Starting phenix.real_space_refine on Sun Mar 17 23:53:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/03_2024/5kel_8240.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/03_2024/5kel_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_8240/03_2024/5kel_8240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/03_2024/5kel_8240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/03_2024/5kel_8240.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kel_8240/03_2024/5kel_8240.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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-5265/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 dihedrals: 6 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: 9 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: 12 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: 15 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 dihedrals: 6 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: 9 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: 12 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: 15 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 dihedrals: 6 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: 9 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: 12 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: 15 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.85, per 1000 atoms: 0.51 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: 7.93 Conformation dependent library (CDL) restraints added in 3.3 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: 2.37 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: 7.18 Time building geometry restraints manager: 8.52 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=" 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 angle pdb=" C VAL A 92 " pdb=" N PRO A 93 " pdb=" CA PRO A 93 " ideal model delta sigma weight residual 119.66 127.33 -7.67 7.20e-01 1.93e+00 1.14e+02 angle pdb=" C ALA A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 126 " ideal model delta sigma weight residual 120.03 130.33 -10.30 9.90e-01 1.02e+00 1.08e+02 angle pdb=" C ALA F 125 " pdb=" N PRO F 126 " pdb=" CA PRO F 126 " ideal model delta sigma weight residual 120.03 130.32 -10.29 9.90e-01 1.02e+00 1.08e+02 ... (remaining 26734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 11586 21.51 - 43.01: 366 43.01 - 64.52: 96 64.52 - 86.03: 87 86.03 - 107.54: 39 Dihedral angle restraints: 12174 sinusoidal: 5328 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 12171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 2940 0.206 - 0.413: 78 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 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.340 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 53.320 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 : 0.015 0.083 19710 Z= 0.946 Angle : 1.819 11.804 26739 Z= 1.195 Chirality : 0.103 1.031 3039 Planarity : 0.015 0.244 3372 Dihedral : 14.922 107.536 7749 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 % Allowed : 0.60 % Favored : 98.96 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.011 TRP B 597 HIS 0.007 0.002 HIS T 90 PHE 0.038 0.006 PHE U 91 TYR 0.062 0.010 TYR Q 79 ARG 0.007 0.001 ARG T 61 *********************** 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 : 2.985 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: A 75 VAL cc_start: 0.9404 (t) cc_final: 0.9134 (p) REVERT: A 251 GLN cc_start: 0.9285 (mp10) cc_final: 0.8882 (pm20) REVERT: B 564 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: H 50 GLU cc_start: 0.8137 (tt0) cc_final: 0.7663 (tm-30) REVERT: H 61 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8566 (mm-30) REVERT: H 68 THR cc_start: 0.8763 (p) cc_final: 0.8558 (t) REVERT: H 80 LEU cc_start: 0.9112 (tp) cc_final: 0.8894 (tp) REVERT: H 103 TRP cc_start: 0.5952 (p90) cc_final: 0.5537 (p90) REVERT: L 17 GLU cc_start: 0.8923 (tt0) cc_final: 0.8712 (tt0) REVERT: L 58 VAL cc_start: 0.8752 (t) cc_final: 0.8393 (p) REVERT: L 81 GLU cc_start: 0.8788 (pt0) cc_final: 0.8308 (tm-30) REVERT: L 105 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8087 (mt-10) REVERT: C 12 VAL cc_start: 0.7496 (m) cc_final: 0.6897 (p) REVERT: C 63 LEU cc_start: 0.8565 (mt) cc_final: 0.8291 (mp) REVERT: C 64 LYS cc_start: 0.8871 (tttt) cc_final: 0.8601 (tptp) REVERT: C 81 LYS cc_start: 0.9193 (tttt) cc_final: 0.8923 (ptmm) REVERT: C 82 ILE cc_start: 0.8011 (mt) cc_final: 0.7675 (mm) REVERT: D 1 ASP cc_start: 0.8103 (m-30) cc_final: 0.7437 (p0) REVERT: D 82 ASP cc_start: 0.8386 (m-30) cc_final: 0.8145 (m-30) REVERT: E 75 VAL cc_start: 0.9329 (t) cc_final: 0.9072 (p) REVERT: E 117 ASP cc_start: 0.8449 (p0) cc_final: 0.8208 (t0) REVERT: E 178 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: E 223 THR cc_start: 0.9113 (m) cc_final: 0.8906 (p) REVERT: E 251 GLN cc_start: 0.9311 (mp10) cc_final: 0.8951 (pm20) REVERT: E 253 LEU cc_start: 0.9593 (mt) cc_final: 0.9377 (tt) REVERT: E 275 TRP cc_start: 0.6975 (m-90) cc_final: 0.5875 (m-90) REVERT: G 564 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8771 (mp0) REVERT: G 588 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8923 (mmmm) REVERT: P 12 MET cc_start: 0.8528 (mtm) cc_final: 0.8282 (mtt) REVERT: P 20 LEU cc_start: 0.9197 (tp) cc_final: 0.8818 (tp) REVERT: P 35 ASN cc_start: 0.8169 (m-40) cc_final: 0.5622 (t0) REVERT: P 80 LEU cc_start: 0.9228 (tp) cc_final: 0.8927 (tp) REVERT: P 82 ASN cc_start: 0.8045 (m-40) cc_final: 0.7218 (m110) REVERT: T 17 GLU cc_start: 0.8710 (tt0) cc_final: 0.8417 (tt0) REVERT: T 58 VAL cc_start: 0.8676 (t) cc_final: 0.8427 (p) REVERT: T 73 LEU cc_start: 0.9428 (tp) cc_final: 0.9078 (tt) REVERT: T 81 GLU cc_start: 0.8758 (pt0) cc_final: 0.8420 (tp30) REVERT: T 105 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7770 (mt-10) REVERT: J 12 VAL cc_start: 0.7672 (m) cc_final: 0.7219 (p) REVERT: J 63 LEU cc_start: 0.8803 (mt) cc_final: 0.8438 (mp) REVERT: J 64 LYS cc_start: 0.9057 (tttt) cc_final: 0.8806 (tptp) REVERT: J 69 ILE cc_start: 0.7640 (mt) cc_final: 0.7407 (mt) REVERT: N 1 ASP cc_start: 0.8207 (m-30) cc_final: 0.7504 (p0) REVERT: N 38 GLN cc_start: 0.8555 (tt0) cc_final: 0.8205 (tt0) REVERT: N 82 ASP cc_start: 0.8752 (m-30) cc_final: 0.8470 (m-30) REVERT: N 103 LYS cc_start: 0.8308 (mttt) cc_final: 0.8053 (mmtm) REVERT: F 35 LEU cc_start: 0.9150 (mt) cc_final: 0.8874 (mp) REVERT: F 75 VAL cc_start: 0.9353 (t) cc_final: 0.9098 (p) REVERT: F 178 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: F 223 THR cc_start: 0.9132 (m) cc_final: 0.8865 (p) REVERT: F 251 GLN cc_start: 0.9250 (mp10) cc_final: 0.8853 (pm20) REVERT: F 275 TRP cc_start: 0.7245 (m-90) cc_final: 0.5827 (m-90) REVERT: I 564 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8759 (mp0) REVERT: I 588 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9089 (mmmm) REVERT: I 608 CYS cc_start: 0.6560 (m) cc_final: 0.6256 (m) REVERT: Q 12 MET cc_start: 0.8392 (mtm) cc_final: 0.8191 (mtt) REVERT: Q 20 LEU cc_start: 0.9260 (tp) cc_final: 0.9047 (tp) REVERT: Q 35 ASN cc_start: 0.8306 (m-40) cc_final: 0.5683 (t0) REVERT: U 17 GLU cc_start: 0.8806 (tt0) cc_final: 0.8540 (tt0) REVERT: U 58 VAL cc_start: 0.8659 (t) cc_final: 0.8351 (p) REVERT: U 87 TYR cc_start: 0.8697 (m-80) cc_final: 0.8074 (m-80) REVERT: M 12 VAL cc_start: 0.7389 (m) cc_final: 0.6899 (p) REVERT: M 63 LEU cc_start: 0.8819 (mt) cc_final: 0.8413 (mp) REVERT: M 69 ILE cc_start: 0.7659 (mt) cc_final: 0.7378 (mt) REVERT: M 75 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8543 (ttp-110) REVERT: M 81 LYS cc_start: 0.9226 (tttt) cc_final: 0.8956 (ptmm) REVERT: O 1 ASP cc_start: 0.8185 (m-30) cc_final: 0.7523 (p0) REVERT: O 23 CYS cc_start: 0.5829 (t) cc_final: 0.4958 (t) REVERT: O 38 GLN cc_start: 0.8463 (tt0) cc_final: 0.8155 (tt0) REVERT: O 82 ASP cc_start: 0.8409 (m-30) cc_final: 0.8139 (m-30) outliers start: 9 outliers final: 4 residues processed: 767 average time/residue: 0.3265 time to fit residues: 367.9570 Evaluate side-chains 417 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 408 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 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: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 514 ASN B 602 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 90 GLN E 39 HIS E 73 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** T 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7554 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 19710 Z= 0.271 Angle : 0.888 14.630 26739 Z= 0.463 Chirality : 0.051 0.244 3039 Planarity : 0.007 0.108 3372 Dihedral : 13.165 88.620 3534 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.55 % Favored : 93.86 % Rotamer: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % 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: 0.63 (0.17), residues: 2361 helix: 0.21 (0.35), residues: 147 sheet: -0.10 (0.18), residues: 678 loop : 0.87 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 35 HIS 0.014 0.002 HIS L 90 PHE 0.018 0.003 PHE F 88 TYR 0.030 0.003 TYR O 36 ARG 0.021 0.001 ARG Q 94 *********************** 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 592 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 589 time to evaluate : 1.907 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: A 75 VAL cc_start: 0.9465 (t) cc_final: 0.9198 (p) REVERT: A 117 ASP cc_start: 0.8822 (p0) cc_final: 0.8548 (p0) REVERT: B 591 ASP cc_start: 0.8947 (p0) cc_final: 0.8738 (m-30) REVERT: H 2 VAL cc_start: 0.8140 (p) cc_final: 0.7877 (t) REVERT: H 43 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8669 (pttm) REVERT: H 100 MET cc_start: 0.6903 (ttt) cc_final: 0.6456 (ttt) REVERT: L 13 VAL cc_start: 0.9376 (m) cc_final: 0.9168 (p) REVERT: L 35 TRP cc_start: 0.7972 (m100) cc_final: 0.7569 (m100) REVERT: C 64 LYS cc_start: 0.8929 (tttt) cc_final: 0.8600 (pttt) REVERT: D 1 ASP cc_start: 0.8083 (m-30) cc_final: 0.7341 (p0) REVERT: D 44 PRO cc_start: 0.9024 (Cg_endo) cc_final: 0.8789 (Cg_exo) REVERT: D 91 TYR cc_start: 0.8242 (m-80) cc_final: 0.7977 (m-80) REVERT: E 35 LEU cc_start: 0.9212 (mp) cc_final: 0.8971 (mp) REVERT: E 75 VAL cc_start: 0.9315 (t) cc_final: 0.9059 (p) REVERT: E 117 ASP cc_start: 0.8697 (p0) cc_final: 0.8317 (p0) REVERT: E 251 GLN cc_start: 0.9261 (mp10) cc_final: 0.8933 (pm20) REVERT: E 275 TRP cc_start: 0.7019 (m-90) cc_final: 0.6748 (m-90) REVERT: G 555 ILE cc_start: 0.9537 (mm) cc_final: 0.9159 (tp) REVERT: G 588 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8987 (mmtp) REVERT: G 595 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8872 (tm-30) REVERT: P 2 VAL cc_start: 0.8102 (p) cc_final: 0.7711 (t) REVERT: P 100 MET cc_start: 0.7507 (ttt) cc_final: 0.7205 (ttt) REVERT: T 13 VAL cc_start: 0.9451 (m) cc_final: 0.9242 (p) REVERT: T 92 TRP cc_start: 0.7759 (p-90) cc_final: 0.7557 (p-90) REVERT: J 100 TYR cc_start: 0.7923 (t80) cc_final: 0.7677 (t80) REVERT: N 1 ASP cc_start: 0.8190 (m-30) cc_final: 0.7385 (p0) REVERT: N 91 TYR cc_start: 0.8178 (m-80) cc_final: 0.7777 (m-80) REVERT: F 69 ASN cc_start: 0.8768 (t0) cc_final: 0.8501 (t0) REVERT: F 75 VAL cc_start: 0.9399 (t) cc_final: 0.9198 (p) REVERT: F 251 GLN cc_start: 0.9318 (mp10) cc_final: 0.8913 (pm20) REVERT: I 555 ILE cc_start: 0.9502 (mm) cc_final: 0.9121 (tt) REVERT: I 570 GLN cc_start: 0.9326 (tp40) cc_final: 0.9123 (tp-100) REVERT: I 588 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9097 (mmmm) REVERT: Q 5 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8436 (tp40) REVERT: Q 18 MET cc_start: 0.7778 (tmm) cc_final: 0.7075 (tmm) REVERT: U 87 TYR cc_start: 0.8747 (m-80) cc_final: 0.8502 (m-80) REVERT: U 98 PHE cc_start: 0.8637 (m-80) cc_final: 0.8322 (m-10) REVERT: M 20 LEU cc_start: 0.8802 (mp) cc_final: 0.8485 (mt) REVERT: M 27 PHE cc_start: 0.6212 (t80) cc_final: 0.5847 (t80) REVERT: M 77 GLN cc_start: 0.7597 (mt0) cc_final: 0.6670 (mt0) REVERT: M 100 MET cc_start: 0.8659 (ttp) cc_final: 0.8242 (ttp) REVERT: O 1 ASP cc_start: 0.8317 (m-30) cc_final: 0.7398 (p0) REVERT: O 44 PRO cc_start: 0.9023 (Cg_endo) cc_final: 0.8697 (Cg_exo) REVERT: O 48 ILE cc_start: 0.8509 (mt) cc_final: 0.8218 (mt) REVERT: O 85 ASP cc_start: 0.8535 (t0) cc_final: 0.8308 (t0) outliers start: 3 outliers final: 0 residues processed: 590 average time/residue: 0.3083 time to fit residues: 271.7150 Evaluate side-chains 388 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.067 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 229 optimal weight: 0.0170 chunk 189 optimal weight: 20.0000 chunk 211 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.1622 ------------------------------------------------------------------------------- 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 B 613 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 C 39 GLN D 38 GLN D 42 GLN D 90 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 GLN G 586 ASN G 602 HIS G 613 HIS P 53 ASN ** 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 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 HIS I 613 HIS Q 53 ASN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 GLN O 27 GLN ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19710 Z= 0.268 Angle : 0.797 9.977 26739 Z= 0.410 Chirality : 0.048 0.229 3039 Planarity : 0.006 0.110 3372 Dihedral : 11.565 84.904 3534 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.55 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: 0.11 (0.17), residues: 2361 helix: 0.15 (0.35), residues: 156 sheet: -0.30 (0.18), residues: 687 loop : 0.38 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 103 HIS 0.004 0.001 HIS T 90 PHE 0.023 0.002 PHE M 98 TYR 0.031 0.003 TYR P 99 ARG 0.006 0.001 ARG G 580 *********************** 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 507 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 2.417 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: A 75 VAL cc_start: 0.9464 (t) cc_final: 0.9253 (p) REVERT: A 117 ASP cc_start: 0.8809 (p0) cc_final: 0.8484 (p0) REVERT: A 137 TYR cc_start: 0.9040 (m-10) cc_final: 0.8836 (m-10) REVERT: B 591 ASP cc_start: 0.8945 (p0) cc_final: 0.8705 (m-30) REVERT: L 13 VAL cc_start: 0.9416 (m) cc_final: 0.9142 (p) REVERT: L 91 PHE cc_start: 0.6490 (m-10) cc_final: 0.6166 (m-10) REVERT: C 64 LYS cc_start: 0.8920 (tttt) cc_final: 0.8564 (tptp) REVERT: C 69 ILE cc_start: 0.7696 (mt) cc_final: 0.7437 (mt) REVERT: C 82 ILE cc_start: 0.8200 (mp) cc_final: 0.7829 (mp) REVERT: D 1 ASP cc_start: 0.8178 (m-30) cc_final: 0.7335 (p0) REVERT: D 103 LYS cc_start: 0.8562 (mppt) cc_final: 0.8345 (mmtm) REVERT: E 35 LEU cc_start: 0.9215 (mp) cc_final: 0.8992 (mm) REVERT: E 75 VAL cc_start: 0.9400 (t) cc_final: 0.9187 (p) REVERT: E 117 ASP cc_start: 0.8735 (p0) cc_final: 0.8423 (p0) REVERT: E 251 GLN cc_start: 0.9451 (mp10) cc_final: 0.9045 (pm20) REVERT: G 588 LYS cc_start: 0.9244 (mmtt) cc_final: 0.9025 (mmtm) REVERT: G 595 GLN cc_start: 0.9132 (tp-100) cc_final: 0.8851 (tm-30) REVERT: P 34 MET cc_start: 0.7351 (mmp) cc_final: 0.5889 (mmp) REVERT: P 55 TYR cc_start: 0.9280 (m-10) cc_final: 0.8927 (m-10) REVERT: P 80 LEU cc_start: 0.9050 (tt) cc_final: 0.8814 (tt) REVERT: T 13 VAL cc_start: 0.9413 (m) cc_final: 0.9094 (p) REVERT: T 83 PHE cc_start: 0.8360 (m-10) cc_final: 0.7699 (m-10) REVERT: T 98 PHE cc_start: 0.8844 (m-80) cc_final: 0.8575 (m-10) REVERT: J 69 ILE cc_start: 0.7727 (mt) cc_final: 0.7521 (mt) REVERT: J 75 ARG cc_start: 0.8974 (ttp-110) cc_final: 0.7922 (ttp-110) REVERT: J 82 ASN cc_start: 0.8902 (t0) cc_final: 0.8685 (m110) REVERT: N 1 ASP cc_start: 0.8288 (m-30) cc_final: 0.7327 (p0) REVERT: N 18 ARG cc_start: 0.9053 (mmt-90) cc_final: 0.8849 (mmp80) REVERT: N 54 ARG cc_start: 0.7890 (ptt90) cc_final: 0.7540 (ptm-80) REVERT: F 69 ASN cc_start: 0.8933 (t0) cc_final: 0.8699 (t0) REVERT: F 251 GLN cc_start: 0.9473 (mp10) cc_final: 0.8969 (pm20) REVERT: I 555 ILE cc_start: 0.9462 (mm) cc_final: 0.8982 (tt) REVERT: Q 91 TYR cc_start: 0.8700 (m-80) cc_final: 0.8280 (m-80) REVERT: U 13 VAL cc_start: 0.9484 (m) cc_final: 0.9194 (p) REVERT: U 83 PHE cc_start: 0.8403 (m-10) cc_final: 0.8096 (m-80) REVERT: U 87 TYR cc_start: 0.8646 (m-80) cc_final: 0.8209 (m-80) REVERT: U 105 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7887 (mp0) REVERT: M 19 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8504 (mmmm) REVERT: M 20 LEU cc_start: 0.8822 (mp) cc_final: 0.8562 (mt) REVERT: M 81 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8800 (tptp) REVERT: O 1 ASP cc_start: 0.8381 (m-30) cc_final: 0.7381 (p0) REVERT: O 91 TYR cc_start: 0.8322 (m-10) cc_final: 0.7924 (m-80) REVERT: O 103 LYS cc_start: 0.8466 (mppt) cc_final: 0.8215 (mmtm) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.3103 time to fit residues: 235.9288 Evaluate side-chains 366 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.164 ------------------------------------------------------------------------------- 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: 10.0000 chunk 160 optimal weight: 0.1980 chunk 110 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 213 optimal weight: 0.2980 chunk 226 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 