Starting phenix.real_space_refine on Mon Mar 18 08:08:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/03_2024/8e5l_27914_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/03_2024/8e5l_27914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/03_2024/8e5l_27914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/03_2024/8e5l_27914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/03_2024/8e5l_27914_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/03_2024/8e5l_27914_neut_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 21 5.49 5 Mg 6 5.21 5 S 102 5.16 5 Be 6 3.05 5 C 12533 2.51 5 N 3540 2.21 5 O 3832 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20058 Number of models: 1 Model: "" Number of chains: 13 Chain: "7" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, '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: 11.61, per 1000 atoms: 0.58 Number of scatterers: 20058 At special positions: 0 Unit cell: (145.32, 126.636, 137.016, 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 21 15.00 Mg 6 11.99 F 18 9.00 O 3832 8.00 N 3540 7.00 C 12533 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: 9.12 Conformation dependent library (CDL) restraints added in 4.0 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: 4.86 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: 3.584A 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: 3.595A 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: 3.554A 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: 3.595A 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: 3.593A 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: 4.250A 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: 5.994A 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: 8.081A pdb=" N GLY e 174 " --> pdb=" O LEU e 313 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE e 315 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 7.691A 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: 6.084A 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: 7.518A 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: 6.931A 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: 6.325A 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: 7.097A pdb=" N MET f 205 " --> pdb=" O LEU f 263 " (cutoff:3.500A) removed outlier: 7.062A 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: 8.299A 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: 3.852A 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: 7.062A 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: 3.854A pdb=" N ILE b 49 " --> pdb=" O ILE b 101 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 5.993A 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: 6.649A 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: 6.932A 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: 6.324A 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: 7.061A pdb=" N GLU b 226 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 8.193A 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: 7.834A 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: 3.852A pdb=" N ILE a 49 " --> pdb=" O ILE a 101 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 5.993A 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: 6.651A 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: 6.084A 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: 7.521A pdb=" N LEU a 263 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.099A 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: 3.852A pdb=" N ILE d 49 " --> pdb=" O ILE d 101 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 5.993A 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: 8.079A 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: 7.692A 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: 7.097A pdb=" N MET d 205 " --> pdb=" O LEU d 263 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLU d 226 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU d 208 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL d 228 " --> pdb=" O LEU d 208 " (cutoff:3.500A) removed outlier: 8.301A 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: 6.25 Time building geometry restraints manager: 9.70 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: 4755 1.33 - 1.45: 3619 1.45 - 1.57: 11764 1.57 - 1.69: 35 1.69 - 1.81: 198 Bond restraints: 20371 Sorted by residual: 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 a1002 " pdb=" F2 BEF a1002 " 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 1.562 -0.086 2.00e-02 2.50e+03 1.86e+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 1.81e+01 ... (remaining 20366 not shown) Histogram of bond angle deviations from ideal: 100.55 - 107.79: 849 107.79 - 115.03: 12423 115.03 - 122.26: 10912 122.26 - 129.50: 3234 129.50 - 136.74: 85 Bond angle restraints: 27503 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 112.58 105.31 7.27 1.22e+00 