Starting phenix.real_space_refine on Mon Mar 18 07:58:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5p_27917/03_2024/8e5p_27917_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5p_27917/03_2024/8e5p_27917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5p_27917/03_2024/8e5p_27917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5p_27917/03_2024/8e5p_27917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5p_27917/03_2024/8e5p_27917_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5p_27917/03_2024/8e5p_27917_neut_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12524 2.51 5 N 3538 2.21 5 O 3824 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "e ARG 30": "NH1" <-> "NH2" Residue "e PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "e TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 211": "OE1" <-> "OE2" Residue "e GLU 214": "OE1" <-> "OE2" Residue "e GLU 218": "OE1" <-> "OE2" Residue "e GLU 226": "OE1" <-> "OE2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "e PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 334": "OE1" <-> "OE2" Residue "e ARG 347": "NH1" <-> "NH2" Residue "e PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 366": "NH1" <-> "NH2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "f ARG 30": "NH1" <-> "NH2" Residue "f PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 128": "NH1" <-> "NH2" Residue "f TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 211": "OE1" <-> "OE2" Residue "f GLU 214": "OE1" <-> "OE2" Residue "f GLU 218": "OE1" <-> "OE2" Residue "f GLU 226": "OE1" <-> "OE2" Residue "f ARG 299": "NH1" <-> "NH2" Residue "f PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 333": "OE1" <-> "OE2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 366": "NH1" <-> "NH2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "c ARG 30": "NH1" <-> "NH2" Residue "c PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 92": "NH1" <-> "NH2" Residue "c TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 128": "NH1" <-> "NH2" Residue "c TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c GLU 214": "OE1" <-> "OE2" Residue "c GLU 218": "OE1" <-> "OE2" Residue "c GLU 226": "OE1" <-> "OE2" Residue "c ARG 299": "NH1" <-> "NH2" Residue "c PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 333": "OE1" <-> "OE2" Residue "c GLU 334": "OE1" <-> "OE2" Residue "c ARG 347": "NH1" <-> "NH2" Residue "c PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 366": "NH1" <-> "NH2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 128": "NH1" <-> "NH2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 214": "OE1" <-> "OE2" Residue "b GLU 218": "OE1" <-> "OE2" Residue "b GLU 226": "OE1" <-> "OE2" Residue "b ARG 299": "NH1" <-> "NH2" Residue "b PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 333": "OE1" <-> "OE2" Residue "b GLU 334": "OE1" <-> "OE2" Residue "b ARG 347": "NH1" <-> "NH2" Residue "b PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 366": "NH1" <-> "NH2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "a ARG 30": "NH1" <-> "NH2" Residue "a PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 92": "NH1" <-> "NH2" Residue "a TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 214": "OE1" <-> "OE2" Residue "a GLU 218": "OE1" <-> "OE2" Residue "a GLU 226": "OE1" <-> "OE2" Residue "a ARG 299": "NH1" <-> "NH2" Residue "a PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 333": "OE1" <-> "OE2" Residue "a ARG 347": "NH1" <-> "NH2" Residue "a PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 366": "NH1" <-> "NH2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 128": "NH1" <-> "NH2" Residue "d TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 214": "OE1" <-> "OE2" Residue "d GLU 218": "OE1" <-> "OE2" Residue "d GLU 226": "OE1" <-> "OE2" Residue "d ARG 299": "NH1" <-> "NH2" Residue "d PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 334": "OE1" <-> "OE2" Residue "d ARG 347": "NH1" <-> "NH2" Residue "d PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 366": "NH1" <-> "NH2" Residue "d ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20038 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'RNA': 8} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "e" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "f" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "c" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "b" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "d" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.34, per 1000 atoms: 0.52 Number of scatterers: 20038 At special positions: 0 Unit cell: (139.7, 116.6, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 102 16.00 P 20 15.00 Mg 6 11.99 F 18 9.00 O 3824 8.00 N 3538 7.00 C 12524 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 12 sheets defined 41.