Starting phenix.real_space_refine on Tue Apr 16 08:03:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1f_35921/04_2024/8j1f_35921_trim_updated.pdb" } resolution = 3.62 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= 0.022 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: 6 Type Number sf(0) Gaussians S 104 5.16 5 Cl 8 4.86 5 C 12448 2.51 5 N 3160 2.21 5 O 3396 1.98 5 H 19280 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 743": "OD1" <-> "OD2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 743": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 369": "OD1" <-> "OD2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 743": "OD1" <-> "OD2" Residue "D PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 420": "OD1" <-> "OD2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 743": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 38396 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9557 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 20, 'TRANS': 566} Chain breaks: 4 Chain: "B" Number of atoms: 9557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9557 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 20, 'TRANS': 566} Chain breaks: 4 Chain: "C" Number of atoms: 9557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9557 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 20, 'TRANS': 566} Chain breaks: 4 Chain: "D" Number of atoms: 9557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 9557 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 20, 'TRANS': 566} Chain breaks: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'XQ3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.56, per 1000 atoms: 0.43 Number of scatterers: 38396 At special positions: 0 Unit cell: (147.87, 147.87, 119.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 8 17.00 S 104 16.00 O 3396 8.00 N 3160 7.00 C 12448 6.00 H 19280 1.00 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: 30.24 Conformation dependent library (CDL) restraints added in 3.7 seconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 8 sheets defined 55.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 163 through 166 No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.661A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 336 through 356 removed outlier: 3.530A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.758A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 453 through 464 removed outlier: 3.657A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 Processing helix chain 'A' and resid 505 through 530 removed outlier: 3.515A pdb=" N PHE A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 568 Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.512A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR A 591 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE A 592 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 595 " --> pdb=" O TYR A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 632 removed outlier: 3.624A pdb=" N PHE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.694A pdb=" N ILE A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 724 Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.913A pdb=" N LYS A 730 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 745 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 163 through 166 No H-bonds generated for 'chain 'B' and resid 163 through 166' Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.661A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 323 through 330 Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.530A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.758A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 446 through 449 No H-bonds generated for 'chain 'B' and resid 446 through 449' Processing helix chain 'B' and resid 453 through 464 removed outlier: 3.657A pdb=" N LEU B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 490 Processing helix chain 'B' and resid 505 through 530 removed outlier: 3.515A pdb=" N PHE B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 568 Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.512A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR B 591 " --> pdb=" O MET B 587 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 595 " --> pdb=" O TYR B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 632 removed outlier: 3.624A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS B 612 " --> pdb=" O LYS B 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 631 " --> pdb=" O GLY B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 679 removed outlier: 3.694A pdb=" N ILE B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 724 Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.912A pdb=" N LYS B 730 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 745 Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 169 through 175 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.661A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 