Starting phenix.real_space_refine on Sun Jun 30 05:58:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/06_2024/8e5l_27914_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/06_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_27914/06_2024/8e5l_27914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/06_2024/8e5l_27914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/06_2024/8e5l_27914_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5l_27914/06_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-5370/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: 11.51, per 1000 atoms: 0.57 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: 8.26 Conformation dependent library (CDL) restraints added in 3.8 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: 3.86 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: 5.66 Time building geometry restraints manager: 8.99 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: 3.720 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: 12.190 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 53.680 Find NCS groups from input model: 1.240 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.190 ------------------------------------------------------------------------------- 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 : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.3791 time to fit residues: 150.7878 Evaluate side-chains 147 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4476 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20371 Z= 0.223 Angle : 0.667 7.183 27503 Z= 0.321 Chirality : 0.043 0.161 3135 Planarity : 0.004 0.054 3525 Dihedral : 10.674 152.083 2917 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.84 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: 0.09 (0.17), residues: 2490 helix: 0.59 (0.16), residues: 1098 sheet: -1.00 (0.24), residues: 402 loop : 0.16 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 381 HIS 0.012 0.002 HIS c 388 PHE 0.016 0.002 PHE b 335 TYR 0.020 0.002 TYR d 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 154 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.415 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: -0.1899 (ttt) cc_final: -0.2163 (ttt) REVERT: e 341 MET cc_start: 0.1416 (mtp) cc_final: 0.0817 (mtm) REVERT: f 21 MET cc_start: 0.1862 (mmm) cc_final: -0.0249 (mtm) REVERT: c 29 MET cc_start: -0.1733 (mtp) cc_final: -0.2189 (ttt) REVERT: c 416 MET cc_start: 0.0912 (ptm) cc_final: 0.0583 (ptt) REVERT: d 21 MET cc_start: -0.1203 (mmm) cc_final: -0.3703 (mtt) REVERT: d 341 MET cc_start: 0.0321 (tpt) cc_final: -0.0993 (tpt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.3200 time to fit residues: 77.5892 Evaluate side-chains 121 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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: 0.9990 chunk 69 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 242 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 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 a 142 ASN ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4598 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20371 Z= 0.170 Angle : 0.576 8.052 27503 Z= 0.273 Chirality : 0.041 0.151 3135 Planarity : 0.003 0.027 3525 Dihedral : 10.412 166.666 2917 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.05 % Allowed : 1.82 % 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: 0.57 (0.17), residues: 2490 helix: 0.83 (0.15), residues: 1104 sheet: -0.73 (0.27), residues: 372 loop : 0.57 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 381 HIS 0.006 0.001 HIS c 239 PHE 0.011 0.001 PHE f 36 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 140 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 2.408 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: e 21 MET cc_start: -0.2589 (ttt) cc_final: -0.2819 (ttt) REVERT: e 341 MET cc_start: 0.1089 (mtp) cc_final: 0.0848 (mtm) REVERT: f 21 MET cc_start: 0.1836 (mmm) cc_final: 0.0291 (mtp) REVERT: c 416 MET cc_start: 0.0718 (ptm) cc_final: 0.0259 (ptt) REVERT: d 21 MET cc_start: -0.0964 (mmm) cc_final: -0.3234 (mtt) REVERT: d 341 MET cc_start: 0.0363 (tpt) cc_final: -0.0863 (tpt) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.3177 time to fit residues: 70.1851 Evaluate