Starting phenix.real_space_refine (version: dev) on Thu Feb 23 04:55:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/02_2023/5kel_8240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/02_2023/5kel_8240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/02_2023/5kel_8240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/02_2023/5kel_8240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/02_2023/5kel_8240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/02_2023/5kel_8240.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "E GLU 245": "OE1" <-> "OE2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 564": "OE1" <-> "OE2" Residue "F GLU 245": "OE1" <-> "OE2" Residue "F TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 564": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19278 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1828 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 889 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "C" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "E" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1828 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 889 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "P" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "T" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "J" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "N" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "F" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1828 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "I" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 889 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "Q" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 952 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "U" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 102} Chain: "M" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 930 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "S" 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 dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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 dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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 dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.05, per 1000 atoms: 0.57 Number of scatterers: 19278 At special positions: 0 Unit cell: (150.65, 148.03, 145.41, 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 84 16.00 O 3837 8.00 N 3210 7.00 C 12147 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 609 " distance=2.02 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 608 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.19 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.21 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.14 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS G 609 " distance=2.02 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 135 " distance=2.02 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 511 " - pdb=" SG CYS G 556 " distance=2.03 Simple disulfide: pdb=" SG CYS G 601 " - pdb=" SG CYS G 608 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.19 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.21 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.15 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS I 609 " distance=2.02 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 135 " distance=2.02 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 511 " - pdb=" SG CYS I 556 " distance=2.03 Simple disulfide: pdb=" SG CYS I 601 " - pdb=" SG CYS I 608 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.19 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.21 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.15 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 S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 5 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 603 " - " ASN A 238 " " NAG E 603 " - " ASN E 238 " " NAG F 603 " - " ASN F 238 " " NAG K 1 " - " ASN A 228 " " NAG R 1 " - " ASN A 268 " " NAG S 1 " - " ASN A 257 " " NAG V 1 " - " ASN B 563 " " NAG W 1 " - " ASN E 228 " " NAG X 1 " - " ASN E 268 " " NAG Y 1 " - " ASN E 257 " " NAG Z 1 " - " ASN G 563 " " NAG a 1 " - " ASN F 228 " " NAG b 1 " - " ASN F 268 " " NAG c 1 " - " ASN F 257 " " NAG d 1 " - " ASN I 563 " Time building additional restraints: 8.92 Conformation dependent library (CDL) restraints added in 2.8 seconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 15.2% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 553 through 576 removed outlier: 3.810A pdb=" N LEU B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 597 removed outlier: 3.580A pdb=" N ARG B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 100 through 101 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 60 through 65 removed outlier: 4.411A pdb=" N SER C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 78 through 85 Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'G' and resid 527 through 532 Processing helix chain 'G' and resid 550 through 552 No H-bonds generated for 'chain 'G' and resid 550 through 552' Processing helix chain 'G' and resid 553 through 576 removed outlier: 3.810A pdb=" N LEU G 571 " --> pdb=" O GLN G 567 " (cutoff:3.500A) Processing helix chain 'G' and resid 584 through 597 removed outlier: 3.579A pdb=" N ARG G 596 " --> pdb=" O PHE G 592 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'P' and resid 52A through 