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 11 through 21 Processing helix chain 'e' and resid 31 through 44 Processing helix chain 'e' and resid 83 through 89 Processing helix chain 'e' and resid 124 through 127 No H-bonds generated for 'chain 'e' and resid 124 through 127' Processing helix chain 'e' and resid 133 through 135 No H-bonds generated for 'chain 'e' and resid 133 through 135' Processing helix chain 'e' and resid 154 through 165 removed outlier: 3.583A pdb=" N LEU e 157 " --> pdb=" O THR e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 198 Processing helix chain 'e' and resid 213 through 220 Processing helix chain 'e' and resid 236 through 256 removed outlier: 3.594A pdb=" N HIS e 256 " --> pdb=" O ARG e 252 " (cutoff:3.500A) Processing helix chain 'e' and resid 267 through 277 Processing helix chain 'e' and resid 294 through 302 Processing helix chain 'e' and resid 326 through 337 removed outlier: 3.555A pdb=" N GLU e 333 " --> pdb=" O GLU e 329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) Processing helix chain 'e' and resid 347 through 351 Processing helix chain 'e' and resid 368 through 370 No H-bonds generated for 'chain 'e' and resid 368 through 370' Processing helix chain 'e' and resid 374 through 389 Proline residue: e 389 - end of helix Processing helix chain 'e' and resid 392 through 403 Processing helix chain 'e' and resid 409 through 416 Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 11 through 21 Processing helix chain 'f' and resid 31 through 44 Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 124 through 127 No H-bonds generated for 'chain 'f' and resid 124 through 127' Processing helix chain 'f' and resid 133 through 135 No H-bonds generated for 'chain 'f' and resid 133 through 135' Processing helix chain 'f' and resid 154 through 165 removed outlier: 3.584A pdb=" N LEU f 157 " --> pdb=" O THR f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 198 Processing helix chain 'f' and resid 213 through 220 Processing helix chain 'f' and resid 236 through 256 removed outlier: 3.595A pdb=" N HIS f 256 " --> pdb=" O ARG f 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 267 through 277 Processing helix chain 'f' and resid 294 through 302 Processing helix chain 'f' and resid 326 through 334 Processing helix chain 'f' and resid 347 through 351 Processing helix chain 'f' and resid 368 through 370 No H-bonds generated for 'chain 'f' and resid 368 through 370' Processing helix chain 'f' and resid 374 through 389 Proline residue: f 389 - end of helix Processing helix chain 'f' and resid 392 through 403 Processing helix chain 'f' and resid 409 through 416 Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 11 through 21 Processing helix chain 'c' and resid 31 through 44 Processing helix chain 'c' and resid 83 through 89 Processing helix chain 'c' and resid 124 through 127 No H-bonds generated for 'chain 'c' and resid 124 through 127' Processing helix chain 'c' and resid 133 through 135 No H-bonds generated for 'chain 'c' and resid 133 through 135' Processing helix chain 'c' and resid 154 through 165 removed outlier: 3.586A pdb=" N LEU c 157 " --> pdb=" O THR c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 198 Processing helix chain 'c' and resid 213 through 220 Processing helix chain 'c' and resid 236 through 256 removed outlier: 3.594A pdb=" N HIS c 256 " --> pdb=" O ARG c 252 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 277 Processing helix chain 'c' and resid 294 through 302 Processing helix chain 'c' and resid 326 through 334 removed outlier: 3.549A pdb=" N GLU c 333 " --> pdb=" O GLU c 329 " (cutoff:3.500A) Processing helix chain 'c' and resid 347 through 351 Processing helix chain 'c' and resid 368 through 370 No H-bonds generated for 'chain 'c' and resid 368 through 370' Processing helix chain 'c' and resid 374 through 389 Proline residue: c 389 - end of helix Processing helix chain 'c' and resid 392 through 403 Processing helix chain 'c' and resid 409 through 416 Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 11 through 21 Processing helix chain 'b' and resid 31 through 44 Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 124 through 127 No H-bonds generated for 'chain 'b' and resid 124 through 127' Processing helix chain 'b' and resid 133 through 135 No H-bonds generated for 'chain 'b' and resid 133 through 135' Processing helix chain 'b' and resid 154 through 165 removed outlier: 3.583A pdb=" N LEU b 157 " --> pdb=" O THR b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 198 Processing helix chain 'b' and resid 213 through 220 Processing helix chain 'b' and resid 236 through 