Starting phenix.real_space_refine on Sun Sep 29 15:23:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjq_0236/09_2024/6hjq_0236.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjq_0236/09_2024/6hjq_0236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjq_0236/09_2024/6hjq_0236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjq_0236/09_2024/6hjq_0236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjq_0236/09_2024/6hjq_0236.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjq_0236/09_2024/6hjq_0236.cif" } resolution = 4.1 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= 0.003 sd= 0.175 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 90 5.16 5 C 14118 2.51 5 N 3780 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22530 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1569 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "H" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "J" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1569 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1569 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 1, 'TRANS': 201} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" 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 Time building chain proxies: 15.05, per 1000 atoms: 0.67 Number of scatterers: 22530 At special positions: 0 Unit cell: (171.402, 176.792, 196.196, 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 90 16.00 O 4542 8.00 N 3780 7.00 C 14118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.02 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 137 " distance=2.01 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.02 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " FUC N 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG W 1 " - " FUC W 3 " NAG-ASN " NAG M 1 " - " ASN A 15 " " NAG N 1 " - " ASN A 27 " " NAG O 1 " - " ASN A 91 " " NAG P 1 " - " ASN A 290 " " NAG Q 1 " - " ASN B 154 " " NAG R 1 " - " ASN C 15 " " NAG S 1 " - " ASN C 27 " " NAG T 1 " - " ASN C 91 " " NAG U 1 " - " ASN C 290 " " NAG V 1 " - " ASN E 15 " " NAG W 1 " - " ASN E 27 " " NAG X 1 " - " ASN E 91 " " NAG Y 1 " - " ASN E 290 " " NAG Z 1 " - " ASN D 154 " " NAG a 1 " - " ASN F 154 " Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 3.0 seconds 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5280 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 66 sheets defined 19.4% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 101 through 110 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 39 through 59 removed outlier: 4.025A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 125 removed outlier: 4.597A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.868A pdb=" N ASP B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.572A pdb=" N TYR B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.977A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.507A pdb=" N ASP G 90 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 91' Processing helix chain 'G' and resid 188 through 192 removed outlier: 4.147A pdb=" N LEU G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 129 removed outlier: 3.725A pdb=" N LEU H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 4.001A pdb=" N TYR H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.977A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.508A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'I' and resid 188 through 192 removed outlier: 4.146A pdb=" N LEU I 192 " --> pdb=" O SER I 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.976A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.742A pdb=" N LYS K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.507A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR K 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing helix chain 'K' and resid 188 through 192 removed outlier: 4.146A pdb=" N LEU K 192 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 removed outlier: 3.725A pdb=" N LEU J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 4.001A pdb=" N TYR J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.725A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 4.000A pdb=" N TYR L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 101 through 110 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'D' and resid 39 through 59 removed outlier: 4.024A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 125 removed outlier: 4.597A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.869A