708A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'Z' and resid 533 through 535 No H-bonds generated for 'chain 'Z' and resid 533 through 535' Processing helix chain 'Z' and resid 536 through 544 removed outlier: 3.693A pdb=" N LEU Z 544 " --> pdb=" O GLN Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 572 through 596 Processing helix chain 'Z' and resid 621 through 625 Processing helix chain 'Z' and resid 628 through 635 Processing helix chain 'Z' and resid 638 through 663 removed outlier: 4.420A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 334 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 473 through 478 Processing helix chain 'E' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR E 482 " --> pdb=" O SER E 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 483 " --> pdb=" O GLU E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 536 through 544 removed outlier: 3.693A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 4.420A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.709A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 198 through 201 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 143 removed outlier: 4.049A pdb=" N GLU I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 334 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 473 through 478 Processing helix chain 'I' and resid 479 through 484 removed outlier: 4.999A pdb=" N TYR I 482 " --> pdb=" O SER I 479 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS I 483 " --> pdb=" O GLU I 480 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 544 removed outlier: 3.692A pdb=" N LEU J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 596 Processing helix chain 'J' and resid 621 through 625 Processing helix chain 'J' and resid 628 through 635 Processing helix chain 'J' and resid 638 through 663 removed outlier: 4.419A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.708A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 184 through 186 No H-bonds generated for 'chain 'K' and resid 184 through 186' Processing helix chain 'K' and resid 198 through 201 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 5.209A pdb=" N VAL Z 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL A 38 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR Z 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR A 40 " --> pdb=" O CYS Z 604 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N CYS Z 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 465 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323 removed outlier: 6.787A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN A 321A" --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS A 296 " --> pdb=" O ASN A 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.810A pdb=" N MET C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.709A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.385A pdb=" N TYR C 173 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 124 removed outlier: 5.385A pdb=" N TYR C 173 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 118 Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 492 through 497 removed outlier: 5.208A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AC9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'E' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR E 465 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 315 through 323 removed outlier: 6.787A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR E 320 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.635A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 10.100A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N CYS E 296 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 10.693A pdb=" N ASN E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET G 34 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.710A pdb=" N TYR G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR G 173 " --> pdb=" O ASP G 141 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR G 173 " --> pdb=" O ASP G 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 148 through 151 Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 114 through 118 Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 492 through 497 removed outlier: 5.209A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'I' and resid 91 through 92 Processing sheet with id=AF2, first strand: chain 'I' and resid 130 through 131 Processing sheet with id=AF3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AF4, first strand: chain 'I' and resid 200 through 202 removed outlier: 6.341A pdb=" N VAL I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR I 465 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR I 359 " --> pdb=" O PHE I 466 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 315 through 323 removed outlier: 6.788A pdb=" N ALA I 316 " --> pdb=" O ILE I 309 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE I 309 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLN I 321A" --> pdb=" O THR I 303 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N GLU I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N ASN I 448 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 11.042A pdb=" N VAL I 292 " --> pdb=" O ILE I 446 " (cutoff:3.500A) removed outlier: 10.101A pdb=" N ILE I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N CYS I 296 " --> pdb=" O ASN I 442 " (cutoff:3.500A) removed outlier: 10.692A pdb=" N ASN I 442 " --> pdb=" O CYS I 296 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.811A pdb=" N MET K 34 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 11 through 12 removed outlier: 4.710A pdb=" N TYR K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR K 173 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 120 through 124 removed outlier: 5.386A pdb=" N TYR K 173 " --> pdb=" O ASP K 141 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 148 through 151 Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 114 through 118 Processing sheet with id=AG9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.779A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2466 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: 9.71 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.31: 4146 1.31 - 1.46: 8860 1.46 - 1.61: 11033 1.61 - 1.76: 18 1.76 - 1.91: 177 Bond restraints: 24234 Sorted by residual: bond pdb=" C4 NAG A 605 " pdb=" C5 NAG A 605 " ideal model delta sigma weight residual 1.532 1.404 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" C4 NAG E 605 " pdb=" C5 NAG E 605 " ideal model delta sigma weight residual 1.532 1.405 0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C4 NAG I 605 " pdb=" C5 NAG I 605 " ideal model delta sigma weight residual 1.532 1.405 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C ASN A 448 " pdb=" O ASN A 448 " ideal model delta sigma weight residual 1.235 1.161 0.075 1.23e-02 6.61e+03 3.69e+01 bond pdb=" C ASN E 448 " pdb=" O ASN E 448 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.23e-02 6.61e+03 3.61e+01 ... (remaining 24229 not shown) Histogram of bond angle deviations from ideal: 82.43 - 93.43: 12 93.43 - 104.43: 482 104.43 - 115.43: 15170 115.43 - 126.43: 16858 126.43 - 137.43: 400 Bond angle restraints: 32922 Sorted by residual: angle pdb=" N PHE C 100E" pdb=" CA PHE C 100E" pdb=" C PHE C 100E" ideal model delta sigma weight residual 109.52 127.32 -17.80 1.55e+00 4.16e-01 1.32e+02 angle pdb=" N PHE G 100E" pdb=" CA PHE G 100E" pdb=" C PHE G 100E" ideal model delta sigma weight residual 109.52 127.31 -17.79 1.55e+00 4.16e-01 1.32e+02 angle pdb=" N PHE K 100E" pdb=" CA PHE K 100E" pdb=" C PHE K 100E" ideal model delta sigma weight residual 109.52 127.30 -17.78 1.55e+00 4.16e-01 1.32e+02 angle pdb=" C5 NAG I 605 " pdb=" C4 NAG I 605 " pdb=" O4 NAG I 605 " ideal model delta sigma weight residual 111.70 82.43 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" C5 NAG E 605 " pdb=" C4 NAG E 605 " pdb=" O4 NAG E 605 " ideal model delta sigma weight residual 111.70 82.47 29.23 3.00e+00 1.11e-01 9.50e+01 ... (remaining 32917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 13870 17.17 - 34.34: 401 34.34 - 51.51: 105 51.51 - 68.68: 42 68.68 - 85.85: 33 Dihedral angle restraints: 14451 sinusoidal: 5691 harmonic: 8760 Sorted by residual: dihedral pdb=" CB CYS I 119 " pdb=" SG CYS I 119 " pdb=" SG CYS I 205 " pdb=" CB CYS I 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.79 44.79 1 1.00e+01 1.00e-02 2.79e+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 -130.78 44.78 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 14448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.045: 3774 1.045 - 2.089: 0 2.089 - 3.134: 0 3.134 - 4.178: 0 4.178 - 5.223: 6 Chirality restraints: 3780 Sorted by residual: chirality pdb=" C1 NAG I 605 " pdb=" ND2 ASN I 448 " pdb=" C2 NAG I 605 " pdb=" O5 NAG I 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C1 NAG E 605 " pdb=" ND2 ASN E 448 " pdb=" C2 NAG E 605 " pdb=" O5 NAG E 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 chirality pdb=" C1 NAG A 605 " pdb=" ND2 ASN A 448 " pdb=" C2 NAG A 605 " pdb=" O5 NAG A 605 " both_signs ideal model delta sigma weight residual False -2.40 2.82 -5.22 2.00e-01 2.50e+01 6.82e+02 ... (remaining 3777 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG M 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.72e+02 pdb=" C7 NAG B 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.320 2.00e-02 2.50e+03 2.79e-01 9.71e+02 pdb=" C7 NAG N 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.493 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.183 2.00e-02 2.50e+03 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 168 2.58 - 3.16: 19178 3.16 - 3.74: 34871 3.74 - 4.32: 50353 4.32 - 4.90: 79106 Nonbonded interactions: 183676 Sorted by model distance: nonbonded pdb=" OD1 ASN E 262 " pdb=" C1 NAG M 1 " model vdw 2.004 2.776 nonbonded pdb=" OD1 ASN A 262 " pdb=" C1 NAG B 1 " model vdw 2.005 2.776 nonbonded