256 removed outlier: 3.596A pdb=" N HIS b 256 " --> pdb=" O ARG b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 267 through 277 Processing helix chain 'b' and resid 294 through 302 Processing helix chain 'b' and resid 326 through 335 removed outlier: 3.643A pdb=" N GLU b 333 " --> pdb=" O GLU b 329 " (cutoff:3.500A) Processing helix chain 'b' and resid 347 through 351 Processing helix chain 'b' and resid 368 through 370 No H-bonds generated for 'chain 'b' and resid 368 through 370' Processing helix chain 'b' and resid 374 through 389 Proline residue: b 389 - end of helix Processing helix chain 'b' and resid 392 through 403 Processing helix chain 'b' and resid 409 through 416 Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 11 through 21 Processing helix chain 'a' and resid 31 through 44 Processing helix chain 'a' and resid 83 through 89 Processing helix chain 'a' and resid 124 through 127 No H-bonds generated for 'chain 'a' and resid 124 through 127' Processing helix chain 'a' and resid 133 through 135 No H-bonds generated for 'chain 'a' and resid 133 through 135' Processing helix chain 'a' and resid 154 through 165 removed outlier: 3.586A pdb=" N LEU a 157 " --> pdb=" O THR a 154 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 198 Processing helix chain 'a' and resid 213 through 220 Processing helix chain 'a' and resid 236 through 256 removed outlier: 3.593A pdb=" N HIS a 256 " --> pdb=" O ARG a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 277 Processing helix chain 'a' and resid 294 through 302 Processing helix chain 'a' and resid 326 through 336 Processing helix chain 'a' and resid 347 through 351 Processing helix chain 'a' and resid 368 through 370 No H-bonds generated for 'chain 'a' and resid 368 through 370' Processing helix chain 'a' and resid 374 through 389 Proline residue: a 389 - end of helix Processing helix chain 'a' and resid 392 through 403 Processing helix chain 'a' and resid 409 through 416 Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 11 through 21 Processing helix chain 'd' and resid 31 through 44 Processing helix chain 'd' and resid 83 through 89 Processing helix chain 'd' and resid 124 through 127 No H-bonds generated for 'chain 'd' and resid 124 through 127' Processing helix chain 'd' and resid 133 through 135 No H-bonds generated for 'chain 'd' and resid 133 through 135' Processing helix chain 'd' and resid 154 through 165 removed outlier: 3.583A pdb=" N LEU d 157 " --> pdb=" O THR d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 198 Processing helix chain 'd' and resid 213 through 220 Processing helix chain 'd' and resid 236 through 256 removed outlier: 3.594A pdb=" N HIS d 256 " --> pdb=" O ARG d 252 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 277 Processing helix chain 'd' and resid 294 through 302 Processing helix chain 'd' and resid 326 through 332 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 368 through 370 No H-bonds generated for 'chain 'd' and resid 368 through 370' Processing helix chain 'd' and resid 374 through 389 Proline residue: d 389 - end of helix Processing helix chain 'd' and resid 392 through 403 Processing helix chain 'd' and resid 409 through 416 Processing sheet with id= A, first strand: chain 'e' and resid 79 through 81 removed outlier: 4.249A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE e 49 " --> pdb=" O ILE e 101 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'e' and resid 173 through 179 removed outlier: 8.082A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE e 176 " --> pdb=" O ILE e 315 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA e 317 " --> pdb=" O ILE e 176 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA e 178 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA e 319 " --> pdb=" O ALA e 178 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL e 203 " --> pdb=" O ILE e 261 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU e 263 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET e 205 " --> pdb=" O LEU e 263 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU e 226 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU e 208 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL e 228 " --> pdb=" O LEU e 208 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ASP e 210 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER e 230 " --> pdb=" O ASP e 210 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'f' and resid 79 through 81 removed outlier: 4.251A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE f 49 " --> pdb=" O ILE f 101 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'f' and resid 173 through 179 removed outlier: 8.079A pdb=" N GLY f 174 " --> pdb=" O LEU f 313 