pdb=" N ASP D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 186 through 202 removed outlier: 3.572A pdb=" N TYR D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 59 removed outlier: 4.025A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 125 removed outlier: 4.597A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.868A pdb=" N ASP F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 181 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.572A pdb=" N TYR F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 removed outlier: 3.532A pdb=" N GLY A 10 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 23 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.405A pdb=" N LEU A 46 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS A 278 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.790A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU A 98 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP A 234 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU A 98 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP A 234 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 4.952A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.781A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.781A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 153 through 157 Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.569A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.687A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR H 53 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER H 132 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU H 182 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL H 134 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU H 180 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU H 136 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER H 178 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN H 138 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU H 176 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 145 through 151 Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 153 through 157 Processing sheet with id=AD2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.782A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE K 111 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.067A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 153 through 157 Processing sheet with id=AD8, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.569A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.687A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.311A pdb=" N SER J 132 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU J 182 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL J 134 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU J 180 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU J 136 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER J 178 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN J 138 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU J 176 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 145 through 151 Processing sheet with id=AE3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.569A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.688A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 145 through 151 Processing sheet with id=AE7, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.515A pdb=" N GLY C 10 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 23 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AE9, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AF1, first strand: chain 'C' and resid 46 through 49 removed outlier: 5.405A pdb=" N LEU C 46 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS C 278 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.789A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU C 98 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP C 234 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE C 258 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU C 98 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP C 234 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AF6, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.952A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 164 through 168 Processing sheet with id=AF8, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AF9, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AG1, first