336 through 356 removed outlier: 3.530A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.758A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 446 through 449 No H-bonds generated for 'chain 'C' and resid 446 through 449' Processing helix chain 'C' and resid 453 through 464 removed outlier: 3.657A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 490 Processing helix chain 'C' and resid 505 through 530 removed outlier: 3.515A pdb=" N PHE C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 568 Processing helix chain 'C' and resid 576 through 595 removed outlier: 3.512A pdb=" N LEU C 590 " --> pdb=" O TRP C 586 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR C 591 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE C 592 " --> pdb=" O ASN C 588 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 595 " --> pdb=" O TYR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 632 removed outlier: 3.624A pdb=" N PHE C 611 " --> pdb=" O GLN C 607 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS C 612 " --> pdb=" O LYS C 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 679 removed outlier: 3.695A pdb=" N ILE C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 679 " --> pdb=" O LYS C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 724 Processing helix chain 'C' and resid 726 through 730 removed outlier: 3.913A pdb=" N LYS C 730 " --> pdb=" O LYS C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 163 through 166 No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.661A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 336 through 356 removed outlier: 3.530A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 373 through 379 Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.758A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 446 through 449 No H-bonds generated for 'chain 'D' and resid 446 through 449' Processing helix chain 'D' and resid 453 through 464 removed outlier: 3.657A pdb=" N LEU D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 490 Processing helix chain 'D' and resid 505 through 530 removed outlier: 3.515A pdb=" N PHE D 525 " --> pdb=" O GLY D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 568 Processing helix chain 'D' and resid 576 through 595 removed outlier: 3.512A pdb=" N LEU D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR D 591 " --> pdb=" O MET D 587 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY D 595 " --> pdb=" O TYR D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 632 removed outlier: 3.624A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS D 612 " --> pdb=" O LYS D 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 626 " --> pdb=" O LEU D 622 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 631 " --> pdb=" O GLY D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 679 removed outlier: 3.694A pdb=" N ILE D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 679 " --> pdb=" O LYS D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 724 Processing helix chain 'D' and resid 726 through 730 removed outlier: 3.913A pdb=" N LYS D 730 " --> pdb=" O LYS D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 745 Processing sheet with id= A, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.936A pdb=" N TRP A 409 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 414 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= C, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.936A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 414 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 418 through 420 Processing sheet with id= E, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.936A pdb=" N TRP C 409 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 414 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 418 through 420 Processing sheet with id= G, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.935A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 414 " --> pdb=" O TYR D 411 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 418 through 420 808 hydrogen bonds defined for protein. 2364 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: 14.26 Time building geometry restraints manager: 31.