Starting phenix.real_space_refine on Fri Feb 16 17:21:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e76_27936/02_2024/8e76_27936.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e76_27936/02_2024/8e76_27936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e76_27936/02_2024/8e76_27936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e76_27936/02_2024/8e76_27936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e76_27936/02_2024/8e76_27936.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e76_27936/02_2024/8e76_27936.pdb" } resolution = 2.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10208 2.51 5 N 2724 2.21 5 O 2912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 39": "OD1" <-> "OD2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 535": "OD1" <-> "OD2" Residue "A PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 148": "OD1" <-> "OD2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 522": "OD1" <-> "OD2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 535": "OD1" <-> "OD2" Residue "C PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 522": "OD1" <-> "OD2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 535": "OD1" <-> "OD2" Residue "D PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 549": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15928 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3982 Classifications: {'peptide': 506} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 480} Chain breaks: 2 Chain: "B" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3982 Classifications: {'peptide': 506} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 480} Chain breaks: 2 Chain: "C" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3982 Classifications: {'peptide': 506} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 480} Chain breaks: 2 Chain: "D" Number of atoms: 3982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3982 Classifications: {'peptide': 506} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 480} Chain breaks: 2 Time building chain proxies: 9.00, per 1000 atoms: 0.57 Number of scatterers: 15928 At special positions: 0 Unit cell: (132.08, 135.2, 78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2912 8.00 N 2724 7.00 C 10208 6.00 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=0, symmetry=0 Time building additional restraints: 6.91 Conformation dependent library (CDL) restraints added in 2.9 seconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3728 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 54.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.184A pdb=" N THR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 7 " --> pdb=" O TYR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 80 through 89 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.599A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 207 through 224 Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 291 through 307 removed outlier: 4.160A pdb=" N GLY A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.884A pdb=" N PHE A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 476 " --> pdb=" O ILE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 511 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'B' and resid 2 through 8 removed outlier: 4.185A pdb=" N THR B 6 " --> pdb=" O GLY B 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 7 " --> pdb=" O TYR B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 80 through 89 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 91 through 99 removed outlier: 3.598A pdb=" N LEU B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 207 through 224 Processing helix chain 'B' and resid 235 through 247 Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 291 through 307 removed outlier: 4.161A pdb=" N GLY B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 317 Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'B' and resid 444 through 456 Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.883A pdb=" N PHE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 492 through 511 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'C' and resid 2 through 8 removed outlier: 4.185A pdb=" N THR C 6 " --> pdb=" O GLY C 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 7 " --> pdb=" O TYR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 80 through 89 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.599A pdb=" N LEU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 154 through 169 Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 207 through 224 Processing helix chain 'C' and resid 235 through 247 Processing helix chain 'C' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 291 through 307 removed outlier: 4.160A pdb=" N GLY C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 317 Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 440 through 443 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 461 through 476 removed outlier: 3.884A pdb=" N PHE C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 476 " --> pdb=" O ILE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 492 through 511 Processing helix chain 'C' and resid 522 through 529 Processing helix chain 'D' and resid 2 through 8 removed outlier: 