strand: chain 'E' and resid 7 through 11 removed outlier: 3.531A pdb=" N GLY E 10 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY F 23 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AG3, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AG4, first strand: chain 'E' and resid 46 through 49 removed outlier: 5.405A pdb=" N LEU E 46 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N CYS E 278 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 54 through 57 removed outlier: 6.790A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU E 98 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP E 234 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.000A pdb=" N GLU E 98 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N TRP E 234 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AG9, first strand: chain 'E' and resid 136 through 141 removed outlier: 4.952A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 164 through 168 Processing sheet with id=AH2, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AH3, first strand: chain 'E' and resid 295 through 296 939 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.78 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7128 1.34 - 1.46: 5661 1.46 - 1.58: 10116 1.58 - 1.70: 3 1.70 - 1.83: 120 Bond restraints: 23028 Sorted by residual: bond pdb=" C1 MAN T 4 " pdb=" C2 MAN T 4 " ideal model delta sigma weight residual 1.526 1.635 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C1 MAN O 4 " pdb=" C2 MAN O 4 " ideal model delta sigma weight residual 1.526 1.634 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C1 MAN T 4 " pdb=" O5 MAN T 4 " ideal model delta sigma weight residual 1.399 1.498 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.498 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 23023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30202 2.28 - 4.56: 910 4.56 - 6.84: 146 6.84 - 9.11: 35 9.11 - 11.39: 9 Bond angle restraints: 31302 Sorted by residual: angle pdb=" C GLY D 134 " pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C GLY B 134 " pdb=" N ASN B 135 " pdb=" CA ASN B 135 " ideal model delta sigma weight residual 121.54 130.94 -9.40 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C GLY F 134 " pdb=" N ASN F 135 " pdb=" CA ASN F 135 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" N GLY A 249 " pdb=" CA GLY A 249 " pdb=" C GLY A 249 " ideal model delta sigma weight residual 113.18 124.57 -11.39 2.37e+00 1.78e-01 2.31e+01 angle pdb=" N GLY C 249 " pdb=" CA GLY C 249 " pdb=" C GLY C 249 " ideal model delta sigma weight residual 113.18 124.56 -11.38 2.37e+00 1.78e-01 2.30e+01 ... (remaining 31297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.77: 13600 20.77 - 41.53: 480 41.53 - 62.30: 68 62.30 - 83.07: 42 83.07 - 103.83: 33 Dihedral angle restraints: 14223 sinusoidal: 5958 harmonic: 8265 Sorted by residual: dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.60 -50.60 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 143.58 -50.58 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 14220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3138 0.088 - 0.177: 414 0.177 - 0.265: 30 0.265 - 0.353: 9 0.353 - 0.442: 3 Chirality restraints: 3594 Sorted by residual: chirality pdb=" C3 BMA T 3 " pdb=" C2 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" O3 BMA T 3 " both_signs ideal model delta sigma weight residual False 2.41 1.97 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" C3 BMA O 3 " pdb=" C2 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" O3 BMA O 3 " both_signs ideal model delta sigma weight residual False 2.41 1.97 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C3 BMA X 3 " pdb=" C2 BMA X 3 " pdb=" C4 BMA X 3 " pdb=" O3 BMA X 3 " both_signs ideal model delta sigma weight residual False 2.41 1.97 0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 3591 not shown) Planarity restraints: 4011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.130 2.00e-02 2.50e+03 1.14e-01 1.64e+02 pdb=" C7 NAG S 2 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " -0.130 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG N 2 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " -0.130 2.00e-02 2.50e+03 1.14e-01 1.63e+02 pdb=" C7 NAG W 2 " -0.018 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " 0.203 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.024 2.00e-02 2.50e+03 ... (remaining 4008 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.10: 