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19248 1.03 - 1.23: 44 1.23 - 1.42: 8180 1.42 - 1.62: 11168 1.62 - 1.81: 184 Bond restraints: 38824 Sorted by residual: bond pdb=" C08 XQ3 A 901 " pdb=" S16 XQ3 A 901 " ideal model delta sigma weight residual 1.549 1.770 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C08 XQ3 B 901 " pdb=" S16 XQ3 B 901 " ideal model delta sigma weight residual 1.549 1.770 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C08 XQ3 C 901 " pdb=" S16 XQ3 C 901 " ideal model delta sigma weight residual 1.549 1.770 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C08 XQ3 D 901 " pdb=" S16 XQ3 D 901 " ideal model delta sigma weight residual 1.549 1.770 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C15 XQ3 A 901 " pdb=" S16 XQ3 A 901 " ideal model delta sigma weight residual 1.570 1.771 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 38819 not shown) Histogram of bond angle deviations from ideal: 70.29 - 83.05: 40 83.05 - 95.81: 4 95.81 - 108.57: 12914 108.57 - 121.34: 50218 121.34 - 134.10: 6904 Bond angle restraints: 70080 Sorted by residual: angle pdb=" C PRO D 638 " pdb=" CA PRO D 638 " pdb=" HA PRO D 638 " ideal model delta sigma weight residual 109.00 70.29 38.71 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C PRO A 638 " pdb=" CA PRO A 638 " pdb=" HA PRO A 638 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C PRO B 638 " pdb=" CA PRO B 638 " pdb=" HA PRO B 638 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C PRO C 638 " pdb=" CA PRO C 638 " pdb=" HA PRO C 638 " ideal model delta sigma weight residual 109.00 70.30 38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" N PRO B 638 " pdb=" CA PRO B 638 " pdb=" HA PRO B 638 " ideal model delta sigma weight residual 110.00 73.41 36.59 3.00e+00 1.11e-01 1.49e+02 ... (remaining 70075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 16969 23.47 - 46.94: 969 46.94 - 70.42: 174 70.42 - 93.89: 52 93.89 - 117.36: 4 Dihedral angle restraints: 18168 sinusoidal: 9808 harmonic: 8360 Sorted by residual: dihedral pdb=" C ASN A 637 " pdb=" N ASN A 637 " pdb=" CA ASN A 637 " pdb=" CB ASN A 637 " ideal model delta harmonic sigma weight residual -122.60 -134.72 12.12 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C ASN D 637 " pdb=" N ASN D 637 " pdb=" CA ASN D 637 " pdb=" CB ASN D 637 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C ASN C 637 " pdb=" N ASN C 637 " pdb=" CA ASN C 637 " pdb=" CB ASN C 637 " ideal model delta harmonic sigma weight residual -122.60 -134.71 12.11 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 18165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3000 0.101 - 0.202: 28 0.202 - 0.303: 0 0.303 - 0.404: 0 0.404 - 0.505: 8 Chirality restraints: 3036 Sorted by residual: chirality pdb=" CA ASN A 637 " pdb=" N ASN A 637 " pdb=" C ASN A 637 " pdb=" CB ASN A 637 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA ASN D 637 " pdb=" N ASN D 637 " pdb=" C ASN D 637 " pdb=" CB ASN D 637 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CA ASN B 637 " pdb=" N ASN B 637 " pdb=" C ASN B 637 " pdb=" CB ASN B 637 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 3033 not shown) Planarity restraints: 5528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 XQ3 D 901 " 0.036 2.00e-02 2.50e+03 4.59e-02 5.26e+01 pdb=" C08 XQ3 D 901 " 0.087 2.00e-02 2.50e+03 pdb=" C09 XQ3 D 901 " -0.070 2.00e-02 2.50e+03 pdb=" C10 XQ3 D 901 " -0.033 2.00e-02 2.50e+03 pdb=" C11 XQ3 D 901 " -0.006 2.00e-02 2.50e+03 pdb=" C12 XQ3 D 901 " 0.027 2.00e-02 2.50e+03 pdb=" C13 XQ3 D 901 " 0.034 2.00e-02 2.50e+03 pdb=" C14 XQ3 D 901 " 0.009 2.00e-02 2.50e+03 pdb=" C15 XQ3 D 901 " -0.024 2.00e-02 2.50e+03 pdb=" S16 XQ3 D 901 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 XQ3 B 901 " -0.036 2.00e-02 2.50e+03 4.58e-02 5.25e+01 pdb=" C08 XQ3 B 901 " -0.087 2.00e-02 2.50e+03 pdb=" C09 XQ3 B 901 " 0.070 2.00e-02 2.50e+03 pdb=" C10 XQ3 B 901 " 0.033 2.00e-02 2.50e+03 pdb=" C11 XQ3 B 901 " 0.006 2.00e-02 2.50e+03 pdb=" C12 XQ3 B 901 " -0.027 2.00e-02 2.50e+03 pdb=" C13 XQ3 B 901 " -0.034 2.00e-02 2.50e+03 pdb=" C14 XQ3 B 901 " -0.009 2.00e-02 2.50e+03 pdb=" C15 XQ3 B 901 " 0.024 2.00e-02 2.50e+03 pdb=" S16 XQ3 B 901 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 XQ3 A 901 " 0.036 2.00e-02 2.50e+03 4.58e-02 5.24e+01 pdb=" C08 XQ3 A 901 " 0.087 2.00e-02 2.50e+03 pdb=" C09 XQ3 A 901 " -0.070 2.00e-02 2.50e+03 pdb=" C10 XQ3 A 901 " -0.033 2.00e-02 2.50e+03 pdb=" C11 XQ3 A 901 " -0.006 2.00e-02 2.50e+03 pdb=" C12 XQ3 A 901 " 0.027 2.00e-02 2.50e+03 pdb=" C13 XQ3 A 901 " 0.034 2.00e-02 2.50e+03 pdb=" C14 XQ3 A 901 " 0.009 2.00e-02 2.50e+03 pdb=" C15 XQ3 A 901 " -0.024 2.00e-02 2.50e+03 pdb=" S16 XQ3 A 901 " -0.060 2.00e-02 2.50e+03 ... (remaining 5525 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 3221 2.20 - 2.80: 82339 2.80 - 3.40: 108872 3.40 - 4.00: 135355 4.00 - 4.60: 210036 Nonbonded interactions: 539823 Sorted by model distance: nonbonded pdb=" OE1 GLU C 760 " pdb=" H GLU C 760 " model vdw 1.606 1.850 nonbonded pdb=" OE1 GLU B 760 " pdb=" H GLU B 760 " model vdw 1.606 1.850 nonbonded pdb=" OE1 GLU D 760 " pdb=" H GLU D 760 " model vdw 1.607 1.850 nonbonded pdb=" OE1 GLU A 760 " pdb=" H GLU A 760 " model vdw 1.607 1.850 nonbonded pdb=" O LEU D 287 " pdb=" H LEU D 291 " model vdw 1.611 1.850 ... (remaining 539818 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 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.620 Extract box with map and model: 7.820 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 117.760 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.221 19544 Z= 0.373 Angle : 0.699 16.725 26488 Z= 0.330 Chirality : 0.043 0.505 3036 Planarity : 0.004 0.062 