54 Processing helix chain 'P' and resid 100 through 101 Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 60 through 65 removed outlier: 4.410A pdb=" N SER J 65 " --> pdb=" O PRO J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 75 No H-bonds generated for 'chain 'J' and resid 73 through 75' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 71 through 74 Processing helix chain 'F' and resid 78 through 85 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'F' and resid 256 through 260 Processing helix chain 'I' and resid 527 through 532 Processing helix chain 'I' and resid 550 through 552 No H-bonds generated for 'chain 'I' and resid 550 through 552' Processing helix chain 'I' and resid 553 through 576 removed outlier: 3.810A pdb=" N LEU I 571 " --> pdb=" O GLN I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 584 through 597 removed outlier: 3.580A pdb=" N ARG I 596 " --> pdb=" O PHE I 592 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 Processing helix chain 'Q' and resid 52A through 54 Processing helix chain 'Q' and resid 100 through 101 Processing helix chain 'U' and resid 79 through 83 Processing helix chain 'M' and resid 40 through 43 Processing helix chain 'M' and resid 60 through 65 removed outlier: 4.410A pdb=" N SER M 65 " --> pdb=" O PRO M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.886A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 69 removed outlier: 4.009A pdb=" N THR A 175 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYR A 109 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA A 177 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN A 107 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 515 through 519 Processing sheet with id=AA5, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.526A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.089A pdb=" N GLY H 16 " --> pdb=" O THR H 82B" (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR H 82B" --> pdb=" O GLY H 16 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.571A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.344A pdb=" N GLY C 16 " --> pdb=" O ASN C 82B" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.183A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.886A pdb=" N GLY E 36 " --> pdb=" O ILE E 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 67 through 69 Processing sheet with id=AC2, first strand: chain 'E' and resid 67 through 69 removed outlier: 4.009A pdb=" N THR E 175 " --> pdb=" O TYR E 109 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR E 109 " --> pdb=" O THR E 175 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 177 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN E 107 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS E 108 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL E 141 " --> pdb=" O CYS E 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN E 110 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY E 143 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 220 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS E 140 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA E 222 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER E 142 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG E 219 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 515 through 519 Processing sheet with id=AC4, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AC5, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.526A pdb=" N MET P 34 " --> pdb=" O GLU P 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 10 through 12 Processing sheet with id=AC7, first strand: chain 'P' and resid 16 through 18 removed outlier: 6.089A pdb=" N GLY P 16 " --> pdb=" O THR P 82B" (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR P 82B" --> pdb=" O GLY P 16 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'T' and resid 4 through 7 Processing sheet with id=AC9, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.572A pdb=" N ALA T 34 " --> pdb=" O GLN T 89 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 10 through 13 Processing sheet with id=AD2, first strand: chain 'J' and resid 4 through 8 removed outlier: 5.344A pdb=" N GLY J 16 " --> pdb=" O ASN J 82B" (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.183A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR N 49 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.886A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 67 through 69 Processing sheet with id=AE1, first strand: chain 'F' and resid 67 through 69 removed outlier: 4.009A pdb=" N THR F 175 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR F 109 " --> pdb=" O THR F 175 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA F 177 " --> pdb=" O ASN F 107 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N ASN F 107 " --> pdb=" O ALA F 177 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS F 108 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL F 141 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ASN F 110 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY F 143 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR F 220 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS F 140 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA F 222 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER F 142 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG F 219 " --> pdb=" O GLU F 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 