202 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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** B 602 HIS ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN D 42 GLN D 90 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19710 Z= 0.199 Angle : 0.729 11.601 26739 Z= 0.372 Chirality : 0.047 0.245 3039 Planarity : 0.005 0.107 3372 Dihedral : 10.291 77.897 3534 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.76 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: -0.06 (0.17), residues: 2361 helix: 0.18 (0.36), residues: 156 sheet: -0.26 (0.19), residues: 645 loop : 0.14 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 531 HIS 0.004 0.001 HIS L 90 PHE 0.039 0.002 PHE H 27 TYR 0.031 0.002 TYR A 232 ARG 0.007 0.000 ARG F 299 *********************** 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 505 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 2.232 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: A 75 VAL cc_start: 0.9465 (t) cc_final: 0.9244 (p) REVERT: A 117 ASP cc_start: 0.8825 (p0) cc_final: 0.8451 (p0) REVERT: A 137 TYR cc_start: 0.9020 (m-10) cc_final: 0.8764 (m-10) REVERT: H 5 GLN cc_start: 0.8838 (tp40) cc_final: 0.8527 (mm110) REVERT: H 34 MET cc_start: 0.6898 (mmp) cc_final: 0.5842 (mmp) REVERT: C 20 LEU cc_start: 0.8786 (mt) cc_final: 0.8583 (mt) REVERT: C 64 LYS cc_start: 0.8919 (tttt) cc_final: 0.8562 (tptp) REVERT: C 82 ILE cc_start: 0.8273 (mp) cc_final: 0.7837 (mp) REVERT: D 1 ASP cc_start: 0.8131 (m-30) cc_final: 0.7294 (p0) REVERT: D 4 MET cc_start: 0.7249 (tpt) cc_final: 0.7045 (tpp) REVERT: D 36 TYR cc_start: 0.7902 (m-80) cc_final: 0.7164 (m-80) REVERT: E 75 VAL cc_start: 0.9392 (t) cc_final: 0.9170 (p) REVERT: E 117 ASP cc_start: 0.8815 (p0) cc_final: 0.8383 (p0) REVERT: E 251 GLN cc_start: 0.9441 (mp10) cc_final: 0.8994 (pm20) REVERT: P 55 TYR cc_start: 0.9234 (m-10) cc_final: 0.8867 (m-10) REVERT: P 80 LEU cc_start: 0.9060 (tt) cc_final: 0.8819 (tt) REVERT: T 13 VAL cc_start: 0.9333 (m) cc_final: 0.9042 (p) REVERT: T 83 PHE cc_start: 0.8266 (m-10) cc_final: 0.7751 (m-80) REVERT: T 98 PHE cc_start: 0.8645 (m-80) cc_final: 0.8355 (m-10) REVERT: J 75 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.7965 (ttp-110) REVERT: J 77 GLN cc_start: 0.7534 (mt0) cc_final: 0.6613 (mt0) REVERT: J 82 ASN cc_start: 0.8920 (t0) cc_final: 0.8713 (m-40) REVERT: J 100 MET cc_start: 0.8651 (ttm) cc_final: 0.8416 (mtp) REVERT: N 1 ASP cc_start: 0.8124 (m-30) cc_final: 0.7275 (p0) REVERT: N 36 TYR cc_start: 0.8299 (m-80) cc_final: 0.7944 (m-80) REVERT: N 54 ARG cc_start: 0.7904 (ptt90) cc_final: 0.7628 (ptm-80) REVERT: N 87 PHE cc_start: 0.8501 (m-80) cc_final: 0.8223 (m-80) REVERT: F 69 ASN cc_start: 0.8932 (t0) cc_final: 0.8655 (t0) REVERT: F 117 ASP cc_start: 0.8870 (p0) cc_final: 0.8256 (p0) REVERT: F 251 GLN cc_start: 0.9481 (mp10) cc_final: 0.8951 (pm20) REVERT: I 555 ILE cc_start: 0.9512 (mm) cc_final: 0.9163 (tp) REVERT: Q 91 TYR cc_start: 0.8624 (m-80) cc_final: 0.8267 (m-80) REVERT: U 83 PHE cc_start: 0.8197 (m-10) cc_final: 0.7979 (m-80) REVERT: M 19 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8522 (mmmm) REVERT: M 27 PHE cc_start: 0.6819 (t80) cc_final: 0.6611 (t80) REVERT: M 46 GLU cc_start: 0.8755 (tp30) cc_final: 0.8409 (tp30) REVERT: M 75 ARG cc_start: 0.8938 (ttp-110) cc_final: 0.8675 (mtm110) REVERT: M 81 LYS cc_start: 0.9132 (tmtt) cc_final: 0.8869 (tptp) REVERT: O 1 ASP cc_start: 0.8339 (m-30) cc_final: 0.7355 (p0) REVERT: O 36 TYR cc_start: 0.7970 (m-80) cc_final: 0.7751 (m-80) REVERT: O 78 MET cc_start: 0.8137 (ppp) cc_final: 0.7863 (ppp) REVERT: O 85 ASP cc_start: 0.8361 (t0) cc_final: 0.8124 (t0) REVERT: O 103 LYS cc_start: 0.8331 (mppt) cc_final: 0.8064 (mmtm) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.3070 time to fit residues: 232.9228 Evaluate side-chains 372 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.123 ------------------------------------------------------------------------------- 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: 9.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 203 optimal weight: 0.0570 chunk 57 optimal weight: 0.5980 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 HIS ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 GLN O 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19710 Z= 0.205 Angle : 0.725 11.265 26739 Z= 0.367 Chirality : 0.047 0.237 3039 Planarity : 0.005 0.064 3372 Dihedral : 9.388 69.316 3534 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.18 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -0.31 (0.17), residues: 2361 helix: 0.00 (0.35), residues: 162 sheet: -0.41 (0.19), residues: 669 loop : -0.04 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 531 HIS 0.013 0.001 HIS U 90 PHE 0.034 0.002 PHE H 27 TYR 0.026 0.002 TYR E 261 ARG 0.009 0.001 ARG Q 94 *********************** 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 500 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 500 time to evaluate : 2.236 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: A 75 VAL cc_start: 0.9487 (t) cc_final: 0.9248 (p) REVERT: A 117 ASP cc_start: 0.8869 (p0) cc_final: 0.8422 (p0) REVERT: H 5 GLN cc_start: 0.8932 (tp40) cc_final: 0.8558 (mm110) REVERT: H 50 GLU cc_start: 0.8163 (tp30) cc_final: 0.7962 (tp30) REVERT: H 100 MET cc_start: 0.7096 (ttp) cc_final: 0.6441 (ttp) REVERT: L 91 PHE cc_start: 0.5511 (m-10) cc_final: 0.5182 (m-10) REVERT: C 20 LEU cc_start: 0.8664 (mt) cc_final: 0.8444 (mt) REVERT: C 63 LEU cc_start: 0.8623 (mt) cc_final: 0.8321 (mt) REVERT: C 64 LYS cc_start: 0.8953 (tttt) cc_final: 0.8531 (tptp) REVERT: C 67 LEU cc_start: 0.8202 (mt) cc_final: 0.7677 (mt) REVERT: C 82 ILE cc_start: 0.8444 (mp) cc_final: 0.7969 (mm) REVERT: C 100 MET cc_start: 0.8271 (tpp) cc_final: 0.7989 (mmm) REVERT: D 1 ASP cc_start: 0.8023 (m-30) cc_final: 0.7087 (p0) REVERT: D 4 MET cc_start: 0.7634 (tpt) cc_final: 0.7160 (tpp) REVERT: D 103 LYS cc_start: 0.8405 (mppt) cc_final: 0.8070 (mmtm) REVERT: E 75 VAL cc_start: 0.9377 (t) cc_final: 0.9151 (p) REVERT: E 99 TYR cc_start: 0.8823 (p90) cc_final: 0.8594 (p90) REVERT: E 117 ASP cc_start: 0.8924 (p0) cc_final: 0.8449 (p0) REVERT: E 251 GLN cc_start: 0.9399 (mp10) cc_final: 0.8974 (pm20) REVERT: P 55 TYR cc_start: 0.9257 (m-10) cc_final: 0.8932 (m-10) REVERT: T 13 VAL cc_start: 0.8925 (m) cc_final: 0.8487 (p) REVERT: T 83 PHE cc_start: 0.8337 (m-10) cc_final: 0.7770 (m-10) REVERT: T 98 PHE cc_start: 0.8657 (m-80) cc_final: 0.8243 (m-10) REVERT: J 46 GLU cc_start: 0.8648 (tp30) cc_final: 0.8168 (tp30) REVERT: J 81 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8163 (tptp) REVERT: J 82 ASN cc_start: 0.8935 (t0) cc_final: 0.8718 (m-40) REVERT: J 100 MET cc_start: 0.8672 (ttm) cc_final: 0.8372 (mtp) REVERT: N 1 ASP cc_start: 0.8099 (m-30) cc_final: 0.7229 (p0) REVERT: N 36 TYR cc_start: 0.8305 (m-80) cc_final: 0.7771 (m-80) REVERT: N 77 ASN cc_start: 0.8534 (t0) cc_final: 0.8289 (t0) REVERT: F 69 ASN cc_start: 0.8910 (t0) cc_final: 0.8645 (t0) REVERT: F 117 ASP cc_start: 0.8919 (p0) cc_final: 0.8243 (p0) REVERT: F 251 GLN cc_start: 0.9476 (mp10) cc_final: 0.8950 (pm20) REVERT: I 534 TYR cc_start: 0.8754 (t80) cc_final: 0.8502 (t80) REVERT: I 555 ILE cc_start: 0.9508 (mm) cc_final: 0.9166 (tp) REVERT: Q 3 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8626 (mm-40) REVERT: Q 5 GLN cc_start: 0.8528 (tp40) cc_final: 0.8095 (tm-30) REVERT: Q 34 MET cc_start: 0.8169 (tpt) cc_final: 0.7640 (tpp) REVERT: U 13 VAL cc_start: 0.8790 (m) cc_final: 0.8562 (p) REVERT: U 83 PHE cc_start: 0.8316 (m-10) cc_final: 0.8072 (m-80) REVERT: M 46 GLU cc_start: 0.8796 (tp30) cc_final: 0.8388 (tp30) REVERT: M 75 ARG cc_start: 0.8928 (ttp-110) cc_final: 0.8672 (mtm110) REVERT: M 81 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8868 (tptp) REVERT: M 82 ILE cc_start: 0.8352 (mm) cc_final: 0.7919 (mm) REVERT: O 1 ASP cc_start: 0.8382 (m-30) cc_final: 0.7336 (p0) REVERT: O 17 ASP cc_start: 0.7051 (m-30) cc_final: 0.6499 (m-30) REVERT: O 71 PHE cc_start: 0.8080 (m-80) cc_final: 0.7854 (m-80) REVERT: O 78 MET cc_start: 0.8309 (ppp) cc_final: 0.8035 (ppp) REVERT: O 83 LEU cc_start: 0.8588 (mt) cc_final: 0.8024 (pt) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.3026 time to fit residues: 228.9943 Evaluate side-chains 365 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 GLN ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 514 ASN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19710 Z= 0.221 Angle : 0.712 9.608 26739 Z= 0.362 Chirality : 0.046 0.234 3039 Planarity : 0.005 0.083 3372 Dihedral : 8.921 59.884 3534 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.44 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 0.24 (0.37), residues: 162 sheet: -0.39 (0.18), residues: 732 loop : -0.10 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP L 35 HIS 0.002 0.001 HIS L 90 PHE 0.039 0.002 PHE H 27 TYR 0.034 0.002 TYR L 96 ARG 0.009 0.001 ARG Q 94 *********************** 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 475 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 2.021 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: A 75 VAL cc_start: 0.9498 (t) cc_final: 0.9269 (p) REVERT: A 117 ASP cc_start: 0.8900 (p0) cc_final: 0.8419 (p0) REVERT: H 5 GLN cc_start: 0.8956 (tp40) cc_final: 0.8581 (mm110) REVERT: H 80 LEU cc_start: 0.8809 (tt) cc_final: 0.8592 (tt) REVERT: H 100 MET cc_start: 0.7066 (ttp) cc_final: 0.6834 (ttp) REVERT: C 20 LEU cc_start: 0.8767 (mt) cc_final: 0.8538 (mt) REVERT: C 50 LEU cc_start: 0.9278 (tp) cc_final: 0.9037 (tp) REVERT: C 64 LYS cc_start: 0.8912 (tttt) cc_final: 0.8521 (tptp) REVERT: C 82 ILE cc_start: 0.8501 (mp) cc_final: 0.8048 (mp) REVERT: D 1 ASP cc_start: 0.7989 (m-30) cc_final: 0.7032 (p0) REVERT: D 4 MET cc_start: 0.7874 (tpt) cc_final: 0.7318 (tpp) REVERT: D 18 ARG cc_start: 0.8509 (mmt-90) cc_final: 0.8265 (mmp80) REVERT: D 103 LYS cc_start: 0.8469 (mppt) cc_final: 0.8132 (mmtm) REVERT: E 117 ASP cc_start: 0.8970 (p0) cc_final: 0.8430 (p0) REVERT: E 251 GLN cc_start: 0.9402 (mp10) cc_final: 0.8951 (pm20) REVERT: G 543 TYR cc_start: 0.8484 (m-80) cc_final: 0.8045 (m-80) REVERT: P 55 TYR cc_start: 0.9268 (m-10) cc_final: 0.8949 (m-10) REVERT: P 80 LEU cc_start: 0.9156 (tt) cc_final: 0.8885 (tt) REVERT: T 13 VAL cc_start: 0.8928 (m) cc_final: 0.8606 (p) REVERT: T 83 PHE cc_start: 0.8411 (m-10) cc_final: 0.7878 (m-80) REVERT: T 98 PHE cc_start: 0.8681 (m-80) cc_final: 0.8292 (m-10) REVERT: J 46 GLU cc_start: 0.8768 (tp30) cc_final: 0.8255 (tp30) REVERT: J 100 MET cc_start: 0.8685 (ttm) cc_final: 0.8365 (mtp) REVERT: N 1 ASP cc_start: 0.8069 (m-30) cc_final: 0.7246 (p0) REVERT: N 18 ARG cc_start: 0.8645 (mmp80) cc_final: 0.8385 (mmp80) REVERT: N 38 GLN cc_start: 0.8709 (tp40) cc_final: 0.8081 (tp-100) REVERT: N 78 MET cc_start: 0.8824 (ppp) cc_final: 0.8502 (ppp) REVERT: N 83 LEU cc_start: 0.8571 (mt) cc_final: 0.8326 (pt) REVERT: F 69 ASN cc_start: 0.8987 (t0) cc_final: 0.8722 (t0) REVERT: F 117 ASP cc_start: 0.8738 (p0) cc_final: 0.8314 (p0) REVERT: F 251 GLN cc_start: 0.9481 (mp10) cc_final: 0.8925 (pm20) REVERT: I 534 TYR cc_start: 0.8830 (t80) cc_final: 0.8600 (t80) REVERT: I 555 ILE cc_start: 0.9520 (mm) cc_final: 0.8999 (tt) REVERT: Q 3 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8667 (mm-40) REVERT: Q 5 GLN cc_start: 0.8498 (tp40) cc_final: 0.8117 (tm-30) REVERT: U 83 PHE cc_start: 0.8284 (m-10) cc_final: 0.7943 (m-80) REVERT: M 46 