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE f 315 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE f 176 " --> pdb=" O ILE f 315 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA f 317 " --> pdb=" O ILE f 176 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA f 178 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA f 319 " --> pdb=" O ALA f 178 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL f 203 " --> pdb=" O ILE f 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU f 263 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU f 226 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU f 208 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL f 228 " --> pdb=" O LEU f 208 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASP f 210 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER f 230 " --> pdb=" O ASP f 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 79 through 81 removed outlier: 4.252A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE c 49 " --> pdb=" O ILE c 101 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 173 through 179 removed outlier: 8.080A pdb=" N GLY c 174 " --> pdb=" O LEU c 313 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE c 315 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE c 176 " --> pdb=" O ILE c 315 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA c 317 " --> pdb=" O ILE c 176 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA c 178 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA c 319 " --> pdb=" O ALA c 178 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL c 203 " --> pdb=" O ILE c 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU c 263 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET c 205 " --> pdb=" O LEU c 263 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU c 226 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU c 208 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL c 228 " --> pdb=" O LEU c 208 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP c 210 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER c 230 " --> pdb=" O ASP c 210 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'b' and resid 79 through 81 removed outlier: 4.250A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'b' and resid 173 through 179 removed outlier: 8.080A pdb=" N GLY b 174 " --> pdb=" O LEU b 313 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE b 315 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE b 176 " --> pdb=" O ILE b 315 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA b 317 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA b 178 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA b 319 " --> pdb=" O ALA b 178 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL b 203 " --> pdb=" O ILE b 261 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU b 263 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET b 205 " --> pdb=" O LEU b 263 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU b 208 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL b 228 " --> pdb=" O LEU b 208 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ASP b 210 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER b 230 " --> pdb=" O ASP b 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'a' and resid 79 through 81 removed outlier: 4.254A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'a' and resid 173 through 179 removed outlier: 8.081A pdb=" N GLY a 174 " --> pdb=" O LEU a 313 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE a 315 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE a 176 " --> pdb=" O ILE a 315 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA a 317 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA a 178 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA a 319 " --> pdb=" O ALA a 178 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL a 203 " --> pdb=" O ILE a 261 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET a 205 " --> pdb=" O LEU a 263 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU a 226 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU a 208 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL a 228 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASP a 210 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER a 230 " --> pdb=" O ASP a 210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 79 through 81 removed outlier: 4.252A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'd' and resid 173 through 179 removed outlier: 8.080A pdb=" N GLY d 174 " --> pdb=" O LEU d 313 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE d 315 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE d 176 " --> pdb=" O ILE d 315 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA d 317 " --> pdb=" O ILE d 176 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA d 178 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA d 319 " --> pdb=" O ALA d 178 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL d 203 " --> pdb=" O ILE d 261 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU d 263 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASP d 210 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N SER d 230 " --> pdb=" O ASP d 210 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.72 Time building geometry restraints manager: 9.