515 through 519 Processing sheet with id=AE3, first strand: chain 'Q' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.526A pdb=" N MET Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'Q' and resid 16 through 18 removed outlier: 6.088A pdb=" N GLY Q 16 " --> pdb=" O THR Q 82B" (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR Q 82B" --> pdb=" O GLY Q 16 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'U' and resid 10 through 13 removed outlier: 3.572A pdb=" N ALA U 34 " --> pdb=" O GLN U 89 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'M' and resid 4 through 8 removed outlier: 5.344A pdb=" N GLY M 16 " --> pdb=" O ASN M 82B" (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 56 through 59 removed outlier: 5.452A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'O' and resid 10 through 13 Processing sheet with id=AF6, first strand: chain 'O' and resid 53 through 54 removed outlier: 6.183A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR O 49 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR O 97 " --> pdb=" O GLN O 90 " (cutoff:3.500A) 738 hydrogen bonds defined for protein. 1710 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: 7.46 Time building geometry restraints manager: 9.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4182 1.32 - 1.45: 5621 1.45 - 1.57: 9790 1.57 - 1.70: 3 1.70 - 1.82: 114 Bond restraints: 19710 Sorted by residual: bond pdb=" N TYR H 99 " pdb=" CA TYR H 99 " ideal model delta sigma weight residual 1.458 1.429 0.029 6.30e-03 2.52e+04 2.16e+01 bond pdb=" CA HIS U 90 " pdb=" C HIS U 90 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.12e+01 bond pdb=" CA HIS L 90 " pdb=" C HIS L 90 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.12e+01 bond pdb=" CA HIS T 90 " pdb=" C HIS T 90 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" CB HIS T 90 " pdb=" CG HIS T 90 " ideal model delta sigma weight residual 1.497 1.434 0.063 1.40e-02 5.10e+03 2.05e+01 ... (remaining 19705 not shown) Histogram of bond angle deviations from ideal: 95.36 - 103.08: 96 103.08 - 110.79: 7024 110.79 - 118.51: 8715 118.51 - 126.22: 10573 126.22 - 133.94: 331 Bond angle restraints: 26739 Sorted by residual: angle pdb=" C2 NAG K 1 " pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 109.64 103.40 6.24 5.38e-01 3.45e+00 1.35e+02 angle pdb=" C2 NAG W 1 " pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 109.64 103.41 6.23 5.38e-01 3.45e+00 1.34e+02 angle pdb=" C2 NAG a 1 " pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 109.64 103.43 6.21 5.38e-01 3.45e+00 1.33e+02 angle pdb=" C VAL F 92 " pdb=" N PRO F 93 " pdb=" CA PRO F 93 " ideal model delta sigma weight residual 119.66 127.38 -7.72 7.20e-01 1.93e+00 1.15e+02 angle pdb=" C VAL E 92 " pdb=" N PRO E 93 " pdb=" CA PRO E 93 " ideal model delta sigma weight residual 119.66 127.35 -7.69 7.20e-01 1.93e+00 1.14e+02 ... (remaining 26734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 11063 17.39 - 34.77: 367 34.77 - 52.16: 102 52.16 - 69.55: 48 69.55 - 86.93: 27 Dihedral angle restraints: 11607 sinusoidal: 4761 harmonic: 6846 Sorted by residual: dihedral pdb=" CB CYS G 601 " pdb=" SG CYS G 601 " pdb=" SG CYS G 608 " pdb=" CB CYS G 608 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS I 601 " pdb=" SG CYS I 601 " pdb=" SG CYS I 608 " pdb=" CB CYS I 608 " ideal model delta sinusoidal sigma weight residual 93.00 151.16 -58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS B 601 " pdb=" SG CYS B 601 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 151.14 -58.14 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 11604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 2949 0.206 - 0.413: 69 0.413 - 0.619: 15 0.619 - 0.825: 0 0.825 - 1.031: 6 Chirality restraints: 3039 Sorted by residual: chirality pdb=" C1 MAN Z 5 " pdb=" O6 BMA Z 3 " pdb=" C2 MAN Z 5 " pdb=" O5 MAN Z 5 " both_signs ideal model delta sigma weight residual False 2.40 1.41 0.99 2.00e-02 2.50e+03 2.44e+03 chirality pdb=" C1 MAN V 5 " pdb=" O6 BMA V 3 " pdb=" C2 MAN V 5 " pdb=" O5 MAN V 5 " both_signs ideal model delta sigma weight residual False 2.40 1.41 0.99 2.00e-02 2.50e+03 2.44e+03 chirality pdb=" C1 MAN d 5 " pdb=" O6 BMA d 3 " pdb=" C2 MAN d 5 " pdb=" O5 MAN d 5 " both_signs ideal model delta sigma weight residual False 2.40 1.41 0.99 2.00e-02 2.50e+03 2.43e+03 ... (remaining 3036 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.284 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG W 2 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.413 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " 0.284 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG a 2 " -0.062 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.014 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " -0.413 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.284 2.00e-02 2.50e+03 2.44e-01 7.42e+02 pdb=" C7 NAG K 2 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.014 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.413 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.205 2.00e-02 2.50e+03 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 60 2.39 - 3.02: 12986 3.02 - 3.65: 28992 3.65 - 4.27: 46890 4.27 - 4.90: 74584 Nonbonded interactions: 163512 Sorted by model distance: nonbonded pdb=" OE1 GLN G 567 " pdb=" CE2 TRP I 531 " model vdw 1.763 3.260 nonbonded pdb=" CE2 TRP B 531 " pdb=" OE1 GLN I 567 " model vdw 1.763 3.260 nonbonded pdb=" OE1 GLN B 567 " pdb=" CE2 TRP G 531 " model