4.185A pdb=" N THR D 6 " --> pdb=" O GLY D 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 7 " --> pdb=" O TYR D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 17 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 80 through 89 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 91 through 99 removed outlier: 3.599A pdb=" N LEU D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 207 through 224 Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 257 through 276 removed outlier: 3.610A pdb=" N ILE D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 291 through 307 removed outlier: 4.160A pdb=" N GLY D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 440 through 443 Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 461 through 476 removed outlier: 3.884A pdb=" N PHE D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL D 476 " --> pdb=" O ILE D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 482 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 492 through 511 Processing helix chain 'D' and resid 522 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 removed outlier: 7.075A pdb=" N PHE A 35 " --> pdb=" O GLN B 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 6.383A pdb=" N LEU A 110 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP A 181 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 112 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 134 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL A 178 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL A 136 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 180 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 138 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 320 removed outlier: 6.557A pdb=" N PHE A 284 " --> pdb=" O TRP A 319 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL A 285 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY A 437 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 419 " --> pdb=" O GLY A 437 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.383A pdb=" N LEU B 110 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP B 181 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 112 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA B 134 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N VAL B 178 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 136 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 180 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR B 138 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.557A pdb=" N PHE B 284 " --> pdb=" O TRP B 319 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 285 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY B 437 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 419 " --> pdb=" O GLY B 437 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.075A pdb=" N PHE C 35 " --> pdb=" O GLN D 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113 removed outlier: 6.384A pdb=" N LEU C 110 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP C 181 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 112 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA C 134 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL C 178 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL C 136 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU C 180 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR C 138 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 318 through 320 removed outlier: 6.558A pdb=" N PHE C 284 " --> pdb=" O TRP C 319 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL C 285 " --> pdb=" O ILE C 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY C 437 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 419 " --> pdb=" O GLY C 437 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 553 through 554 Processing sheet with id=AB2, first strand: chain 'D' and resid 110 through 113 removed outlier: 6.383A pdb=" N LEU D 110 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ASP D 181 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 112 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 134 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL D 178 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 136 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU D 180 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR D 138 " --> pdb=" O LEU D 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.558A pdb=" N PHE D 284 " --> pdb=" O TRP D 319 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL D 285 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY D 437 " --> pdb=" O PHE D 417 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 419 " --> pdb=" O GLY D 437 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 2010 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: 5.28 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5182 1.34 - 1.45: 2603 1.45 - 1.57: 8359 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 16276 Sorted by residual: bond pdb=" C ASN A 395 " pdb=" N PRO A 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.56e+00 bond pdb=" C ASN C 395 " pdb=" N PRO C 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.54e+00 bond pdb=" C ASN D 395 " pdb=" N PRO D 