3 2.10 - 2.80: 5961 2.80 - 3.50: 28694 3.50 - 4.20: 50702 4.20 - 4.90: 86582 Nonbonded interactions: 171942 Sorted by model distance: nonbonded pdb=" CG2 THR E 6 " pdb=" O PHE F 138 " model vdw 1.406 3.460 nonbonded pdb=" CG2 THR C 6 " pdb=" O PHE D 138 " model vdw 1.411 3.460 nonbonded pdb=" CG2 THR A 6 " pdb=" O PHE B 138 " model vdw 1.439 3.460 nonbonded pdb=" OG SER F 151 " pdb=" O THR F 156 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 151 " pdb=" O THR B 156 " model vdw 2.203 3.040 ... (remaining 171937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = (chain 'N' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'X' } 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: 10.960 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: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 53.550 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.006 0.109 23028 Z= 0.377 Angle : 0.940 11.392 31302 Z= 0.488 Chirality : 0.059 0.442 3594 Planarity : 0.007 0.114 3996 Dihedral : 12.717 103.832 8853 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 0.13 % Allowed : 4.77 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.13), residues: 2847 helix: -2.12 (0.17), residues: 477 sheet: -1.30 (0.16), residues: 897 loop : -2.50 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 255 HIS 0.009 0.002 HIS D 111 PHE 0.022 0.003 PHE F 9 TYR 0.026 0.003 TYR E 102 ARG 0.003 0.001 ARG E 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 2.478 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: G 34 MET cc_start: 0.9015 (mmm) cc_final: 0.8682 (mmt) REVERT: G 46 GLU cc_start: 0.8308 (tt0) cc_final: 0.8106 (tt0) REVERT: G 76 LYS cc_start: 0.9606 (mttt) cc_final: 0.9376 (mttm) REVERT: H 4 MET cc_start: 0.8625 (mmm) cc_final: 0.8210 (mmm) REVERT: H 136 LEU cc_start: 0.8253 (tp) cc_final: 0.8013 (tt) REVERT: H 146 LYS cc_start: 0.8189 (mmtp) cc_final: 0.7882 (tptt) REVERT: H 193 TYR cc_start: 0.7756 (m-10) cc_final: 0.7369 (m-80) REVERT: H 211 ASN cc_start: 0.6687 (m-40) cc_final: 0.6244 (p0) REVERT: I 3 GLN cc_start: 0.8166 (pm20) cc_final: 0.7011 (pm20) REVERT: I 34 MET cc_start: 0.9256 (mmm) cc_final: 0.8868 (mmt) REVERT: I 99 MET cc_start: 0.8975 (mmt) cc_final: 0.8772 (mmm) REVERT: I 198 ILE cc_start: 0.9026 (mt) cc_final: 0.8826 (pt) REVERT: I 213 ARG cc_start: 0.7606 (ttt180) cc_final: 0.6701 (tpt170) REVERT: I 215 GLU cc_start: 0.5589 (pt0) cc_final: 0.5015 (mm-30) REVERT: K 1 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8494 (tm-30) REVERT: K 3 GLN cc_start: 0.8109 (pm20) cc_final: 0.7161 (pm20) REVERT: K 34 MET cc_start: 0.9184 (mmm) cc_final: 0.8866 (mmt) REVERT: K 99 MET cc_start: 0.8919 (mmt) cc_final: 0.8564 (mmm) REVERT: K 198 ILE cc_start: 0.9122 (mt) cc_final: 0.8917 (pt) REVERT: K 213 ARG cc_start: 0.7828 (ttt180) cc_final: 0.6690 (tpt170) REVERT: K 215 GLU cc_start: 0.6477 (pt0) cc_final: 0.5982 (mm-30) REVERT: J 146 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8124 (tmmt) REVERT: L 4 MET cc_start: 0.8819 (mmm) cc_final: 0.8571 (mmm) REVERT: L 136 LEU cc_start: 0.8929 (tp) cc_final: 0.8677 (tt) REVERT: L 193 TYR cc_start: 0.7710 (m-10) cc_final: 0.7091 (m-80) REVERT: D 149 MET cc_start: 0.9013 (mmt) cc_final: 0.8708 (mmm) REVERT: F 149 MET cc_start: 0.9070 (mmt) cc_final: 0.8691 (mmm) outliers start: 3 outliers final: 3 residues processed: 238 average time/residue: 0.5118 time to fit residues: 167.2946 Evaluate side-chains 93 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.0270 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 ASN G 207 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 167 GLN H 190 HIS I 77 ASN I 158 ASN K 77 ASN K 158 ASN K 207 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN J 167 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 161 GLN L 167 GLN L 190 HIS C 108 GLN C 250 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 250 ASN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23028 Z= 0.221 Angle : 0.680 11.455 31302 Z= 0.352 Chirality : 0.046 0.325 3594 Planarity : 0.004 0.054 3996 Dihedral : 10.763 78.772 3936 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.15), residues: 2847 helix: 0.15 (0.22), residues: 471 sheet: -0.89 (0.16), residues: 945 loop : -1.92 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 153 HIS 0.004 0.001 HIS E 276 PHE 0.013 0.001 PHE C 99 TYR 0.013 0.001 TYR H 91 ARG 0.005 0.001 ARG D 127 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.381 