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4633 1.33 - 1.45: 3721 1.45 - 1.57: 11764 1.57 - 1.69: 33 1.69 - 1.81: 198 Bond restraints: 20349 Sorted by residual: bond pdb=" BE BEF a1002 " pdb=" F2 BEF a1002 " ideal model delta sigma weight residual 1.476 1.564 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" BE BEF c1002 " pdb=" F2 BEF c1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" BE BEF b1002 " pdb=" F2 BEF b1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" BE BEF e1002 " pdb=" F2 BEF e1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" BE BEF f1002 " pdb=" F2 BEF f1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 20344 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.77: 837 107.77 - 115.02: 12414 115.02 - 122.27: 10930 122.27 - 129.52: 3203 129.52 - 136.77: 85 Bond angle restraints: 27469 Sorted by residual: angle pdb=" N ASP f 322 " pdb=" CA ASP f 322 " pdb=" C ASP f 322 " ideal model delta sigma weight residual 112.58 105.29 7.29 1.22e+00 6.72e-01 3.57e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.74 6.59 1.21e+00 6.83e-01 2.97e+01 angle pdb=" N GLU c 334 " pdb=" CA GLU c 334 " pdb=" C GLU c 334 " ideal model delta sigma weight residual 111.33 105.03 6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" F2 BEF e1002 " pdb=" BE BEF e1002 " pdb=" F3 BEF e1002 " ideal model delta sigma weight residual 119.96 105.53 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF c1002 " pdb=" BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.54 14.42 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 12388 29.83 - 59.65: 147 59.65 - 89.48: 48 89.48 - 119.31: 2 119.31 - 149.14: 6 Dihedral angle restraints: 12591 sinusoidal: 5397 harmonic: 7194 Sorted by residual: dihedral pdb=" O1B ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PB ADP d1000 " pdb=" PA ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.13 -149.14 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP c1000 " pdb=" O3A ADP c1000 " pdb=" PB ADP c1000 " pdb=" PA ADP c1000 " ideal model delta sinusoidal sigma weight residual -60.00 89.09 -149.10 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP d1000 " pdb=" O3A ADP d1000 " pdb=" PA ADP d1000 " pdb=" PB ADP d1000 " ideal model delta sinusoidal sigma weight residual -60.00 84.35 -144.35 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2607 0.052 - 0.104: 406 0.104 - 0.155: 109 0.155 - 0.207: 7 0.207 - 0.259: 1 Chirality restraints: 3130 Sorted by residual: chirality pdb=" C3' A 7 1 " pdb=" C4' A 7 1 " pdb=" O3' A 7 1 " pdb=" C2' A 7 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.74 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL d 330 " pdb=" N VAL d 330 " pdb=" C VAL d 330 " pdb=" CB VAL d 330 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.99e-01 chirality pdb=" C3' U 7 2 " pdb=" C4' U 7 2 " pdb=" O3' U 7 2 " pdb=" C2' U 7 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 3127 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C ILE b 331 " -0.112 2.00e-02 2.50e+03 pdb=" O ILE b 331 " 0.043 2.00e-02 2.50e+03 pdb=" N TYR b 332 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE e 331 " -0.028 2.00e-02 2.50e+03 5.66e-02 3.20e+01 pdb=" C ILE e 331 " 0.098 2.00e-02 2.50e+03 pdb=" O ILE e 331 " -0.038 2.00e-02 2.50e+03 pdb=" N TYR e 332 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE c 331 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ILE c 331 " -0.086 2.00e-02 2.50e+03 pdb=" O ILE c 331 " 0.033 2.00e-02 2.50e+03 pdb=" N TYR c 332 " 0.028 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 72 2.02 - 2.74: 1678 2.74 - 3.46: 29280 3.46 - 4.18: 46631 4.18 - 4.90: 83743 Nonbonded interactions: 161404 Sorted by model distance: nonbonded pdb=" O2' U 7 5 " pdb=" OG1 THR e 286 " model vdw 1.299 2.440 nonbonded pdb=" NH2 ARG b 173 " pdb=" CD ARG a 212 " model vdw 1.351 3.520 nonbonded pdb=" C5' U 7 5 " pdb=" CG2 THR d 286 " model vdw 1.381 3.860 nonbonded pdb=" NH2 ARG b 173 " pdb=" NE ARG a 212 " model vdw 1.392 3.200 nonbonded pdb=" N2 G 7 3 " pdb=" CG2 VAL c 284 " model vdw 1.408 3.540 ... (remaining 