6.72e-01 3.55e+01 angle pdb=" N GLU e 334 " pdb=" CA GLU e 334 " pdb=" C GLU e 334 " ideal model delta sigma weight residual 111.33 104.73 6.60 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 111.33 105.04 6.29 1.21e+00 6.83e-01 2.70e+01 angle pdb=" F2 BEF c1002 " pdb=" BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" F2 BEF d1002 " pdb=" BE BEF d1002 " pdb=" F3 BEF d1002 " ideal model delta sigma weight residual 119.96 105.55 14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 12396 29.81 - 59.62: 154 59.62 - 89.43: 45 89.43 - 119.24: 2 119.24 - 149.05: 10 Dihedral angle restraints: 12607 sinusoidal: 5413 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 89.05 -149.05 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP e1000 " pdb=" O3A ADP e1000 " pdb=" PB ADP e1000 " pdb=" PA ADP e1000 " ideal model delta sinusoidal sigma weight residual -60.00 88.97 -148.98 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 84.41 -144.41 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 12604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2600 0.052 - 0.103: 412 0.103 - 0.155: 112 0.155 - 0.206: 10 0.206 - 0.258: 1 Chirality restraints: 3135 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 1.66e+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 9.08e-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 0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 3132 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 331 " 0.032 2.00e-02 2.50e+03 6.48e-02 4.19e+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 5.67e-02 3.21e+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 " 0.024 2.00e-02 2.50e+03 4.93e-02 2.43e+01 pdb=" C ILE c 331 " -0.085 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 3522 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 72 2.02 - 2.74: 1684 2.74 - 3.46: 29306 3.46 - 4.18: 46682 4.18 - 4.90: 83834 Nonbonded interactions: 161578 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 1.352 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 161573 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: 4.290 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: 12.700 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 58.770 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.170 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: 80.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 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 0.087 20371 Z= 0.222 Angle : 0.641 14.413 27503 Z= 0.351 Chirality : 0.042 0.258 3135 Planarity : 0.004 0.065 3525 Dihedral : 11.889 149.051 7951 Min Nonbonded Distance : 1.299 Molprobity Statistics. All-atom Clashscore : 26.62 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 0.001 0.000 HIS e 295 PHE 0.007 0.001 PHE a 36 TYR 0.016 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 272 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 237 time to evaluate : 2.412 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: f 21 MET cc_start: 0.1134 (mmm) cc_final: -0.0692 (ttt) REVERT: c 29 MET cc_start: -0.1502 (mtp) cc_final: -0.2173 (ttt) REVERT: b 29 MET cc_start: -0.1529 (mtp) cc_final: -0.2115 (ttt) REVERT: d 21 MET cc_start: -0.0973 (mmm) cc_final: -0.4030 (ttt) outliers start: 35 outliers final: 8 residues processed: 269 average time/residue: 0.3649 time to fit residues: 143.5820 Evaluate side-chains 147 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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: 0.0970 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 193 optimal weight: 40.0000 chunk 74 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 193 GLN e 220 GLN e 241 GLN e 256 HIS ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 193 GLN f 256 HIS c 25 ASN c 117 ASN c 295 HIS c 340 ASN c 388 HIS b 25 ASN b 220 GLN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 256 HIS a 135 ASN a 256 HIS d 193 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 256 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4482 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20371 Z= 0.221 Angle : 0.664 7.882 27503 Z= 0.320 Chirality : 0.043 0.164 3135 Planarity : 0.004 0.045 3525 Dihedral : 10.601 152.819 2917 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: 0.08 (0.17), residues: 2490 helix: 0.60 (0.16), residues: 1092 sheet: -0.99 (0.24), residues: 402 loop : 0.12 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 381 HIS 0.013 0.002 HIS c 388 PHE 0.015 0.002 PHE d 355 TYR 0.018 0.002 TYR d 332 ARG 0.009 0.001 ARG b 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 154 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.581 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: e 21 MET cc_start: -0.1896 (ttt) cc_final: -0.2126 (ttt) REVERT: e 341 MET cc_start: 0.1382 (mtp) cc_final: 0.0939 (mtm) REVERT: f 21 MET cc_start: 0.1873 (mmm) cc_final: -0.0228 (mtm) REVERT: c 29 MET cc_start: -0.1705 (mtp) cc_final: -0.2157 (ttt) REVERT: c 416 MET cc_start: 0.0684 (ptm) cc_final: 0.0374 (ptt) REVERT: d 21 MET cc_start: -0.0987 (mmm) cc_final: -0.3516 (mtt) REVERT: d 341 MET cc_start: 0.0280 (tpt) cc_final: -0.0991 (tpt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3323 time to fit residues: 79.4377 Evaluate side-chains 121 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.372 ------------------------------------------------------------------------------- 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: 0.0020 chunk 69 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 152 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.0030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 32 GLN e 241 GLN ** f 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** c 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 172 GLN ** b 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4447 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20371 Z= 0.132 Angle : 0.543 7.531 27503 Z= 0.253 Chirality : 0.041 0.150 3135 Planarity : 0.003 0.029 3525 Dihedral : 10.160 158.917 2917 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: 0.61 (0.17), residues: 2490 helix: 0.92 (0.16), residues: 1104 sheet: -0.71 (0.27), residues: 372 loop : 0.50 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 381 HIS 0.006 0.001 HIS c 239 PHE 0.010 0.001 PHE a 413 TYR 0.017 0.001 TYR f 332 ARG 0.004 0.000 ARG c 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 146 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.366 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: e 21 MET cc_start: -0.2760 (ttt) cc_final: -0.3043 (ttt) REVERT: f 21 MET cc_start: 0.1601 (mmm) cc_final: -0.0212 (mtm) REVERT: c 29 MET cc_start: -0.1666 (mtp) cc_final: -0.2203 (ttt) REVERT: c 416 MET cc_start: 0.0698 (ptm) cc_final: 0.0284 (ptt) REVERT: b 245 MET cc_start: 0.4604 (ptp) cc_final: 0.4210 (ptp) REVERT: d 21 MET cc_start: -0.0839 (mmm) cc_final: -0.3272 (mtt) REVERT: d 341 MET cc_start: 0.0453 (tpt) cc_final: -0.0767 (tpt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.3292 time to fit residues: 76.0195 Evaluate side-chains 117 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.628 ------------------------------------------------------------------------------- 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: 9.9990 chunk 168 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 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 42 HIS e 142 ASN e 241 GLN f 42 HIS ** f 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 ASN f 193 GLN ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 193 GLN ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 241 GLN ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN a 241 GLN d 135 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5066 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20371 Z= 0.317 Angle : 0.799 9.856 27503 Z= 0.393 Chirality : 0.045 0.208 3135 Planarity : 0.005 0.052 3525 Dihedral : 10.824 161.831 2917 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.45 % 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: -0.01 (0.17), residues: 2490 helix: 0.02 (0.14), residues: 1098 sheet: -0.82 (0.26), residues: 360 loop : 0.57 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP f 381 HIS 0.011 0.002 HIS c 239 PHE 0.037 0.003 PHE e 300 TYR 0.019 0.003 TYR f 332 ARG 0.012 0.001 ARG f 221 *********************** 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 134 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 2.440 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: e 29 MET cc_start: -0.0049 (tmm) cc_final: -0.0573 (tmm) REVERT: e 245 MET cc_start: 0.4064 (ptt) cc_final: 0.3615 (ptt) REVERT: f 21 MET cc_start: 0.2209 (mmm) cc_final: -0.0043 (mtp) REVERT: b 245 MET cc_start: 0.5479 (ptp) cc_final: 0.4951 (ptp) REVERT: a 245 MET cc_start: 0.6100 (ptp) cc_final: 0.5506 (ptp) REVERT: d 21 MET cc_start: -0.0668 (mmm) cc_final: -0.2651 (mtp) REVERT: d 341 MET cc_start: 0.1162 (tpt) cc_final: 0.0889 (tpt) outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.3159 time to fit residues: 67.7637 Evaluate side-chains 112 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 2.459 ------------------------------------------------------------------------------- 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: 10.0000 chunk 135 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 203 optimal weight: 0.0970 chunk 165 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 241 GLN f 172 GLN c 172 GLN ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 25 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4879 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20371 Z= 0.145 Angle : 0.570 7.399 27503 Z= 0.270 Chirality : 0.041 0.199 3135 Planarity : 0.003 0.028 3525 Dihedral : 10.278 152.116 2917 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: 0.52 (0.17), residues: 2490 helix: 0.65 (0.15), residues: 1110 sheet: -0.65 (0.26), residues: 366 loop : 0.66 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 381 HIS 0.007 0.001 HIS b 344 PHE 0.015 0.001 PHE e 300 TYR 0.018 0.001 TYR f 332 ARG 0.002 0.000 ARG f 221 *********************** 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 120 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 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: e 21 MET cc_start: -0.2756 (ttt) cc_final: -0.3040 (ttt) REVERT: e 29 MET cc_start: -0.0288 (tmm) cc_final: -0.0973 (tmm) REVERT: f 21 MET cc_start: 0.2298 (mmm) cc_final: -0.0134 (mtm) REVERT: b 245 MET cc_start: 0.5372 (ptp) cc_final: 0.4876 (ptp) REVERT: a 29 MET cc_start: -0.0894 (ttt) cc_final: -0.1710 (tmm) REVERT: d 21 MET cc_start: -0.0579 (mmm) cc_final: -0.2105 (mtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3156 time to fit residues: 60.3434 Evaluate side-chains 107 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.661 ------------------------------------------------------------------------------- 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: 20.0000 chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN f 142 ASN c 172 GLN c 190 ASN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN d 172 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4981 moved from start: 0.7526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20371 Z= 0.164 Angle : 0.594 8.050 27503 Z= 0.282 Chirality : 0.041 0.139 3135 Planarity : 0.003 0.029 3525 Dihedral : 10.257 159.199 2917 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 0.79 (0.17), residues: 2490 helix: 0.85 (0.15), residues: 1110 sheet: -0.60 (0.26), residues: 372 loop : 0.88 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.007 0.001 HIS c 239 PHE 0.025 0.001 PHE f 36 TYR 0.017 0.002 TYR b 72 ARG 0.004 0.000 ARG c 128 *********************** 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 120 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 2.480 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: e 21 MET cc_start: -0.2773 (ttt) cc_final: -0.3025 (ttt) REVERT: a 245 MET cc_start: 0.5027 (ptp) cc_final: 0.3932 (ptt) REVERT: d 21 MET cc_start: -0.0589 (mmm) cc_final: -0.2196 (mtt) REVERT: d 341 MET cc_start: 0.0340 (tpt) cc_final: -0.0138 (tpt) outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.3177 time to fit residues: 60.8897 Evaluate side-chains 110 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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: 10.0000 chunk 26 optimal weight: 0.1980 chunk 136 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN f 142 ASN ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 HIS ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 142 ASN ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN d 172 GLN d 241 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5073 moved from start: 0.8400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20371 Z= 0.181 Angle : 0.598 7.933 27503 Z= 0.288 Chirality : 0.041 0.151 3135 Planarity : 0.003 0.030 3525 Dihedral : 10.339 160.251 2917 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.05 % Allowed : 1.21 % Favored : 98.74 % 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: 0.73 (0.17), residues: 2490 helix: 0.82 (0.15), residues: 1110 sheet: -0.62 (0.26), residues: 372 loop : 0.81 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.007 0.001 HIS c 42 PHE 0.020 0.001 PHE d 121 TYR 0.013 0.001 TYR d 332 ARG 0.004 0.000 ARG c 160 *********************** 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 123 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.340 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: e 21 MET cc_start: -0.2234 (ttt) cc_final: -0.2467 (ttt) REVERT: f 1 MET cc_start: 0.5501 (pmm) cc_final: 0.4199 (ptp) REVERT: a 29 MET cc_start: -0.1030 (ttm) cc_final: -0.1831 (ptm) REVERT: d 21 MET cc_start: -0.0061 (mmm) cc_final: -0.2131 (mtt) REVERT: d 341 MET cc_start: 0.0613 (tpt) cc_final: 0.0180 (tpt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.3241 time to fit residues: 63.2722 Evaluate side-chains 108 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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: 0.0670 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 187 optimal weight: 6.