GLU cc_start: 0.8847 (tp30) cc_final: 0.8406 (tp30) REVERT: M 75 ARG cc_start: 0.9098 (ttp-110) cc_final: 0.8801 (mtm110) REVERT: M 81 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8810 (tptp) REVERT: O 1 ASP cc_start: 0.8392 (m-30) cc_final: 0.7359 (p0) REVERT: O 17 ASP cc_start: 0.6970 (m-30) cc_final: 0.6463 (m-30) REVERT: O 78 MET cc_start: 0.8404 (ppp) cc_final: 0.8078 (ppp) REVERT: O 83 LEU cc_start: 0.8673 (mt) cc_final: 0.8188 (pt) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.3018 time to fit residues: 216.4694 Evaluate side-chains 350 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 0.3980 chunk 128 optimal weight: 8.9990 chunk 165 optimal weight: 0.0060 chunk 190 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 90 GLN E 39 HIS ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS I 514 ASN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 HIS ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19710 Z= 0.257 Angle : 0.721 9.506 26739 Z= 0.368 Chirality : 0.046 0.228 3039 Planarity : 0.005 0.064 3372 Dihedral : 8.323 58.205 3534 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.95 % Favored : 92.67 % Rotamer: Outliers : 0.10 % Allowed : 1.69 % Favored : 98.21 % 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: -0.68 (0.17), residues: 2361 helix: 0.12 (0.36), residues: 180 sheet: -0.58 (0.18), residues: 822 loop : -0.34 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 35 HIS 0.009 0.001 HIS U 90 PHE 0.041 0.002 PHE P 27 TYR 0.037 0.002 TYR H 32 ARG 0.007 0.001 ARG Q 94 *********************** 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 439 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 437 time to evaluate : 2.369 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: A 117 ASP cc_start: 0.8946 (p0) cc_final: 0.8469 (p0) REVERT: L 91 PHE cc_start: 0.6197 (m-10) cc_final: 0.5877 (m-10) REVERT: C 20 LEU cc_start: 0.8784 (mt) cc_final: 0.8561 (mt) REVERT: C 64 LYS cc_start: 0.8824 (tttt) cc_final: 0.8486 (tptp) REVERT: C 82 ILE cc_start: 0.8435 (mp) cc_final: 0.8015 (mp) REVERT: D 1 ASP cc_start: 0.7901 (m-30) cc_final: 0.6851 (p0) REVERT: D 4 MET cc_start: 0.7802 (tpt) cc_final: 0.7478 (tpp) REVERT: D 18 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.8257 (mmp80) REVERT: D 78 MET cc_start: 0.8500 (ppp) cc_final: 0.8239 (ppp) REVERT: D 103 LYS cc_start: 0.8423 (mppt) cc_final: 0.8077 (mmtm) REVERT: E 117 ASP cc_start: 0.9049 (p0) cc_final: 0.8529 (p0) REVERT: E 251 GLN cc_start: 0.9475 (mp10) cc_final: 0.9007 (pm20) REVERT: G 543 TYR cc_start: 0.8618 (m-80) cc_final: 0.8209 (m-80) REVERT: G 565 THR cc_start: 0.9376 (m) cc_final: 0.9039 (t) REVERT: P 55 TYR cc_start: 0.9251 (m-10) cc_final: 0.9045 (m-10) REVERT: P 80 LEU cc_start: 0.9214 (tt) cc_final: 0.9010 (tt) REVERT: T 13 VAL cc_start: 0.8985 (m) cc_final: 0.8616 (p) REVERT: T 98 PHE cc_start: 0.8699 (m-80) cc_final: 0.8328 (m-10) REVERT: J 46 GLU cc_start: 0.8956 (tp30) cc_final: 0.8694 (tp30) REVERT: N 4 MET cc_start: 0.7555 (tpt) cc_final: 0.7352 (tpp) REVERT: N 38 GLN cc_start: 0.8634 (tp40) cc_final: 0.8380 (tp40) REVERT: N 78 MET cc_start: 0.8800 (ppp) cc_final: 0.8493 (ppp) REVERT: F 69 ASN cc_start: 0.9101 (t0) cc_final: 0.8826 (t0) REVERT: F 117 ASP cc_start: 0.8805 (p0) cc_final: 0.8364 (p0) REVERT: F 251 GLN cc_start: 0.9494 (mp10) cc_final: 0.8932 (pm20) REVERT: I 534 TYR cc_start: 0.8922 (t80) cc_final: 0.8714 (t80) REVERT: Q 3 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8448 (mp10) REVERT: Q 5 GLN cc_start: 0.8502 (tp40) cc_final: 0.8057 (tm-30) REVERT: Q 80 LEU cc_start: 0.9232 (tt) cc_final: 0.9019 (tt) REVERT: Q 91 TYR cc_start: 0.8559 (m-80) cc_final: 0.8145 (m-80) REVERT: Q 100 MET cc_start: 0.7320 (ptm) cc_final: 0.7079 (ptm) REVERT: U 35 TRP cc_start: 0.7860 (m100) cc_final: 0.7620 (m100) REVERT: U 83 PHE cc_start: 0.8390 (m-10) cc_final: 0.7829 (m-10) REVERT: U 98 PHE cc_start: 0.8741 (m-80) cc_final: 0.8431 (m-10) REVERT: M 46 GLU cc_start: 0.8814 (tp30) cc_final: 0.8362 (tp30) REVERT: M 75 ARG cc_start: 0.9138 (ttp-110) cc_final: 0.8866 (mtm110) REVERT: M 81 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8819 (tptp) REVERT: O 78 MET cc_start: 0.8344 (ppp) cc_final: 0.8072 (ppp) REVERT: O 83 LEU cc_start: 0.8682 (mt) cc_final: 0.8194 (pt) REVERT: O 103 LYS cc_start: 0.8187 (mppt) cc_final: 0.7842 (mmtt) outliers start: 2 outliers final: 0 residues processed: 437 average time/residue: 0.3123 time to fit residues: 204.5238 Evaluate side-chains 339 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.178 ------------------------------------------------------------------------------- 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: 4.9990 chunk 134 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 177 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** M 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19710 Z= 0.207 Angle : 0.707 13.481 26739 Z= 0.358 Chirality : 0.045 0.232 3039 Planarity : 0.005 0.066 3372 Dihedral : 7.640 57.675 3534 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.95 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 0.16 (0.36), residues: 180 sheet: -0.48 (0.18), residues: 804 loop : -0.41 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 35 HIS 0.005 0.001 HIS U 90 PHE 0.042 0.002 PHE P 27 TYR 0.026 0.002 TYR H 32 ARG 0.007 0.000 ARG P 94 *********************** 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 446 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.320 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: A 117 ASP cc_start: 0.8978 (p0) cc_final: 0.8489 (p0) REVERT: A 162 TYR cc_start: 0.8942 (m-10) cc_final: 0.8736 (m-10) REVERT: H 18 MET cc_start: 0.8157 (tmm) cc_final: 0.7851 (tmm) REVERT: C 20 LEU cc_start: 0.8780 (mt) cc_final: 0.8552 (mt) REVERT: C 64 LYS cc_start: 0.8824 (tttt) cc_final: 0.8550 (pttt) REVERT: C 82 ILE cc_start: 0.8440 (mp) cc_final: 0.8027 (mp) REVERT: D 1 ASP cc_start: 0.7989 (m-30) cc_final: 0.6904 (p0) REVERT: D 4 MET cc_start: 0.7753 (tpt) cc_final: 0.7463 (tpp) REVERT: D 18 ARG cc_start: 0.8495 (mmt-90) cc_final: 0.8263 (mmp80) REVERT: D 78 MET cc_start: 0.8531 (ppp) cc_final: 0.8298 (ppp) REVERT: D 103 LYS cc_start: 0.8412 (mppt) cc_final: 0.8076 (mmtm) REVERT: E 117 ASP cc_start: 0.9052 (p0) cc_final: 0.8483 (p0) REVERT: E 251 GLN cc_start: 0.9474 (mp10) cc_final: 0.8999 (pm20) REVERT: G 543 TYR cc_start: 0.8544 (m-80) cc_final: 0.8154 (m-80) REVERT: T 83 PHE cc_start: 0.8515 (m-10) cc_final: 0.8063 (m-10) REVERT: T 98 PHE cc_start: 0.8656 (m-80) cc_final: 0.8325 (m-10) REVERT: J 75 ARG cc_start: 0.8744 (mtm-85) cc_final: 0.8446 (ttp-110) REVERT: J 77 GLN cc_start: 0.8124 (mt0) cc_final: 0.6778 (mt0) REVERT: N 38 GLN cc_start: 0.8475 (tp40) cc_final: 0.8159 (tp40) REVERT: N 78 MET cc_start: 0.8837 (ppp) cc_final: 0.8557 (ppp) REVERT: N 98 PHE cc_start: 0.6549 (p90) cc_final: 0.6100 (p90) REVERT: F 69 ASN cc_start: 0.9106 (t0) cc_final: 0.8849 (t0) REVERT: F 117 ASP cc_start: 0.8897 (p0) cc_final: 0.8418 (p0) REVERT: F 251 GLN cc_start: 0.9482 (mp10) cc_final: 0.8901 (pm20) REVERT: Q 3 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8530 (mp10) REVERT: Q 12 MET cc_start: 0.8212 (ptm) cc_final: 0.7749 (tmm) REVERT: Q 33 TRP cc_start: 0.7904 (p90) cc_final: 0.7614 (p90) REVERT: Q 91 TYR cc_start: 0.8575 (m-80) cc_final: 0.8175 (m-80) REVERT: U 13 VAL cc_start: 0.9055 (m) cc_final: 0.8788 (p) REVERT: U 83 PHE cc_start: 0.8268 (m-10) cc_final: 0.7971 (m-10) REVERT: U 98 PHE cc_start: 0.8752 (m-80) cc_final: 0.8509 (m-10) REVERT: M 19 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8350 (mmmm) REVERT: M 75 ARG cc_start: 0.9143 (ttp-110) cc_final: 0.8864 (mtm110) REVERT: M 81 LYS cc_start: 0.9121 (tmtt) cc_final: 0.8827 (tptp) REVERT: O 17 ASP cc_start: 0.6931 (m-30) cc_final: 0.6461 (m-30) REVERT: O 78 MET cc_start: 0.8391 (ppp) cc_final: 0.8103 (ppp) REVERT: O 83 LEU cc_start: 0.8631 (mt) cc_final: 0.8094 (pt) REVERT: O 103 LYS cc_start: 0.8149 (mppt) cc_final: 0.7851 (mmtm) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.3119 time to fit residues: 209.5777 Evaluate side-chains 338 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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: 4.9990 chunk 197 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 189 optimal weight: 0.0370 chunk 198 optimal weight: 0.9980 chunk 209 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.7262 ------------------------------------------------------------------------------- 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 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100BASN D 90 GLN ** G 595 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 I 602 HIS Q 3 GLN M 100BASN ** 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: 0.7668 moved from start: 0.6335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19710 Z= 0.193 Angle : 0.716 12.091 26739 Z= 0.362 Chirality : 0.046 0.235 3039 Planarity : 0.004 0.065 3372 Dihedral : 7.255 57.487 3534 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.16 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -0.63 (0.17), residues: 2361 helix: 0.17 (0.37), residues: 180 sheet: -0.34 (0.18), residues: 777 loop : -0.47 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP L 35 HIS 0.004 0.001 HIS A 39 PHE 0.045 0.002 PHE P 27 TYR 0.022 0.002 TYR H 32 ARG 0.007 0.000 ARG C 75 *********************** 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 459 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 2.242 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: A 117 ASP cc_start: 0.8876 (p0) cc_final: 0.8493 (p0) REVERT: A 162 TYR cc_start: 0.8891 (m-10) cc_final: 0.8680 (m-10) REVERT: H 43 LYS cc_start: 0.9151 (mmtt) cc_final: 0.8889 (mttt) REVERT: H 48 VAL cc_start: 0.9275 (t) cc_final: 0.8879 (t) REVERT: C 20 LEU cc_start: 0.8699 (mt) cc_final: 0.8408 (mt) REVERT: C 64 LYS cc_start: 0.8829 (tttt) cc_final: 0.8576 (pttt) REVERT: C 82 ILE cc_start: 0.8550 (mp) cc_final: 0.8109 (mp) REVERT: D 1 ASP cc_start: 0.7876 (m-30) cc_final: 0.6885 (p0) REVERT: D 4 MET cc_start: 0.7668 (tpt) cc_final: 0.7446 (tpp) REVERT: D 18 ARG cc_start: 0.8483 (mmt-90) cc_final: 0.8238 (mmp80) REVERT: D 78 MET cc_start: 0.8564 (ppp) cc_final: 0.8296 (ppp) REVERT: D 91 TYR cc_start: 0.7711 (m-80) cc_final: 0.6255 (m-80) REVERT: D 103 LYS cc_start: 0.8481 (mppt) cc_final: 0.8149 (mmtm) REVERT: E 117 ASP cc_start: 0.9071 (p0) cc_final: 0.8453 (p0) REVERT: E 251 GLN cc_start: 0.9459 (mp10) cc_final: 0.8983 (pm20) REVERT: G 543 TYR cc_start: 0.8446 (m-80) cc_final: 0.8033 (m-80) REVERT: P 80 LEU cc_start: 0.9091 (tt) cc_final: 0.8744 (tt) REVERT: T 83 PHE cc_start: 0.8468 (m-10) cc_final: 0.8231 (m-10) REVERT: T 98 PHE cc_start: 0.8681 (m-80) cc_final: 0.8299 (m-10) REVERT: J 75 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8473 (ttp-110) REVERT: J 77 GLN cc_start: 0.8105 (mt0) cc_final: 0.6787 (mt0) REVERT: N 38 GLN cc_start: 0.8402 (tp40) cc_final: 0.7659 (tp40) REVERT: N 78 MET cc_start: 0.8834 (ppp) cc_final: 0.8575 (ppp) REVERT: N 98 PHE cc_start: 0.6766 (p90) cc_final: 0.6388 (p90) REVERT: N 105 GLU cc_start: 0.6590 (tt0) cc_final: 0.6379 (tt0) REVERT: F 69 ASN cc_start: 0.9120 (t0) cc_final: 0.8819 (t0) REVERT: F 117 ASP cc_start: 0.8936 (p0) cc_final: 0.8455 (p0) REVERT: F 232 TYR cc_start: 0.8657 (m-10) cc_final: 0.8448 (m-10) REVERT: F 251 GLN cc_start: 0.9473 (mp10) cc_final: 0.9094 (mm-40) REVERT: I 550 ASN