161399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 3.440 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: 12.350 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 52.140 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3583 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 : 0.003 0.088 20349 Z= 0.223 Angle : 0.641 14.431 27469 Z= 0.351 Chirality : 0.041 0.259 3130 Planarity : 0.004 0.065 3524 Dihedral : 11.506 149.136 7935 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Rotamer: Outliers : 1.63 % Allowed : 4.11 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.83 (0.16), residues: 2490 helix: 0.26 (0.15), residues: 1134 sheet: -2.06 (0.22), residues: 378 loop : -0.69 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP a 381 HIS 0.002 0.000 HIS e 295 PHE 0.007 0.001 PHE b 36 TYR 0.017 0.001 TYR d 332 ARG 0.003 0.000 ARG b 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 21 MET cc_start: 0.2762 (mmm) cc_final: 0.1609 (ttt) REVERT: c 29 MET cc_start: -0.3216 (mtp) cc_final: -0.3706 (ttt) REVERT: c 341 MET cc_start: -0.1671 (ttm) cc_final: -0.1969 (tmm) outliers start: 35 outliers final: 9 residues processed: 198 average time/residue: 0.3119 time to fit residues: 95.5249 Evaluate side-chains 126 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 193 optimal weight: 40.0000 chunk 74 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 172 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 256 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 HIS a 172 GLN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3934 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20349 Z= 0.226 Angle : 0.687 8.551 27469 Z= 0.325 Chirality : 0.043 0.204 3130 Planarity : 0.004 0.051 3524 Dihedral : 10.052 157.458 2901 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.85 % Favored : 98.11 % Rotamer: Outliers : 0.05 % Allowed : 1.45 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -0.03 (0.17), residues: 2490 helix: 0.63 (0.16), residues: 1098 sheet: -1.07 (0.24), residues: 408 loop : -0.08 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 381 HIS 0.004 0.001 HIS a 388 PHE 0.019 0.002 PHE b 335 TYR 0.021 0.002 TYR b 332 ARG 0.008 0.001 ARG e 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 117 time to evaluate : 2.158 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: f 21 MET cc_start: 0.3003 (mmm) cc_final: 0.2131 (mtt) REVERT: f 29 MET cc_start: -0.2248 (mtp) cc_final: -0.2476 (ttm) REVERT: b 396 MET cc_start: 0.5299 (mtp) cc_final: 0.4343 (mtp) outliers start: 1 outliers final: 0 residues processed: 118 average time/residue: 0.3128 time to fit residues: 58.6550 Evaluate side-chains 105 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 0.0030 chunk 69 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 30.0000 chunk 61 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 overall best weight: 2.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 25 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 HIS b 241 GLN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4067 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20349 Z= 0.186 Angle : 0.599 7.216 27469 Z= 0.283 Chirality : 0.041 0.153 3130 Planarity : 0.004 0.061 3524 Dihedral : 9.825 157.555 2901 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.05 % Allowed : 1.63 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.46 (0.17), residues: 2490 helix: 0.77 (0.16), residues: 1098 sheet: -0.51 (0.26), residues: 390 loop : 0.35 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 381 HIS 0.008 0.001 HIS c 42 PHE 0.015 0.001 PHE e 413 TYR 0.013 0.001 TYR f 332 ARG 0.007 0.001 ARG b 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.556 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: f 21 MET cc_start: 0.3035 (mmm) cc_final: 0.2344 (mtt) REVERT: f 29 MET cc_start: -0.1910 (mtp) cc_final: -0.2294 (ttm) REVERT: b 396 MET cc_start: 0.5636 (mtp) cc_final: 0.5069 (mtp) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.2937 time to fit residues: 52.8363 Evaluate side-chains 103 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 32 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 193 GLN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4118 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20349 Z= 0.149 Angle : 0.559 11.419 27469 Z= 0.260 Chirality : 0.040 0.189 3130 Planarity : 0.003 0.035 3524 Dihedral : 9.696 156.494 2901 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.17), residues: 2490 helix: 0.97 (0.16), residues: 1098 sheet: -0.30 (0.26), residues: 384 loop : 0.47 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.003 0.001 HIS f 344 PHE 0.008 0.001 PHE f 355 TYR 0.018 0.001 TYR f 332 ARG 0.006 0.000 ARG e 