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.45e+00 bond pdb=" C ASN B 395 " pdb=" N PRO B 396 " ideal model delta sigma weight residual 1.334 1.349 -0.016 8.40e-03 1.42e+04 3.43e+00 bond pdb=" CB ARG D 247 " pdb=" CG ARG D 247 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.30e+00 ... (remaining 16271 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.12: 397 106.12 - 113.07: 8771 113.07 - 120.02: 5641 120.02 - 126.97: 7070 126.97 - 133.93: 169 Bond angle restraints: 22048 Sorted by residual: angle pdb=" N GLU A 405 " pdb=" CA GLU A 405 " pdb=" C GLU A 405 " ideal model delta sigma weight residual 113.43 106.93 6.50 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N GLU B 405 " pdb=" CA GLU B 405 " pdb=" C GLU B 405 " ideal model delta sigma weight residual 113.43 106.94 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N GLU D 405 " pdb=" CA GLU D 405 " pdb=" C GLU D 405 " ideal model delta sigma weight residual 113.43 106.94 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N GLU C 405 " pdb=" CA GLU C 405 " pdb=" C GLU C 405 " ideal model delta sigma weight residual 113.43 106.94 6.49 1.26e+00 6.30e-01 2.65e+01 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 113.43 109.30 4.13 1.26e+00 6.30e-01 1.07e+01 ... (remaining 22043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 8613 16.18 - 32.35: 871 32.35 - 48.53: 192 48.53 - 64.71: 44 64.71 - 80.88: 24 Dihedral angle restraints: 9744 sinusoidal: 3912 harmonic: 5832 Sorted by residual: dihedral pdb=" CA CYS D 151 " pdb=" C CYS D 151 " pdb=" N TYR D 152 " pdb=" CA TYR D 152 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA CYS A 151 " pdb=" C CYS A 151 " pdb=" N TYR A 152 " pdb=" CA TYR A 152 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA CYS B 151 " pdb=" C CYS B 151 " pdb=" N TYR B 152 " pdb=" CA TYR B 152 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1247 0.032 - 0.064: 843 0.064 - 0.095: 242 0.095 - 0.127: 112 0.127 - 0.159: 20 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA PHE B 445 " pdb=" N PHE B 445 " pdb=" C PHE B 445 " pdb=" CB PHE B 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE D 445 " pdb=" N PHE D 445 " pdb=" C PHE D 445 " pdb=" CB PHE D 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA PHE A 445 " pdb=" N PHE A 445 " pdb=" C PHE A 445 " pdb=" CB PHE A 445 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 2461 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 309 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO C 310 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 310 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 310 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 309 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 310 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 309 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 310 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 310 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 310 " -0.022 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 499 2.70 - 3.25: 16453 3.25 - 3.80: 28301 3.80 - 4.35: 37030 4.35 - 4.90: 58382 Nonbonded interactions: 140665 Sorted by model distance: nonbonded pdb=" O GLY D 150 " pdb=" OH TYR D 195 " model vdw 2.155 2.440 nonbonded pdb=" O GLY B 150 " pdb=" OH TYR B 195 " model vdw 2.155 2.440 nonbonded pdb=" O GLY C 150 " pdb=" OH TYR C 195 " model vdw 2.156 2.440 nonbonded pdb=" O GLY A 150 " pdb=" OH TYR A 195 " model vdw 2.156 2.440 nonbonded pdb=" OD1 ASP A 213 " pdb=" OH TYR A 246 " model vdw 2.192 2.440 ... (remaining 140660 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.030 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.100 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 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 : 0.007 0.049 16276 Z= 0.483 Angle : 0.722 9.110 22048 Z= 0.396 Chirality : 0.047 0.159 2464 Planarity : 0.004 0.041 2844 Dihedral : 14.221 80.882 6016 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -2.28 (0.17), residues: 2000 helix: -1.20 (0.15), residues: 944 sheet: -0.49 (0.39), residues: 192 loop : -2.03 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 127 HIS 0.004 0.001 HIS B 511 PHE 0.019 0.002 PHE D 35 TYR 0.015 0.002 TYR A 74 ARG 0.006 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 154 MET cc_start: 0.4035 (tpp) cc_final: 0.3753 (tpp) REVERT: B 269 LEU cc_start: 0.7271 (mt) cc_final: 0.7051 (mt) REVERT: C 63 MET cc_start: 0.5901 (mmp) cc_final: 0.5471 (mmt) outliers start: 0 outliers final: 2 residues processed: 329 average time/residue: 1.0158 time to fit residues: 378.2982 Evaluate side-chains 190 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 ASP Chi-restraints excluded: chain D residue 500 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 41 GLN A 66 GLN A 174 GLN A 459 HIS A 480 HIS ** B 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 66 GLN B 115 HIS B 174 GLN B 217 GLN B 281 ASN B 459 HIS B 480 HIS C 41 GLN C 66 GLN C 174 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 459 HIS D 28 HIS D 41 GLN D 66 GLN D 174 GLN D 459 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16276 Z= 0.264 Angle : 0.675 8.526 22048 Z= 0.348 Chirality : 0.044 0.230 2464 Planarity : 0.005 0.057 2844 Dihedral : 5.053 33.432 2212 