side-chains 119 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.435 ------------------------------------------------------------------------------- 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: 2.9990 chunk 116 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 142 ASN e 241 GLN f 142 ASN f 193 GLN c 193 GLN c 241 GLN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 241 GLN a 25 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4899 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20371 Z= 0.221 Angle : 0.647 8.998 27503 Z= 0.310 Chirality : 0.042 0.271 3135 Planarity : 0.004 0.041 3525 Dihedral : 10.584 174.947 2917 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.09 % Allowed : 2.66 % 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: 0.48 (0.17), residues: 2490 helix: 0.64 (0.15), residues: 1110 sheet: -0.60 (0.27), residues: 360 loop : 0.57 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP d 381 HIS 0.009 0.001 HIS c 239 PHE 0.016 0.002 PHE b 111 TYR 0.020 0.002 TYR f 332 ARG 0.008 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 131 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 2.545 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: e 29 MET cc_start: 0.0062 (tmm) cc_final: -0.0450 (tmm) REVERT: f 21 MET cc_start: 0.2030 (mmm) cc_final: -0.0041 (mtt) REVERT: b 245 MET cc_start: 0.5275 (ptp) cc_final: 0.4646 (ptp) REVERT: a 245 MET cc_start: 0.5851 (ptp) cc_final: 0.5258 (ptt) REVERT: d 21 MET cc_start: -0.0690 (mmm) cc_final: -0.2688 (mtp) REVERT: d 396 MET cc_start: 0.4003 (tpp) cc_final: 0.3662 (mmt) outliers start: 2 outliers final: 2 residues processed: 131 average time/residue: 0.3039 time to fit residues: 64.0174 Evaluate side-chains 111 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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: 10.0000 chunk 3 optimal weight: 3.9990 chunk 177 optimal weight: 0.0470 chunk 98 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.9884 ------------------------------------------------------------------------------- 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 ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 42 HIS ** a 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4854 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20371 Z= 0.149 Angle : 0.554 7.047 27503 Z= 0.262 Chirality : 0.040 0.137 3135 Planarity : 0.003 0.025 3525 Dihedral : 10.299 173.783 2917 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 0.85 (0.17), residues: 2490 helix: 1.01 (0.15), residues: 1104 sheet: -0.52 (0.26), residues: 366 loop : 0.72 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 381 HIS 0.007 0.001 HIS b 344 PHE 0.008 0.001 PHE f 36 TYR 0.017 0.001 TYR d 332 ARG 0.003 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 124 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.757 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: e 21 MET cc_start: -0.2650 (ttt) cc_final: -0.2851 (ttt) REVERT: e 29 MET cc_start: 0.0070 (tmm) cc_final: -0.0613 (tmm) REVERT: f 21 MET cc_start: 0.2102 (mmm) cc_final: -0.0228 (mtm) REVERT: d 21 MET cc_start: -0.0617 (mmm) cc_final: -0.2397 (mtt) REVERT: d 341 MET cc_start: 0.0428 (tpt) cc_final: -0.0288 (tpt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3129 time to fit residues: 62.1976 Evaluate side-chains 108 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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: 3.9990 chunk 215 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 0.0270 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 42 HIS e 172 GLN e 241 GLN c 172 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 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 190 ASN ** 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: 0.5033 moved from start: 0.7766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20371 Z= 0.194 Angle : 0.624 8.861 27503 Z= 0.298 Chirality : 0.042 0.169 3135 Planarity : 0.003 0.027 3525 Dihedral : 10.495 174.572 2917 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.23 % 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: 0.76 (0.17), residues: 2490 helix: 0.85 (0.15), residues: 1110 sheet: -0.65 (0.26), residues: 366 loop : 0.84 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP d 381 