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.279 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: f 21 MET cc_start: 0.2982 (mmm) cc_final: 0.2263 (mtt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3108 time to fit residues: 54.7286 Evaluate side-chains 103 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 0.0570 chunk 98 optimal weight: 20.0000 chunk 203 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN a 256 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4383 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20349 Z= 0.228 Angle : 0.651 11.583 27469 Z= 0.310 Chirality : 0.042 0.199 3130 Planarity : 0.003 0.036 3524 Dihedral : 9.859 155.484 2901 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.67 (0.17), residues: 2490 helix: 0.78 (0.16), residues: 1098 sheet: -0.22 (0.27), residues: 396 loop : 0.60 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.005 0.001 HIS a 344 PHE 0.013 0.001 PHE c 335 TYR 0.020 0.002 TYR a 72 ARG 0.005 0.001 ARG e 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.351 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: f 21 MET cc_start: 0.3262 (mmm) cc_final: 0.2292 (mtt) REVERT: f 245 MET cc_start: 0.4546 (ptp) cc_final: 0.3794 (ptt) REVERT: c 327 MET cc_start: 0.5452 (tpt) cc_final: 0.5081 (tpp) REVERT: b 21 MET cc_start: 0.0394 (ttt) cc_final: 0.0107 (ttt) REVERT: d 341 MET cc_start: -0.1179 (mmt) cc_final: -0.1682 (mmp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.3030 time to fit residues: 52.8916 Evaluate side-chains 102 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 0.9980 chunk 215 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 238 optimal weight: 0.7980 chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4286 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20349 Z= 0.136 Angle : 0.573 8.425 27469 Z= 0.264 Chirality : 0.041 0.161 3130 Planarity : 0.003 0.031 3524 Dihedral : 9.653 154.879 2901 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.91 (0.17), residues: 2490 helix: 1.03 (0.16), residues: 1104 sheet: -0.12 (0.27), residues: 384 loop : 0.64 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 381 HIS 0.003 0.001 HIS f 344 PHE 0.011 0.001 PHE b 355 TYR 0.017 0.001 TYR f 332 ARG 0.003 0.000 ARG b 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.266 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: e 21 MET cc_start: -0.3511 (ttt) cc_final: -0.3757 (ttt) REVERT: f 21 MET cc_start: 0.3177 (mmm) cc_final: 0.2192 (mtt) REVERT: f 245 MET cc_start: 0.4512 (ptp) cc_final: 0.4063 (ptt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3024 time to fit residues: 52.6051 Evaluate side-chains 101 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 256 HIS ** f 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 HIS ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 ASN ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 ASN b 199 HIS ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN a 126 ASN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 142 ASN d 256 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4733 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 20349 Z= 0.335 Angle : 0.831 11.431 27469 Z= 0.406 Chirality : 0.046 0.213 3130 Planarity : 0.005 0.062 3524 Dihedral : 10.251 158.015 2901 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 28.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.38 (0.17), residues: 2490 helix: 0.43 (0.15), residues: 1068 sheet: -0.38 (0.26), residues: 396 loop : 0.60 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP d 381 HIS 0.007 0.002 HIS b 239 PHE 0.035 0.002 PHE d 413 TYR 0.015 0.002 TYR d 332 ARG 0.018 0.001 ARG f 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.189 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: e 21 MET cc_start: -0.3189 (ttt) cc_final: -0.3546 (ttt) REVERT: f 21 MET cc_start: 0.3734 (mmm) cc_final: 0.2736 (mtt) REVERT: c 327 MET cc_start: 0.5159 (tpt) cc_final: 0.4714 (tpp) REVERT: b 21 MET cc_start: 0.0894 (ttt) cc_final: 0.0669 (ttt) REVERT: b 396 MET cc_start: 0.5131 (mtt) cc_final: 0.4816 (mtt) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3086 time to fit residues: 54.5245 Evaluate side-chains 99 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4576 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 20349 Z= 0.155 Angle : 0.586 7.465 27469 Z= 0.280 Chirality : 0.042 0.182 3130 Planarity : 0.003 0.033 3524 Dihedral : 9.753 154.015 2901 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.84 (0.17), residues: 2490 helix: 0.88 (0.16), residues: 1098 sheet: -0.15 (0.26), residues: 396 loop : 0.75 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 381 HIS 0.005 0.001 HIS f 344 PHE 0.013 0.001 PHE f 121 TYR 0.022 0.001 TYR b 332 