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.46 % Allowed : 14.29 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.18), residues: 2000 helix: 0.05 (0.16), residues: 960 sheet: -0.35 (0.40), residues: 200 loop : -1.65 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 319 HIS 0.014 0.001 HIS B 298 PHE 0.024 0.002 PHE B 434 TYR 0.023 0.002 TYR D 487 ARG 0.013 0.001 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.5396 (mmm) cc_final: 0.5145 (mmm) REVERT: B 406 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5570 (mttt) REVERT: D 304 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7335 (mm) outliers start: 42 outliers final: 9 residues processed: 212 average time/residue: 0.8566 time to fit residues: 211.3854 Evaluate side-chains 169 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 492 THR Chi-restraints excluded: chain C residue 284 PHE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 395 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16276 Z= 0.195 Angle : 0.593 8.040 22048 Z= 0.304 Chirality : 0.042 0.195 2464 Planarity : 0.004 0.056 2844 Dihedral : 4.635 20.774 2208 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.63 % Allowed : 14.93 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.74 (0.19), residues: 2000 helix: 0.36 (0.17), residues: 964 sheet: -0.32 (0.40), residues: 200 loop : -1.51 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 319 HIS 0.010 0.001 HIS B 298 PHE 0.020 0.002 PHE A 445 TYR 0.027 0.001 TYR D 164 ARG 0.004 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 169 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 395 ASN cc_start: 0.7634 (p0) cc_final: 0.7343 (p0) REVERT: B 406 LYS cc_start: 0.6245 (OUTLIER) cc_final: 0.5855 (mttt) REVERT: D 304 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7468 (mm) outliers start: 45 outliers final: 7 residues processed: 196 average time/residue: 0.8082 time to fit residues: 186.0954 Evaluate side-chains 154 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 492 THR Chi-restraints excluded: chain D residue 551 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** B 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16276 Z= 0.472 Angle : 0.752 11.837 22048 Z= 0.386 Chirality : 0.048 0.211 2464 Planarity : 0.005 0.051 2844 Dihedral : 4.982 21.838 2208 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.99 % Allowed : 15.52 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.71 (0.18), residues: 2000 helix: 0.20 (0.16), residues: 968 sheet: -0.50 (0.42), residues: 168 loop : -1.17 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 319 HIS 0.007 0.001 HIS A 28 PHE 0.038 0.002 PHE A 434 TYR 0.020 0.002 TYR A 100 ARG 0.017 0.001 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 135 time to evaluate : 1.982 Fit side-chains REVERT: B 108 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.5160 (mtm110) REVERT: B 395 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7023 (p0) REVERT: C 434 PHE cc_start: 0.6745 (m-10) cc_final: 0.6295 (m-10) outliers start: 51 outliers final: 15 residues processed: 169 average time/residue: 0.9513 time to fit residues: 184.8534 Evaluate side-chains 128 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 108 ARG Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 151 CYS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 HIS D 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16276 Z= 0.173 Angle : 0.606 10.880 22048 Z= 0.305 Chirality : 0.043 0.230 2464 Planarity : 0.004 0.048 2844 Dihedral : 4.557 19.733 2208 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.23 % Allowed : 17.74 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.40 (0.19), residues: 2000 helix: 0.60 (0.17), residues: 960 sheet: -0.46 (0.43), residues: 168 loop : -1.17 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 319 HIS 0.008 0.001 HIS B 298 PHE 0.022 0.002 PHE B 445 TYR 0.014 0.001 TYR B 208 ARG 0.004 0.000 ARG A 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: B 395 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6802 (p0) REVERT: C 434 PHE cc_start: 0.6570 (m-10) cc_final: 0.6273 (m-10) outliers start: 21 outliers final: 7 residues processed: 133 average time/residue: 1.1060 time to fit residues: 167.0536 Evaluate side-chains 119 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 193 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16276 Z= 0.260 Angle : 0.609 16.321 22048 Z= 0.306 Chirality : 0.043 0.235 2464 Planarity : 0.004 0.045 2844 Dihedral : 4.397 21.833 2208 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.58 % Allowed : 17.97 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.17 (0.19), residues: 2000 helix: 0.74 (0.17), residues: 976 sheet: -0.36 (0.43), residues: 168 loop : -1.00 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 319 HIS 0.007 0.001 HIS B 298 PHE 0.017 0.002 PHE B 445 TYR 0.013 0.001 TYR A 164 ARG 0.004 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.897 Fit side-chains REVERT: B 63 MET cc_start: 0.6713 (mmp) cc_final: 0.6346 (mmp) outliers start: 27 outliers final: 9 residues processed: 133 average time/residue: 1.1203 time to fit residues: 168.8550 Evaluate side-chains 116 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.0470 chunk 162 