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: G 34 MET cc_start: 0.8839 (mmm) cc_final: 0.8626 (tpp) REVERT: H 4 MET cc_start: 0.8533 (mmm) cc_final: 0.8096 (mmm) REVERT: H 146 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7905 (ttpp) REVERT: H 193 TYR cc_start: 0.7951 (m-10) cc_final: 0.7537 (m-80) REVERT: H 211 ASN cc_start: 0.6452 (m-40) cc_final: 0.6157 (p0) REVERT: I 34 MET cc_start: 0.9112 (mmm) cc_final: 0.8765 (mmt) REVERT: I 215 GLU cc_start: 0.5737 (pt0) cc_final: 0.5107 (mm-30) REVERT: K 1 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8576 (tm-30) REVERT: K 34 MET cc_start: 0.9126 (mmm) cc_final: 0.8383 (mmt) REVERT: K 99 MET cc_start: 0.9007 (mmt) cc_final: 0.8515 (mmm) REVERT: K 215 GLU cc_start: 0.6552 (pt0) cc_final: 0.5992 (mm-30) REVERT: J 4 MET cc_start: 0.8169 (mmm) cc_final: 0.7842 (mmm) REVERT: J 146 LYS cc_start: 0.8636 (mmtp) cc_final: 0.8274 (tmmt) REVERT: L 4 MET cc_start: 0.8782 (mmm) cc_final: 0.8509 (mmm) REVERT: L 193 TYR cc_start: 0.7789 (m-10) cc_final: 0.7491 (m-80) REVERT: D 149 MET cc_start: 0.8964 (mmt) cc_final: 0.8629 (mmm) REVERT: F 59 MET cc_start: 0.8994 (mmm) cc_final: 0.8757 (mmm) REVERT: F 149 MET cc_start: 0.9039 (mmt) cc_final: 0.8665 (mmm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.4593 time to fit residues: 90.9395 Evaluate side-chains 78 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 256 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 205 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN G 109 ASN H 6 GLN H 37 GLN I 77 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 37 GLN J 190 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN F 169 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23028 Z= 0.234 Angle : 0.625 9.709 31302 Z= 0.322 Chirality : 0.044 0.189 3594 Planarity : 0.004 0.049 3996 Dihedral : 9.345 67.877 3936 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.15), residues: 2847 helix: 1.17 (0.24), residues: 474 sheet: -0.66 (0.16), residues: 972 loop : -1.71 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 153 HIS 0.006 0.001 HIS J 190 PHE 0.013 0.001 PHE E 213 TYR 0.018 0.002 TYR A 95 ARG 0.005 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.429 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: B 17 MET cc_start: 0.9033 (ttt) cc_final: 0.8802 (ttt) REVERT: G 34 MET cc_start: 0.9061 (mmm) cc_final: 0.8653 (mmt) REVERT: G 99 MET cc_start: 0.9069 (mmm) cc_final: 0.8721 (mmm) REVERT: H 4 MET cc_start: 0.8513 (mmm) cc_final: 0.8106 (mmm) REVERT: H 193 TYR cc_start: 0.7887 (m-10) cc_final: 0.7417 (m-80) REVERT: H 211 ASN cc_start: 0.6536 (m-40) cc_final: 0.6288 (p0) REVERT: I 34 MET cc_start: 0.9163 (mmm) cc_final: 0.8806 (mmt) REVERT: I 215 GLU cc_start: 0.5444 (pt0) cc_final: 0.4830 (mm-30) REVERT: K 1 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8487 (tm-30) REVERT: K 3 GLN cc_start: 0.8182 (pm20) cc_final: 0.7012 (pm20) REVERT: K 34 MET cc_start: 0.9200 (mmm) cc_final: 0.8441 (mmt) REVERT: K 46 GLU cc_start: 0.8202 (tt0) cc_final: 0.7710 (tt0) REVERT: K 77 ASN cc_start: 0.9328 (m-40) cc_final: 0.8882 (t0) REVERT: K 211 ASP cc_start: 0.7713 (m-30) cc_final: 0.7483 (t0) REVERT: K 215 GLU cc_start: 0.6329 (pt0) cc_final: 0.5704 (mm-30) REVERT: J 4 MET cc_start: 0.8339 (mmm) cc_final: 0.8041 (mmm) REVERT: J 150 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8689 (mmmm) REVERT: L 4 MET cc_start: 0.8767 (mmm) cc_final: 0.8389 (mmm) REVERT: L 193 TYR cc_start: 0.7505 (m-10) cc_final: 0.7009 (m-80) REVERT: E 230 MET cc_start: 0.8817 (mtp) cc_final: 0.8542 (mtm) REVERT: D 149 MET cc_start: 0.8940 (mmt) cc_final: 0.8664 (mmm) REVERT: F 59 MET cc_start: 0.9065 (mmm) cc_final: 0.8844 (mmm) REVERT: F 149 MET cc_start: 0.9025 (mmt) cc_final: 0.8650 (mmm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.4697 time to fit residues: 73.0671 Evaluate side-chains 74 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 172 optimal weight: 30.0000 chunk 257 optimal weight: 5.9990 chunk 272 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 150 ASN ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 77 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN J 37 GLN L 6 GLN L 37 GLN L 161 GLN C 32 HIS C 150 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 HIS E 150 ASN ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23028 Z= 0.353 Angle : 0.689 9.738 31302 Z= 0.353 Chirality : 0.045 0.193 3594 Planarity : 0.004 0.049 3996 Dihedral : 8.874 59.762 3936 