HIS 0.008 0.001 HIS c 239 PHE 0.014 0.001 PHE b 111 TYR 0.018 0.002 TYR c 332 ARG 0.009 0.001 ARG a 238 *********************** 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 121 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.244 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 21 MET cc_start: -0.2476 (ttt) cc_final: -0.3009 (ttt) REVERT: f 21 MET cc_start: 0.3404 (mmm) cc_final: 0.0201 (mtm) REVERT: d 21 MET cc_start: -0.0077 (mmm) cc_final: -0.2390 (mtt) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.3345 time to fit residues: 64.7104 Evaluate side-chains 109 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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: 9.9990 chunk 26 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 174 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 241 GLN ** b 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 HIS d 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20371 Z= 0.134 Angle : 0.550 6.863 27503 Z= 0.260 Chirality : 0.041 0.145 3135 Planarity : 0.003 0.028 3525 Dihedral : 10.298 177.911 2917 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.05 % Allowed : 1.26 % Favored : 98.69 % 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: 0.82 (0.17), residues: 2490 helix: 0.99 (0.15), residues: 1140 sheet: -0.51 (0.26), residues: 372 loop : 0.69 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 381 HIS 0.006 0.001 HIS c 239 PHE 0.020 0.001 PHE d 121 TYR 0.014 0.001 TYR b 72 ARG 0.003 0.000 ARG a 28 *********************** 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 122 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.278 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: e 21 MET cc_start: -0.2513 (ttt) cc_final: -0.2793 (ttt) REVERT: d 21 MET cc_start: -0.0138 (mmm) cc_final: -0.2186 (mtt) REVERT: d 341 MET cc_start: 0.1008 (tpt) cc_final: 0.0621 (tpt) outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.3087 time to fit residues: 59.9949 Evaluate side-chains 110 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.8343 > 50: distance: 72 - 75: 14.709 distance: 75 - 76: 18.297 distance: 76 - 77: 13.237 distance: 76 - 79: 7.880 distance: 77 - 78: 5.490 distance: 77 - 81: 6.842 distance: 81 - 82: 9.932 distance: 82 - 83: 11.810 distance: 82 - 85: 5.607 distance: 83 - 84: 4.772 distance: 83 - 88: 7.194 distance: 85 - 86: 3.870 distance: 85 - 87: 5.075 distance: 88 - 89: 11.044 distance: 89 - 90: 8.438 distance: 89 - 92: 11.356 distance: 90 - 91: 12.022 distance: 90 - 99: 11.566 distance: 92 - 93: 8.250 distance: 93 - 94: 4.469 distance: 93 - 95: 19.113 distance: 94 - 96: 8.751 distance: 95 - 97: 10.834 distance: 96 - 98: 16.498 distance: 97 - 98: 6.433 distance: 99 - 100: 4.805 distance: 100 - 101: 9.849 distance: 100 - 103: 4.507 distance: 101 - 102: 9.712 distance: 101 - 107: 8.436 distance: 103 - 104: 6.028 distance: 104 - 105: 8.893 distance: 104 - 106: 9.892 distance: 108 - 109: 8.816 distance: 108 - 111: 9.870 distance: 109 - 110: 13.523 distance: 109 - 116: 13.448 distance: 111 - 112: 9.419 distance: 112 - 113: 23.814 distance: 113 - 114: 21.790 distance: 113 - 115: 18.810 distance: 116 - 117: 27.013 distance: 116 - 122: 22.911 distance: 117 - 118: 11.534 distance: 117 - 120: 22.447 distance: 118 - 119: 4.949 distance: 118 - 123: 8.193 distance: 120 - 121: 26.020 distance: 121 - 122: 16.455 distance: 123 - 124: 9.369 distance: 124 - 125: 20.422 distance: 124 - 127: 4.110 distance: 126 - 155: 23.884 distance: 128 - 129: 12.316 distance: 129 - 130: 3.940 distance: 129 - 132: 12.191 distance: 130 - 131: 8.880 distance: 130 - 134: 9.872 distance: 131 - 162: 14.993 distance: 132 - 133: 7.473 distance: 134 - 135: 3.993 distance: 135 - 136: 8.103 distance: 135 - 138: 4.409 distance: 136 - 137: 11.803 distance: 136 - 145: 7.224 distance: 137 - 169: 14.313 distance: 138 - 139: 7.215 distance: 139 - 140: 7.181 distance: 140 - 141: 3.949 distance: 141 - 142: 4.754 distance: 142 - 143: 11.974 distance: 142 - 144: 18.411 distance: 145 - 146: 6.639 distance: 146 - 147: 11.984 distance: 146 - 149: 9.908 distance: 147 - 148: 8.565 distance: 147 - 155: 5.216 distance: 148 - 176: 9.096 distance: 149 - 150: 7.094 distance: 150 - 152: 11.506 distance: 151 - 153: 3.559 distance: 152 - 154: 5.941 distance: 153 - 154: 9.460