vdw 1.764 3.260 nonbonded pdb=" CD2 TRP B 531 " pdb=" OE1 GLN I 567 " model vdw 1.809 3.260 nonbonded pdb=" OE1 GLN G 567 " pdb=" CD2 TRP I 531 " model vdw 1.809 3.260 ... (remaining 163507 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 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'K' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'S' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12147 2.51 5 N 3210 2.21 5 O 3837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.050 Check model and map are aligned: 0.290 Process input model: 53.570 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.014 0.083 19710 Z= 0.934 Angle : 1.799 11.804 26739 Z= 1.209 Chirality : 0.102 1.031 3039 Planarity : 0.015 0.244 3372 Dihedral : 11.205 86.932 7182 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 1.27 % Allowed : 3.43 % Favored : 95.30 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.17), residues: 2361 helix: -0.19 (0.36), residues: 171 sheet: 0.51 (0.19), residues: 642 loop : 1.76 (0.17), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 758 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 767 average time/residue: 0.3398 time to fit residues: 383.6546 Evaluate side-chains 386 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 382 time to evaluate : 2.216 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 4 average time/residue: 0.2051 time to fit residues: 4.2493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 514 ASN B 602 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN D 42 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN J 39 GLN F 73 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 19710 Z= 0.306 Angle : 0.857 14.574 26739 Z= 0.471 Chirality : 0.052 0.439 3039 Planarity : 0.007 0.108 3372 Dihedral : 6.833 58.223 2967 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.21 % Favored : 94.07 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % 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: 0.72 (0.17), residues: 2361 helix: 0.43 (0.37), residues: 147 sheet: -0.10 (0.18), residues: 696 loop : 0.97 (0.17), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 563 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 563 average time/residue: 0.3244 time to fit residues: 272.3450 Evaluate side-chains 367 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 144 optimal weight: 0.0370 chunk 58 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 79 GLN D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN G 602 HIS ** P 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN T 45 GLN T 79 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 508 GLN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 HIS Q 53 ASN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 19710 Z= 0.278 Angle : 0.766 9.294 26739 Z= 0.414 Chirality : 0.048 0.365 3039 Planarity : 0.006 0.098 3372 Dihedral : 6.546 53.358 2967 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.38 % Favored : 94.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.17), residues: 2361 helix: 0.24 (0.35), residues: 153 sheet: -0.21 (0.18), residues: 690 loop : 0.42 (0.17), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.3272 time to fit residues: 239.3592 Evaluate side-chains 338 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 0.5980 chunk 226 optimal weight: 20.0000 chunk 111 optimal weight: 0.0170 chunk 202 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.5224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN B 602 HIS B 613 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 GLN G 602 HIS G 613 HIS P 53 ASN ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 613 HIS ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 19710 Z= 0.287 Angle : 0.752 15.248 26739 Z= 0.401 Chirality : 0.047 0.351 3039 Planarity : 0.006 0.090 3372 Dihedral : 6.305 44.688 2967 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.14 % Favored : 93.48 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % 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: -0.23 (0.17), residues: 2361 helix: 0.38 (0.37), residues: 162 sheet: -0.38 (0.18), residues: 699 loop : -0.00 (0.17), residues: 1500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 453 average time/residue: 0.3149 time to fit residues: 216.8537 Evaluate side-chains 321 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 168 optimal weight: 0.0070 chunk 93 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 203 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 570 GLN B 602 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 HIS ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 19710 Z= 0.232 Angle : 0.714 11.421 26739 Z= 0.380 Chirality : 0.047 0.343 3039 Planarity : 0.005 0.063 3372 Dihedral : 6.022 39.213 2967 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.78 % Favored : 92.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % 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: -0.35 (0.17), residues: 2361 helix: 0.29 (0.37), residues: 162 sheet: -0.26 (0.18), residues: 678 loop : -0.20 (0.17), residues: 1521 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.3145 time to fit residues: 220.1749 Evaluate side-chains 323 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 chunk 187 optimal weight: 0.5980 chunk 104 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 118 optimal weight: 0.3980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 19710 Z= 0.207 Angle : 0.696 10.742 26739 Z= 0.370 Chirality : 0.047 0.342 3039 Planarity : 0.005 0.071 3372 Dihedral : 5.827 33.714 2967 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.86 % Favored : 92.