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2847 helix: 1.39 (0.24), residues: 474 sheet: -0.51 (0.16), residues: 963 loop : -1.62 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 153 HIS 0.007 0.002 HIS E 276 PHE 0.015 0.002 PHE B 140 TYR 0.020 0.002 TYR F 157 ARG 0.012 0.001 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.599 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: G 46 GLU cc_start: 0.8445 (tt0) cc_final: 0.7892 (tt0) REVERT: G 99 MET cc_start: 0.9157 (mmm) cc_final: 0.8610 (mmm) REVERT: H 4 MET cc_start: 0.8505 (mmm) cc_final: 0.8072 (mmm) REVERT: H 193 TYR cc_start: 0.7354 (m-10) cc_final: 0.6822 (m-80) REVERT: I 3 GLN cc_start: 0.7992 (pm20) cc_final: 0.7740 (pm20) REVERT: I 34 MET cc_start: 0.9263 (mmm) cc_final: 0.8808 (mmt) REVERT: I 77 ASN cc_start: 0.9361 (m-40) cc_final: 0.8894 (t0) REVERT: I 99 MET cc_start: 0.8974 (mmm) cc_final: 0.8773 (mmm) REVERT: I 215 GLU cc_start: 0.5554 (pt0) cc_final: 0.4790 (mm-30) REVERT: K 34 MET cc_start: 0.9360 (mmm) cc_final: 0.8987 (mmt) REVERT: K 46 GLU cc_start: 0.8208 (tt0) cc_final: 0.7787 (tt0) REVERT: K 211 ASP cc_start: 0.7507 (m-30) cc_final: 0.7212 (t0) REVERT: J 4 MET cc_start: 0.8439 (mmm) cc_final: 0.7980 (mmm) REVERT: J 150 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8643 (mmmm) REVERT: L 4 MET cc_start: 0.8740 (mmm) cc_final: 0.8081 (mmm) REVERT: L 24 ARG cc_start: 0.8187 (mtp-110) cc_final: 0.7787 (ttm-80) REVERT: C 317 MET cc_start: 0.8803 (ttt) cc_final: 0.8538 (ttm) REVERT: E 230 MET cc_start: 0.8919 (mtp) cc_final: 0.8695 (mtm) REVERT: D 59 MET cc_start: 0.8935 (mmm) cc_final: 0.8657 (mmt) REVERT: D 149 MET cc_start: 0.8892 (mmt) cc_final: 0.8651 (mmm) REVERT: F 59 MET cc_start: 0.9105 (mmm) cc_final: 0.8871 (mmm) REVERT: F 149 MET cc_start: 0.9006 (mmt) cc_final: 0.8656 (mmm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.4836 time to fit residues: 70.7419 Evaluate side-chains 67 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 23028 Z= 0.301 Angle : 0.638 9.287 31302 Z= 0.328 Chirality : 0.044 0.183 3594 Planarity : 0.004 0.046 3996 Dihedral : 8.386 58.810 3936 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.16), residues: 2847 helix: 1.79 (0.25), residues: 474 sheet: -0.38 (0.17), residues: 960 loop : -1.53 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 153 HIS 0.006 0.001 HIS H 190 PHE 0.012 0.001 PHE B 140 TYR 0.022 0.002 TYR F 159 ARG 0.009 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.459 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: G 99 MET cc_start: 0.9135 (mmm) cc_final: 0.8658 (mmm) REVERT: H 146 LYS cc_start: 0.7864 (mppt) cc_final: 0.7044 (tmmt) REVERT: H 193 TYR cc_start: 0.7309 (m-10) cc_final: 0.6627 (m-80) REVERT: I 3 GLN cc_start: 0.8033 (pm20) cc_final: 0.7746 (pm20) REVERT: I 34 MET cc_start: 0.9333 (mmm) cc_final: 0.8913 (mmt) REVERT: I 77 ASN cc_start: 0.9361 (m-40) cc_final: 0.8916 (t0) REVERT: K 34 MET cc_start: 0.9395 (mmm) cc_final: 0.8982 (mmt) REVERT: K 46 GLU cc_start: 0.8240 (tt0) cc_final: 0.7743 (tt0) REVERT: K 211 ASP cc_start: 0.7333 (m-30) cc_final: 0.6951 (t0) REVERT: J 4 MET cc_start: 0.8462 (mmm) cc_final: 0.8005 (mmm) REVERT: J 150 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8606 (mmmm) REVERT: L 4 MET cc_start: 0.8688 (mmm) cc_final: 0.8104 (mmm) REVERT: L 24 ARG cc_start: 0.8191 (mtp-110) cc_final: 0.7882 (ttm-80) REVERT: L 123 ASP cc_start: 0.8835 (p0) cc_final: 0.8584 (p0) REVERT: E 230 MET cc_start: 0.8925 (mtp) cc_final: 0.8695 (mtm) REVERT: F 59 MET cc_start: 0.9016 (mmm) cc_final: 0.8800 (mmm) REVERT: F 149 MET cc_start: 0.9002 (mmt) cc_final: 0.8756 (mmm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4293 time to fit residues: 58.9771 Evaluate side-chains 66 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 272 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN L 156 GLN C 130 HIS ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23028 Z= 0.235 Angle : 0.603 9.069 31302 Z= 0.308 Chirality : 0.044 0.184 3594 Planarity : 0.004 0.046 3996 Dihedral : 7.881 57.591 3936 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2847 helix: 2.06 (0.25), residues: 474 sheet: -0.19 (0.17), residues: 942 loop : -1.48 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 153 HIS 0.005 0.001 HIS E 276 PHE 0.010 0.001 PHE I 95 TYR 0.011 0.001 TYR H 193 ARG 0.007 0.001 ARG K 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 99 MET cc_start: 0.9088 (mmm) cc_final: 0.8625 (mmm) REVERT: H 146 LYS cc_start: 