pdb=" OD1 ASN I 262 " pdb=" C1 NAG N 1 " model vdw 2.005 2.776 nonbonded pdb=" O3 NAG B 1 " pdb=" O7 NAG B 1 " model vdw 2.036 2.440 nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.036 2.440 ... (remaining 183671 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' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } 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: 1.730 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: 0.020 Extract box with map and model: 8.910 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 60.790 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.017 0.128 24234 Z= 1.108 Angle : 1.890 29.269 32922 Z= 1.196 Chirality : 0.221 5.223 3780 Planarity : 0.014 0.279 4170 Dihedral : 10.405 85.845 8703 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.50 % Allowed : 2.41 % Favored : 97.08 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: 0.89 (0.15), residues: 2982 helix: -0.58 (0.23), residues: 423 sheet: 1.04 (0.16), residues: 963 loop : 0.82 (0.16), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 367 time to evaluate : 2.712 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 outliers start: 9 outliers final: 3 residues processed: 376 average time/residue: 0.4600 time to fit residues: 252.0842 Evaluate side-chains 155 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 2.703 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1965 time to fit residues: 4.6391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 374 HIS E 425 ASN ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 ASN I 374 HIS I 425 ASN ** K 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 24234 Z= 0.262 Angle : 0.799 14.371 32922 Z= 0.412 Chirality : 0.055 0.955 3780 Planarity : 0.004 0.038 4170 Dihedral : 5.417 27.160 3237 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.02 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % 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: 0.70 (0.15), residues: 2982 helix: 0.33 (0.25), residues: 429 sheet: 0.82 (0.16), residues: 1020 loop : 0.40 (0.16), residues: 1533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 2.841 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: 3 outliers final: 1 residues processed: 190 average time/residue: 0.3708 time to fit residues: 109.9106 Evaluate side-chains 129 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2479 time to fit residues: 4.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 218 optimal weight: 0.3980 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 425 ASN ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 543 ASN ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 543 ASN K 100DHIS ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 24234 Z= 0.310 Angle : 0.754 14.055 32922 Z= 0.389 Chirality : 0.046 0.325 3780 Planarity : 0.004 0.055 4170 Dihedral : 5.308 31.640 3237 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.34 (0.15), residues: 2982 helix: 0.28 (0.25), residues: 429 sheet: 0.81 (0.17), residues: 921 loop : -0.05 (0.16), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 2.585 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 outliers start: 7 outliers final: 2 residues processed: 151 average time/residue: 0.3649 time to fit residues: 87.9643 Evaluate side-chains 118 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 2.915 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.5076 time to fit residues: 5.2732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 273 optimal weight: 0.1980 chunk 289 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 374 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN E 258 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 24234 Z= 0.327 Angle : 0.719 14.074 32922 Z= 0.375 Chirality : 0.046 0.409 3780 Planarity : 0.004 0.061 4170 Dihedral : 5.367 37.193 3237 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.11 (0.16), residues: 2982 helix: 0.50 (0.26), residues: 411 sheet: 0.40 (0.16), residues: 963 loop : -0.16 (0.16), residues: 1608 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 2.672 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: 2 outliers final: 1 residues processed: 136 average time/residue: 0.3661 time to fit residues: 79.2494 Evaluate side-chains 107 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 2.586 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2005 time to fit residues: 3.8960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 0.0040 chunk 215 optimal weight: 9.9990 chunk 119 optimal weight: 0.0970 chunk 247 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 260 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN E 357 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24234 Z= 0.184 Angle : 0.626 13.909 32922 Z= 0.324 Chirality : 0.044 0.380 3780 Planarity : 0.004 0.040 4170 Dihedral : 5.121 34.842 3237 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2982 helix: 0.52 (0.26), residues: 429 sheet: 0.53 (0.16), residues: 942 loop : -0.20 (0.16), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.758 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: 137 average time/residue: 0.3693 time to fit residues: 81.4474 Evaluate side-chains 105 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 57 optimal weight: 30.0000 chunk 170 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 37 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 24234 Z= 0.336 Angle : 0.695 11.588 32922 Z= 0.363 Chirality : 0.045 0.255 3780 Planarity : 0.004 0.060 4170 Dihedral : 5.320 36.181 3237 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.15), residues: 2982 helix: 0.33 (0.25), residues: 414 sheet: 0.35 (0.16), residues: 948 loop : -0.48 (0.16), residues: 1620 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.759 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: 125 average time/residue: 0.3672 time to fit residues: 74.2947 Evaluate side-chains 101 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 9.9990 chunk 32 optimal weight: 0.0370 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 289 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 176 optimal weight: 30.0000 chunk 133 optimal weight: 7.9990 overall best weight: 3.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 24234 Z= 0.268 Angle : 0.638 11.331 32922 Z= 0.336 Chirality : 0.044 0.254 3780 Planarity : 0.004 0.043 4170 Dihedral : 5.187 32.821 3237 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.20 (0.15), residues: 2982 helix: 0.48 (0.26), residues: 414 sheet: 0.31 (0.17), residues: 930 loop : -0.50 (0.16), residues: 1638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.930 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: 123 average time/residue: 0.3699 time to fit residues: 73.6938 Evaluate side-chains 99 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 24234 Z= 0.153 Angle : 0.590 11.620 32922 Z= 0.308 Chirality : 0.043 0.244 3780 Planarity : 0.004 0.042 4170 Dihedral : 4.877 31.058 3237 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.09 (0.16), residues: 2982 helix: 0.36 (0.25), residues: 450 sheet: 0.33 (0.16), residues: 1008 loop : -0.38 (0.17), residues: 1524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.741 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: 138 average time/residue: 0.3816 time to fit residues: 83.5512 Evaluate side-chains 99 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 40.0000 chunk 252 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 254 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN L 37 GLN L 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 24234 Z= 0.364 Angle : 0.703 10.489 32922 Z= 0.370 Chirality : 0.045 0.260 3780 Planarity : 0.004 0.043 4170 Dihedral : 5.315 32.185 3237 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.47 (0.15), residues: 2982 helix: 0.18 (0.25), residues: 432 sheet: 0.13 (0.16), residues: 1002 loop : -0.70 (0.16), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.857 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: 119 average time/residue: 0.3727 time to fit residues: 72.2189 Evaluate side-chains 93 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 198 optimal weight: 20.0000 chunk 298 optimal weight: 30.0000 chunk 275 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24234 Z= 0.203 Angle : 0.621 11.080 32922 Z= 0.327 Chirality : 0.044 0.260 3780 Planarity : 0.004 0.041 4170 Dihedral : 5.062 31.747 3237 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.34 (0.15), residues: 2982 helix: 0.20 (0.25), residues: 450 sheet: 0.16 (0.16), residues: 1011 loop : -0.55 (0.17), residues: 1521 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5964 Ramachandran restraints generated. 2982 Oldfield, 0 Emsley, 2982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 3.199 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: 122 average time/residue: 0.3602 time to fit residues: 72.1343 Evaluate side-chains 98 residues out of total 2643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 219 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 238 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN ** C 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 37 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 ASN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.040707 restraints weight = 207993.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041583 restraints weight = 125896.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042746 restraints weight = 84790.065| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 24234 Z= 0.248 Angle : 0.627 10.496 32922 Z= 0.332 Chirality : 0.044 0.247 3780 Planarity : 0.004 0.043 4170 Dihedral : 5.144 31.504 3237 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.41 (0.15), residues: 2982 helix: 0.22 (0.25), residues: 432 sheet: 0.17 (0.16), residues: 1002 loop : -0.65 (0.16), residues: 1548 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3363.45 seconds wall clock time: 64 minutes 7.64 seconds (3847.64 seconds total)