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 298 HIS ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16276 Z= 0.177 Angle : 0.596 14.312 22048 Z= 0.297 Chirality : 0.042 0.244 2464 Planarity : 0.004 0.043 2844 Dihedral : 4.309 18.850 2208 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.17 % Allowed : 18.79 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.13 (0.19), residues: 2000 helix: 0.79 (0.17), residues: 972 sheet: -0.34 (0.43), residues: 168 loop : -1.00 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 319 HIS 0.008 0.001 HIS B 298 PHE 0.020 0.001 PHE B 445 TYR 0.013 0.001 TYR B 208 ARG 0.012 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 2.082 Fit side-chains REVERT: B 63 MET cc_start: 0.6603 (mmp) cc_final: 0.6321 (mmp) outliers start: 20 outliers final: 12 residues processed: 121 average time/residue: 0.9713 time to fit residues: 135.7742 Evaluate side-chains 116 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 85 MET Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.0010 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.7093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16276 Z= 0.258 Angle : 0.601 14.180 22048 Z= 0.301 Chirality : 0.043 0.245 2464 Planarity : 0.004 0.042 2844 Dihedral : 4.245 19.836 2208 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.29 % Allowed : 18.91 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.02 (0.19), residues: 2000 helix: 0.86 (0.17), residues: 976 sheet: -0.34 (0.43), residues: 168 loop : -0.85 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 319 HIS 0.011 0.001 HIS D 298 PHE 0.018 0.001 PHE A 445 TYR 0.014 0.001 TYR A 164 ARG 0.004 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: B 63 MET cc_start: 0.6676 (mmp) cc_final: 0.6410 (mmp) outliers start: 22 outliers final: 11 residues processed: 123 average time/residue: 1.0097 time to fit residues: 142.4840 Evaluate side-chains 109 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 HIS ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.7248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16276 Z= 0.240 Angle : 0.614 14.014 22048 Z= 0.306 Chirality : 0.043 0.245 2464 Planarity : 0.004 0.043 2844 Dihedral : 4.245 18.701 2208 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.70 % Allowed : 19.44 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 2000 helix: 0.84 (0.17), residues: 980 sheet: -0.32 (0.43), residues: 168 loop : -0.86 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 546 HIS 0.013 0.001 HIS D 298 PHE 0.018 0.002 PHE A 445 TYR 0.013 0.001 TYR A 49 ARG 0.004 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.989 Fit side-chains revert: symmetry clash REVERT: B 63 MET cc_start: 0.6656 (mmp) cc_final: 0.6400 (mmp) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 1.0350 time to fit residues: 133.9910 Evaluate side-chains 108 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 132 optimal weight: 30.0000 chunk 199 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 158 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN D 298 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.7370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16276 Z= 0.178 Angle : 0.610 13.873 22048 Z= 0.304 Chirality : 0.043 0.222 2464 Planarity : 0.004 0.042 2844 Dihedral : 4.189 18.659 2208 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.76 % Allowed : 19.61 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.04 (0.19), residues: 2000 helix: 0.86 (0.17), residues: 976 sheet: -0.21 (0.40), residues: 200 loop : -0.86 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.016 0.001 HIS D 298 PHE 0.019 0.002 PHE A 445 TYR 0.012 0.001 TYR C 164 ARG 0.003 0.000 ARG C 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 2.043 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 113 average time/residue: 1.0523 time to fit residues: 135.9678 Evaluate side-chains 109 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 395 ASN Chi-restraints excluded: chain C residue 232 GLU Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 553 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 3.9990 chunk 146 optimal weight: 0.0060 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 158 optimal weight: 0.0070 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 overall best weight: 0.9816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS D 298 HIS ** D 479 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.051575 restraints weight = 46154.018| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.26 r_work: 0.2711 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16276 Z= 0.179 Angle : 0.597 13.571 22048 Z= 0.300 Chirality : 0.042 0.192 2464 Planarity : 0.004 0.041 2844 Dihedral : 4.117 18.736 2208 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.64 % Allowed : 19.96 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.19), residues: 2000 helix: 0.90 (0.17), residues: 980 sheet: -0.15 (0.40), residues: 200 loop : -0.84 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 546 HIS 0.019 0.001 HIS D 298 PHE 0.019 0.002 PHE B 445 TYR 0.012 0.001 TYR B 208 ARG 0.003 0.000 ARG C 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.46 seconds wall clock time: 74 minutes 17.99 seconds (4457.99 seconds total)