0.7828 (mppt) cc_final: 0.7063 (tmmt) REVERT: H 193 TYR cc_start: 0.7105 (m-10) cc_final: 0.6497 (m-80) REVERT: I 3 GLN cc_start: 0.8038 (pm20) cc_final: 0.7750 (pm20) REVERT: I 34 MET cc_start: 0.9325 (mmm) cc_final: 0.8982 (mmt) REVERT: I 77 ASN cc_start: 0.9327 (m-40) cc_final: 0.8940 (t0) REVERT: K 34 MET cc_start: 0.9372 (mmm) cc_final: 0.8897 (mmt) REVERT: K 46 GLU cc_start: 0.8251 (tt0) cc_final: 0.7716 (tt0) REVERT: K 77 ASN cc_start: 0.9328 (m-40) cc_final: 0.9000 (t0) REVERT: K 211 ASP cc_start: 0.7022 (m-30) cc_final: 0.6611 (t0) REVERT: J 4 MET cc_start: 0.8486 (mmm) cc_final: 0.8110 (mmm) REVERT: J 150 LYS cc_start: 0.9087 (ptpp) cc_final: 0.8621 (mmmm) REVERT: L 4 MET cc_start: 0.8669 (mmm) cc_final: 0.8280 (tpp) REVERT: E 230 MET cc_start: 0.8893 (mtp) cc_final: 0.8689 (mtm) REVERT: F 149 MET cc_start: 0.8952 (mmt) cc_final: 0.8728 (mmm) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4186 time to fit residues: 57.1270 Evaluate side-chains 63 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 10.0000 chunk 30 optimal weight: 0.0970 chunk 155 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 271 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN L 167 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23028 Z= 0.244 Angle : 0.603 9.489 31302 Z= 0.307 Chirality : 0.044 0.188 3594 Planarity : 0.004 0.045 3996 Dihedral : 7.553 57.296 3936 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2847 helix: 2.09 (0.25), residues: 492 sheet: -0.08 (0.17), residues: 939 loop : -1.49 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 153 HIS 0.005 0.001 HIS A 276 PHE 0.010 0.001 PHE K 95 TYR 0.012 0.001 TYR H 193 ARG 0.006 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.534 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: H 4 MET cc_start: 0.8456 (mmm) cc_final: 0.8094 (mmm) REVERT: H 146 LYS cc_start: 0.7830 (mppt) cc_final: 0.7049 (tmmt) REVERT: H 193 TYR cc_start: 0.6866 (m-10) cc_final: 0.6197 (m-80) REVERT: H 195 CYS cc_start: 0.4098 (p) cc_final: 0.3489 (p) REVERT: I 34 MET cc_start: 0.9358 (mmm) cc_final: 0.9017 (mmt) REVERT: I 77 ASN cc_start: 0.9318 (m-40) cc_final: 0.8956 (t0) REVERT: K 1 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8702 (tm-30) REVERT: K 3 GLN cc_start: 0.8012 (pm20) cc_final: 0.7025 (pm20) REVERT: K 34 MET cc_start: 0.9333 (mmm) cc_final: 0.8878 (mmt) REVERT: K 46 GLU cc_start: 0.8272 (tt0) cc_final: 0.7793 (tt0) REVERT: K 77 ASN cc_start: 0.9335 (m-40) cc_final: 0.9006 (t0) REVERT: K 211 ASP cc_start: 0.7088 (m-30) cc_final: 0.6652 (t0) REVERT: J 4 MET cc_start: 0.8526 (mmm) cc_final: 0.8187 (mmm) REVERT: J 150 LYS cc_start: 0.9083 (ptpp) cc_final: 0.8598 (mmmm) REVERT: L 4 MET cc_start: 0.8659 (mmm) cc_final: 0.8097 (mmm) REVERT: E 230 MET cc_start: 0.8895 (mtp) cc_final: 0.8685 (mtm) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4085 time to fit residues: 57.3243 Evaluate side-chains 67 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 213 optimal weight: 8.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 156 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23028 Z= 0.396 Angle : 0.700 12.204 31302 Z= 0.356 Chirality : 0.045 0.203 3594 Planarity : 0.004 0.045 3996 Dihedral : 7.684 58.778 3936 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2847 helix: 1.87 (0.24), residues: 474 sheet: -0.21 (0.17), residues: 933 loop : -1.49 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 153 HIS 0.006 0.002 HIS E 276 PHE 0.015 0.002 PHE B 3 TYR 0.016 0.002 TYR H 86 ARG 0.008 0.001 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.564 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: I 34 MET cc_start: 0.9382 (mmm) cc_final: 0.9053 (mmt) REVERT: I 77 ASN cc_start: 0.9239 (m-40) cc_final: 0.8912 (t0) REVERT: I 99 MET cc_start: 0.9181 (mmm) cc_final: 0.8884 (mmm) REVERT: K 1 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8789 (tm-30) REVERT: K 34 MET cc_start: 0.9360 (mmm) cc_final: 0.8968 (mmt) REVERT: K 77 ASN cc_start: 0.9323 (m-40) cc_final: 0.9017 (t0) REVERT: K 211 ASP cc_start: 0.7176 (m-30) cc_final: 0.6695 (t0) REVERT: J 4 MET cc_start: 0.8553 (mmm) cc_final: 0.8073 (mmm) REVERT: L 4 MET cc_start: 0.8660 (mmm) cc_final: 0.7924 (mmm) REVERT: E 230 MET cc_start: 0.8946 (mtp) cc_final: 0.8716 (mtm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4141 time to fit residues: 52.9297 Evaluate side-chains 65 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 198 