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % 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: -0.39 (0.17), residues: 2361 helix: 0.44 (0.38), residues: 162 sheet: -0.31 (0.18), residues: 759 loop : -0.23 (0.17), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.3218 time to fit residues: 221.2685 Evaluate side-chains 322 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 602 HIS H 5 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 39 HIS G 567 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS I 514 ASN I 567 GLN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 19710 Z= 0.312 Angle : 0.753 13.105 26739 Z= 0.400 Chirality : 0.046 0.309 3039 Planarity : 0.005 0.069 3372 Dihedral : 5.921 31.511 2967 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 20.78 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.73 % Favored : 92.80 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % 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: -0.67 (0.17), residues: 2361 helix: 0.57 (0.39), residues: 162 sheet: -0.61 (0.18), residues: 810 loop : -0.38 (0.17), residues: 1389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 416 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 416 average time/residue: 0.3186 time to fit residues: 201.0662 Evaluate side-chains 298 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.4980 chunk 134 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN L 90 HIS ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 44 GLN G 551 GLN ** P 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 73 ASN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 19710 Z= 0.356 Angle : 0.796 11.679 26739 Z= 0.421 Chirality : 0.048 0.324 3039 Planarity : 0.006 0.072 3372 Dihedral : 6.140 38.770 2967 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.96 % Favored : 91.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2361 helix: 0.20 (0.38), residues: 162 sheet: -0.72 (0.18), residues: 771 loop : -0.62 (0.17), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.3254 time to fit residues: 200.7988 Evaluate side-chains 287 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 44 GLN ** P 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 HIS ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN F 73 ASN I 514 ASN I 551 GLN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 HIS ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 19710 Z= 0.273 Angle : 0.773 17.252 26739 Z= 0.412 Chirality : 0.047 0.327 3039 Planarity : 0.006 0.129 3372 Dihedral : 6.077 46.354 2967 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 22.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.30 % Favored : 91.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.90 (0.17), residues: 2361 helix: 0.18 (0.39), residues: 162 sheet: -0.62 (0.18), residues: 768 loop : -0.61 (0.17), residues: 1431 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.3303 time to fit residues: 207.7993 Evaluate side-chains 285 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.7980 chunk 135 optimal weight: 0.1980 chunk 105 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 214 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 143 optimal weight: 8.9990 chunk 113 optimal weight: 0.4980 chunk 147 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100BASN D 42 GLN E 44 GLN E 62 GLN G 570 GLN ** P 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN J 39 GLN ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 HIS Q 3 GLN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 19710 Z= 0.207 Angle : 0.746 12.233 26739 Z= 0.392 Chirality : 0.047 0.332 3039 Planarity : 0.005 0.117 3372 Dihedral : 5.892 46.726 2967 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.13 % Favored : 91.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.91 (0.17), residues: 2361 helix: 0.10 (0.39), residues: 162 sheet: -0.59 (0.19), residues: 756 loop : -0.64 (0.17), residues: 1443 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.3124 time to fit residues: 206.1282 Evaluate side-chains 293 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 163 optimal weight: 0.0770 overall best weight: 2.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 551 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 44 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN J 82BASN ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.066560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051354 restraints weight = 103267.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052749 restraints weight = 60944.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053673 restraints weight = 42569.016| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19710 Z= 0.255 Angle : 0.742 10.574 26739 Z= 0.397 Chirality : 0.046 0.299 3039 Planarity : 0.005 0.076 3372 Dihedral : 5.898 45.927 2967 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.39 % Favored : 91.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2361 helix: 0.17 (0.38), residues: 162 sheet: -0.63 (0.18), residues: 756 loop : -0.70 (0.17), residues: 1443 =============================================================================== Job complete usr+sys time: 4453.02 seconds wall clock time: 81 minutes 39.03 seconds (4899.03 seconds total)