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 HIS ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4959 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20371 Z= 0.123 Angle : 0.559 7.720 27503 Z= 0.263 Chirality : 0.041 0.147 3135 Planarity : 0.003 0.031 3525 Dihedral : 10.036 157.968 2917 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 0.68 (0.17), residues: 2490 helix: 0.96 (0.15), residues: 1134 sheet: -0.92 (0.25), residues: 402 loop : 0.74 (0.22), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 381 HIS 0.007 0.001 HIS c 42 PHE 0.019 0.001 PHE d 121 TYR 0.014 0.001 TYR d 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 119 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.523 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 1 MET cc_start: 0.5061 (pmm) cc_final: 0.4191 (ptp) REVERT: a 29 MET cc_start: -0.0644 (ttm) cc_final: -0.1037 (ptm) REVERT: d 21 MET cc_start: -0.0084 (mmm) cc_final: -0.2175 (mtt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3161 time to fit residues: 59.8641 Evaluate side-chains 110 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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: 9.9990 chunk 208 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 133 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 145 optimal weight: 0.1980 chunk 234 optimal weight: 0.5980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN f 32 GLN ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN d 42 HIS ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5135 moved from start: 0.9155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20371 Z= 0.184 Angle : 0.616 8.089 27503 Z= 0.293 Chirality : 0.041 0.186 3135 Planarity : 0.003 0.030 3525 Dihedral : 10.359 165.084 2917 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 0.80 (0.15), residues: 1146 sheet: -0.99 (0.25), residues: 402 loop : 0.76 (0.22), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.006 0.001 HIS b 42 PHE 0.018 0.001 PHE d 121 TYR 0.015 0.002 TYR c 72 ARG 0.004 0.000 ARG c 128 *********************** 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 118 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.344 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: e 21 MET cc_start: -0.2754 (ttt) cc_final: -0.3462 (ttt) REVERT: f 1 MET cc_start: 0.5268 (pmm) cc_final: 0.4502 (ptp) REVERT: a 29 MET cc_start: -0.1183 (ttm) cc_final: -0.2504 (ptm) REVERT: d 21 MET cc_start: -0.0315 (mmm) cc_final: -0.2666 (mtm) REVERT: d 341 MET cc_start: 0.0737 (tpt) cc_final: 0.0160 (tpt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3478 time to fit residues: 65.6809 Evaluate side-chains 108 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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: 1.9990 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 246 optimal weight: 0.0060 chunk 226 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 220 GLN ** c 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5006 moved from start: 0.9138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20371 Z= 0.125 Angle : 0.572 8.068 27503 Z= 0.268 Chirality : 0.041 0.142 3135 Planarity : 0.003 0.030 3525 Dihedral : 10.072 160.039 2917 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 0.79 (0.17), residues: 2490 helix: 1.07 (0.15), residues: 1110 sheet: -0.86 (0.25), residues: 402 loop : 0.75 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 381 HIS 0.004 0.001 HIS c 239 PHE 0.037 0.001 PHE b 335 TYR 0.014 0.001 TYR d 332 ARG 0.003 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 119 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.537 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: -0.2855 (ttt) cc_final: -0.3528 (ttt) REVERT: f 1 MET cc_start: 0.5215 (pmm) cc_final: 0.4350 (ptp) REVERT: a 29 MET cc_start: -0.1246 (ttm) cc_final: -0.2529 (ptm) REVERT: d 21 MET cc_start: -0.0138 (mmm) cc_final: -0.2028 (mtp) REVERT: d 341 MET cc_start: 0.0833 (tpt) cc_final: 0.0243 (tpt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3421 time to fit residues: 64.2594 Evaluate side-chains 107 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.745 ------------------------------------------------------------------------------- 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: 7.9990 chunk 180 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** f 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 241 GLN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 241 GLN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.028032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.021935 restraints weight = 358365.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.022485 restraints weight = 263663.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.022896 restraints weight = 211199.228| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.9615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20371 Z= 0.164 Angle : 0.603 10.618 27503 Z= 0.286 Chirality : 0.041 0.162 3135 Planarity : 0.003 0.030 3525 Dihedral : 10.197 166.467 2917 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.67 % 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: 0.66 (0.17), residues: 2490 helix: 0.98 (0.15), residues: 1134 sheet: -1.08 (0.24), residues: 438 loop : 0.82 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.007 0.001 HIS c 239 PHE 0.023 0.001 PHE b 335 TYR 0.014 0.001 TYR d 332 ARG 0.004 0.000 ARG b 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3243.40 seconds wall clock time: 60 minutes 15.60 seconds (3615.60 seconds total)