ARG 0.004 0.000 ARG f 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 2.484 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: e 21 MET cc_start: -0.3506 (ttt) cc_final: -0.3836 (ttt) REVERT: f 21 MET cc_start: 0.4187 (mmm) cc_final: 0.3526 (mtt) REVERT: f 245 MET cc_start: 0.4682 (ptt) cc_final: 0.4102 (ptt) REVERT: b 21 MET cc_start: 0.0559 (ttt) cc_final: 0.0197 (ttt) REVERT: b 186 MET cc_start: 0.7192 (pmm) cc_final: 0.6800 (pmm) REVERT: b 396 MET cc_start: 0.5129 (mtt) cc_final: 0.4896 (mtt) REVERT: a 1 MET cc_start: 0.6518 (pmm) cc_final: 0.5781 (pmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3071 time to fit residues: 52.7769 Evaluate side-chains 98 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 0.3980 chunk 208 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 234 optimal weight: 40.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 126 ASN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 moved from start: 0.8548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20349 Z= 0.252 Angle : 0.700 10.192 27469 Z= 0.341 Chirality : 0.043 0.165 3130 Planarity : 0.004 0.031 3524 Dihedral : 10.001 155.677 2901 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 24.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.56 (0.17), residues: 2490 helix: 0.61 (0.15), residues: 1110 sheet: -0.34 (0.26), residues: 384 loop : 0.67 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.005 0.001 HIS a 344 PHE 0.014 0.002 PHE d 62 TYR 0.017 0.002 TYR d 332 ARG 0.007 0.001 ARG f 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 1 MET cc_start: 0.6618 (pmm) cc_final: 0.6363 (ptt) REVERT: e 21 MET cc_start: -0.3254 (ttt) cc_final: -0.3851 (ttt) REVERT: f 21 MET cc_start: 0.4854 (mmm) cc_final: 0.3672 (mtt) REVERT: b 21 MET cc_start: 0.1382 (ttt) cc_final: 0.0782 (ttt) REVERT: b 396 MET cc_start: 0.5322 (mtt) cc_final: 0.4947 (mtt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3007 time to fit residues: 50.1079 Evaluate side-chains 97 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 246 optimal weight: 0.0870 chunk 226 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 GLN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4708 moved from start: 0.8722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20349 Z= 0.155 Angle : 0.583 7.046 27469 Z= 0.279 Chirality : 0.042 0.173 3130 Planarity : 0.003 0.077 3524 Dihedral : 9.724 154.232 2901 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.86 (0.17), residues: 2490 helix: 0.90 (0.16), residues: 1110 sheet: 0.03 (0.26), residues: 396 loop : 0.66 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 381 HIS 0.005 0.001 HIS d 344 PHE 0.012 0.001 PHE f 121 TYR 0.015 0.001 TYR b 332 ARG 0.004 0.000 ARG f 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4980 Ramachandran restraints generated. 2490 Oldfield, 0 Emsley, 2490 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.515 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: e 1 MET cc_start: 0.6441 (pmm) cc_final: 0.6144 (ptp) REVERT: e 21 MET cc_start: -0.3275 (ttt) cc_final: -0.3787 (ttt) REVERT: f 21 MET cc_start: 0.4942 (mmm) cc_final: 0.3512 (mtt) REVERT: b 21 MET cc_start: 0.1435 (ttt) cc_final: 0.1118 (ttt) REVERT: b 396 MET cc_start: 0.5252 (mtt) cc_final: 0.4867 (mtt) REVERT: d 416 MET cc_start: 0.2028 (ptt) cc_final: 0.1553 (ptt) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2745 time to fit residues: 46.2687 Evaluate side-chains 97 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 11 optimal weight: 0.1980 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 ASN ** f 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 ASN d 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.030273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.024029 restraints weight = 390328.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.024036 restraints weight = 333010.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.024320 restraints weight = 332228.914| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.9591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20349 Z= 0.231 Angle : 0.672 8.324 27469 Z= 0.327 Chirality : 0.043 0.326 3130 Planarity : 0.004 0.032 3524 Dihedral : 9.938 156.070 2901 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 23.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.67 (0.17), residues: 2490 helix: 0.74 (0.16), residues: 1104 sheet: -0.28 (0.26), residues: 384 loop : 0.67 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 381 HIS 0.005 0.001 HIS e 344 PHE 0.018 0.002 PHE d 50 TYR 0.015 0.002 TYR c 72 ARG 0.005 0.001 ARG f 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3016.04 seconds wall clock time: 56 minutes 24.21 seconds (3384.21 seconds total)