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23028 Z= 0.183 Angle : 0.604 11.510 31302 Z= 0.306 Chirality : 0.044 0.174 3594 Planarity : 0.004 0.043 3996 Dihedral : 7.268 57.491 3936 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2847 helix: 2.26 (0.25), residues: 477 sheet: -0.08 (0.17), residues: 936 loop : -1.34 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 127 HIS 0.005 0.001 HIS D 26 PHE 0.011 0.001 PHE B 9 TYR 0.037 0.001 TYR E 161 ARG 0.007 0.001 ARG L 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.478 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: H 4 MET cc_start: 0.8397 (mmm) cc_final: 0.8043 (mmm) REVERT: H 146 LYS cc_start: 0.7894 (mppt) cc_final: 0.7324 (tppt) REVERT: I 34 MET cc_start: 0.9365 (mmm) cc_final: 0.9036 (mmt) REVERT: I 77 ASN cc_start: 0.9195 (m-40) cc_final: 0.8917 (t0) REVERT: I 99 MET cc_start: 0.9100 (mmm) cc_final: 0.8893 (mmm) REVERT: K 1 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8773 (tm-30) REVERT: K 34 MET cc_start: 0.9334 (mmm) cc_final: 0.8965 (mmt) REVERT: K 46 GLU cc_start: 0.8229 (tt0) cc_final: 0.7792 (tt0) REVERT: K 77 ASN cc_start: 0.9314 (m-40) cc_final: 0.9026 (t0) REVERT: K 211 ASP cc_start: 0.7155 (m-30) cc_final: 0.6669 (t0) REVERT: J 4 MET cc_start: 0.8514 (mmm) cc_final: 0.8228 (mmm) REVERT: J 150 LYS cc_start: 0.9070 (ptpp) cc_final: 0.8471 (mmtp) REVERT: F 98 LEU cc_start: 0.9427 (tp) cc_final: 0.9214 (tp) REVERT: F 149 MET cc_start: 0.9045 (mmt) cc_final: 0.8770 (mmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4110 time to fit residues: 56.3295 Evaluate side-chains 68 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 3.9990 chunk 267 optimal weight: 0.5980 chunk 163 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 258 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 37 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23028 Z= 0.330 Angle : 0.658 10.214 31302 Z= 0.333 Chirality : 0.044 0.176 3594 Planarity : 0.004 0.045 3996 Dihedral : 7.331 57.738 3936 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2847 helix: 2.07 (0.25), residues: 477 sheet: -0.15 (0.17), residues: 942 loop : -1.38 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 153 HIS 0.006 0.001 HIS E 276 PHE 0.012 0.001 PHE B 3 TYR 0.029 0.002 TYR E 161 ARG 0.007 0.001 ARG E 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.790 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: H 4 MET cc_start: 0.8453 (mmm) cc_final: 0.8063 (mmm) REVERT: H 146 LYS cc_start: 0.7967 (mppt) cc_final: 0.7387 (tppt) REVERT: I 34 MET cc_start: 0.9387 (mmm) cc_final: 0.9048 (mmt) REVERT: I 77 ASN cc_start: 0.9213 (m-40) cc_final: 0.8899 (t0) REVERT: K 1 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8773 (tm-30) REVERT: K 34 MET cc_start: 0.9333 (mmm) cc_final: 0.8940 (mmt) REVERT: K 77 ASN cc_start: 0.9302 (m-40) cc_final: 0.8983 (t0) REVERT: K 211 ASP cc_start: 0.7145 (m-30) cc_final: 0.6697 (t0) REVERT: J 4 MET cc_start: 0.8493 (mmm) cc_final: 0.8016 (mmm) REVERT: J 150 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8551 (mmtp) REVERT: L 4 MET cc_start: 0.8624 (mmm) cc_final: 0.8053 (mmm) REVERT: F 98 LEU cc_start: 0.9478 (tp) cc_final: 0.9260 (tp) REVERT: F 149 MET cc_start: 0.9061 (mmt) cc_final: 0.8787 (mmm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3979 time to fit residues: 52.0368 Evaluate side-chains 66 residues out of total 2451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 37 GLN H 167 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN L 32 ASN L 37 GLN ** C 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.030246 restraints weight = 154845.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.031141 restraints weight = 88197.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.031722 restraints weight = 61586.672| |-----------------------------------------------------------------------------| r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23028 Z= 0.168 Angle : 0.595 9.929 31302 Z= 0.300 Chirality : 0.043 0.164 3594 Planarity : 0.004 0.042 3996 Dihedral : 6.930 56.501 3936 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2847 helix: 2.42 (0.25), residues: 477 sheet: 0.02 (0.17), residues: 939 loop : -1.25 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 149 HIS 0.008 0.001 HIS D 26 PHE 0.011 0.001 PHE B 9 TYR 0.023 0.001 TYR A 161 ARG 0.008 0.000 ARG H 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3489.23 seconds wall clock time: 65 minutes 20.73 seconds (3920.73 seconds total)