cc_start: 0.8704 (t0) cc_final: 0.8293 (t0) REVERT: Q 50 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7105 (mm-30) REVERT: Q 91 TYR cc_start: 0.8564 (m-80) cc_final: 0.8181 (m-80) REVERT: U 13 VAL cc_start: 0.8980 (m) cc_final: 0.8758 (p) REVERT: U 83 PHE cc_start: 0.8346 (m-10) cc_final: 0.8048 (m-10) REVERT: U 98 PHE cc_start: 0.8714 (m-80) cc_final: 0.8464 (m-10) REVERT: M 19 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8367 (mmmm) REVERT: M 46 GLU cc_start: 0.8794 (tp30) cc_final: 0.8511 (tp30) REVERT: M 75 ARG cc_start: 0.9128 (ttp-110) cc_final: 0.8849 (mtm110) REVERT: M 81 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8821 (tptp) REVERT: O 18 ARG cc_start: 0.9242 (mmt90) cc_final: 0.8859 (mmp80) REVERT: O 78 MET cc_start: 0.8382 (ppp) cc_final: 0.7969 (ppp) REVERT: O 103 LYS cc_start: 0.8108 (mppt) cc_final: 0.7827 (mmtm) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.3003 time to fit residues: 209.0814 Evaluate side-chains 344 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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: 8.9990 chunk 135 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 73 ASN ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 39 HIS E 62 GLN E 221 GLN ** G 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 19710 Z= 0.429 Angle : 0.881 11.381 26739 Z= 0.450 Chirality : 0.049 0.304 3039 Planarity : 0.006 0.061 3372 Dihedral : 8.006 59.785 3534 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.34 % Favored : 91.32 % Rotamer: Outliers : 0.10 % Allowed : 0.25 % Favored : 99.65 % 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: -1.04 (0.17), residues: 2361 helix: 0.23 (0.38), residues: 174 sheet: -0.70 (0.18), residues: 816 loop : -0.75 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP L 35 HIS 0.008 0.002 HIS U 90 PHE 0.060 0.003 PHE P 27 TYR 0.035 0.003 TYR L 96 ARG 0.016 0.001 ARG J 94 ********************** 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 390 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 388 time to evaluate : 2.097 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: A 117 ASP cc_start: 0.9014 (p0) cc_final: 0.8576 (p0) REVERT: L 92 TRP cc_start: 0.6152 (p90) cc_final: 0.5827 (p90) REVERT: C 20 LEU cc_start: 0.8731 (mt) cc_final: 0.8522 (mt) REVERT: C 64 LYS cc_start: 0.8907 (tttt) cc_final: 0.8646 (tptp) REVERT: C 72 ASP cc_start: 0.7956 (t70) cc_final: 0.7509 (t0) REVERT: C 75 ARG cc_start: 0.8079 (pmt-80) cc_final: 0.6595 (pmt-80) REVERT: C 82 ILE cc_start: 0.8463 (mp) cc_final: 0.8042 (mp) REVERT: D 18 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.8291 (mmp80) REVERT: D 78 MET cc_start: 0.8634 (ppp) cc_final: 0.8352 (ppp) REVERT: D 103 LYS cc_start: 0.8329 (mppt) cc_final: 0.7937 (mmtm) REVERT: E 117 ASP cc_start: 0.9170 (p0) cc_final: 0.8506 (p0) REVERT: E 251 GLN cc_start: 0.9587 (mp10) cc_final: 0.9120 (pm20) REVERT: G 543 TYR cc_start: 0.8883 (m-80) cc_final: 0.8641 (m-80) REVERT: G 578 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8870 (mm-30) REVERT: P 55 TYR cc_start: 0.9253 (m-10) cc_final: 0.9046 (m-10) REVERT: P 80 LEU cc_start: 0.9270 (tt) cc_final: 0.8967 (tt) REVERT: T 35 TRP cc_start: 0.7805 (m100) cc_final: 0.7100 (m100) REVERT: J 77 GLN cc_start: 0.8128 (mt0) cc_final: 0.7635 (mt0) REVERT: J 86 ASP cc_start: 0.8128 (m-30) cc_final: 0.7738 (m-30) REVERT: N 38 GLN cc_start: 0.8401 (tp40) cc_final: 0.7512 (tp-100) REVERT: N 78 MET cc_start: 0.8894 (ppp) cc_final: 0.8611 (ppp) REVERT: N 98 PHE cc_start: 0.6565 (p90) cc_final: 0.6179 (p90) REVERT: F 117 ASP cc_start: 0.9051 (p0) cc_final: 0.8663 (p0) REVERT: F 251 GLN cc_start: 0.9535 (mp10) cc_final: 0.9025 (pm20) REVERT: Q 5 GLN cc_start: 0.8557 (tp40) cc_final: 0.7912 (tm-30) REVERT: U 83 PHE cc_start: 0.8440 (m-10) cc_final: 0.8133 (m-10) REVERT: U 96 TYR cc_start: 0.8944 (m-80) cc_final: 0.8672 (m-10) REVERT: M 46 GLU cc_start: 0.8876 (tp30) cc_final: 0.8500 (tp30) REVERT: M 81 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8777 (tptp) REVERT: O 18 ARG cc_start: 0.9238 (mmt90) cc_final: 0.8843 (mmp80) REVERT: O 78 MET cc_start: 0.8536 (ppp) cc_final: 0.8126 (ppp) REVERT: O 83 LEU cc_start: 0.8675 (mt) cc_final: 0.8207 (pt) REVERT: O 103 LYS cc_start: 0.8112 (mppt) cc_final: 0.7805 (mmtm) outliers start: 2 outliers final: 0 residues processed: 388 average time/residue: 0.3216 time to fit residues: 186.9778 Evaluate side-chains 290 residues out of total 2028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.197 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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** B 567 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 44 GLN G 516 HIS ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN F 73 ASN O 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050323 restraints weight = 105512.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051716 restraints weight = 62332.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.052631 restraints weight = 43474.496| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 19710 Z= 0.281 Angle : 0.782 11.859 26739 Z= 0.400 Chirality : 0.047 0.250 3039 Planarity : 0.005 0.073 3372 Dihedral : 7.783 57.903 3534 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.26 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -1.03 (0.17), residues: 2361 helix: 0.17 (0.38), residues: 180 sheet: -0.59 (0.18), residues: 774 loop : -0.80 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP L 35 HIS 0.005 0.001 HIS U 90 PHE 0.045 0.002 PHE Q 27 TYR 0.025 0.002 TYR P 91 ARG 0.016 0.001 ARG P 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4534.57 seconds wall clock time: 82 minutes 36.96 seconds (4956.96 seconds total)