3276 Dihedral : 14.752 117.359 7124 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.41 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.18), residues: 2308 helix: 0.16 (0.14), residues: 1288 sheet: -2.44 (0.58), residues: 84 loop : -1.84 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 409 HIS 0.003 0.001 HIS B 309 PHE 0.015 0.001 PHE B 615 TYR 0.018 0.001 TYR B 236 ARG 0.004 0.000 ARG C 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 MET cc_start: 0.7376 (ppp) cc_final: 0.7104 (ppp) REVERT: A 713 MET cc_start: 0.8715 (tmm) cc_final: 0.8408 (tmm) REVERT: B 314 MET cc_start: 0.6355 (mtt) cc_final: 0.6135 (mtt) REVERT: B 482 MET cc_start: 0.8032 (mmp) cc_final: 0.7826 (mmp) REVERT: B 680 MET cc_start: 0.7369 (ppp) cc_final: 0.7088 (ppp) REVERT: B 713 MET cc_start: 0.8702 (tmm) cc_final: 0.8404 (tmm) REVERT: C 680 MET cc_start: 0.7389 (ppp) cc_final: 0.7116 (ppp) REVERT: C 713 MET cc_start: 0.8706 (tmm) cc_final: 0.8407 (tmm) REVERT: D 482 MET cc_start: 0.8046 (mmp) cc_final: 0.7843 (mmp) REVERT: D 680 MET cc_start: 0.7389 (ppp) cc_final: 0.7113 (ppp) REVERT: D 713 MET cc_start: 0.8711 (tmm) cc_final: 0.8412 (tmm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.7354 time to fit residues: 282.1263 Evaluate side-chains 213 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 30.0000 chunk 118 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 19544 Z= 0.544 Angle : 0.811 12.382 26488 Z= 0.421 Chirality : 0.050 0.511 3036 Planarity : 0.006 0.066 3276 Dihedral : 8.469 101.819 2644 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.14 % Favored : 88.52 % Rotamer: Outliers : 0.48 % Allowed : 6.97 % Favored : 92.55 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -2.05 (0.17), residues: 2308 helix: -0.61 (0.13), residues: 1364 sheet: -3.60 (0.52), residues: 84 loop : -2.24 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 409 HIS 0.004 0.001 HIS D 243 PHE 0.026 0.003 PHE C 615 TYR 0.020 0.002 TYR B 621 ARG 0.006 0.001 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 228 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7444 (t80) cc_final: 0.7170 (t80) REVERT: A 713 MET cc_start: 0.8857 (tmm) cc_final: 0.8626 (tmm) REVERT: A 743 ASP cc_start: 0.7239 (t0) cc_final: 0.6946 (t0) REVERT: B 346 TYR cc_start: 0.7431 (t80) cc_final: 0.7161 (t80) REVERT: B 482 MET cc_start: 0.8214 (mmp) cc_final: 0.7902 (mmp) REVERT: B 713 MET cc_start: 0.8854 (tmm) cc_final: 0.8625 (tmm) REVERT: B 743 ASP cc_start: 0.7236 (t0) cc_final: 0.6946 (t0) REVERT: C 680 MET cc_start: 0.7485 (ppp) cc_final: 0.7239 (ppp) REVERT: C 713 MET cc_start: 0.8854 (tmm) cc_final: 0.8619 (tmm) REVERT: C 743 ASP cc_start: 0.7240 (t0) cc_final: 0.6940 (t0) REVERT: D 482 MET cc_start: 0.8222 (mmp) cc_final: 0.7913 (mmp) REVERT: D 602 TYR cc_start: 0.6938 (m-80) cc_final: 0.6733 (m-80) REVERT: D 680 MET cc_start: 0.7461 (ppp) cc_final: 0.7216 (ppp) REVERT: D 713 MET cc_start: 0.8858 (tmm) cc_final: 0.8622 (tmm) REVERT: D 743 ASP cc_start: 0.7241 (t0) cc_final: 0.6944 (t0) outliers start: 10 outliers final: 6 residues processed: 236 average time/residue: 0.6791 time to fit residues: 250.8707 Evaluate side-chains 226 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 175 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 30.0000 chunk 211 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 209 optimal weight: 30.0000 chunk 71 optimal weight: 0.8980 chunk 169 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19544 Z= 0.221 Angle : 0.632 12.580 26488 Z= 0.318 Chirality : 0.044 0.514 3036 Planarity : 0.004 0.060 3276 Dihedral : 8.561 113.754 2644 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.75 % Favored : 91.07 % Rotamer: Outliers : 0.10 % Allowed : 9.28 % Favored : 90.62 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.18), residues: 2308 helix: -0.12 (0.14), residues: 1320 sheet: -3.50 (0.52), residues: 84 loop : -2.20 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 409 HIS 0.003 0.001 HIS D 309 PHE 0.019 0.002 PHE A 756 TYR 0.018 0.002 TYR C 553 ARG 0.005 0.000 ARG C 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 TYR cc_start: 0.6853 (m-80) cc_final: 0.6614 (m-80) REVERT: A 713 MET cc_start: 0.8858 (tmm) cc_final: 0.8653 (tmm) REVERT: A 743 ASP cc_start: 0.6900 (t0) cc_final: 0.6595 (t0) REVERT: B 602 TYR cc_start: 0.6886 (m-80) cc_final: 0.6648 (m-80) REVERT: B 713 MET cc_start: 0.8858 (tmm) cc_final: 0.8644 (tmm) REVERT: B 743 ASP cc_start: 0.6902 (t0) cc_final: 0.6599 (t0) REVERT: C 602 TYR cc_start: 0.6897 (m-80) cc_final: 0.6656 (m-80) REVERT: C 713 MET cc_start: 0.8860 (tmm) cc_final: 0.8647 (tmm) REVERT: C 743 ASP cc_start: 0.6942 (t0) cc_final: 0.6644 (t0) REVERT: D 602 TYR cc_start: 0.6885 (m-80) cc_final: 0.6646 (m-80) REVERT: D 680 MET cc_start: 0.7420 (ppp) cc_final: 0.7200 (ppp) REVERT: D 713 MET cc_start: 0.8859 (tmm) cc_final: 0.8648 (tmm) REVERT: D 743 ASP cc_start: 0.6952 (t0) cc_final: 0.6652 (t0) outliers start: 2 outliers final: 2 residues processed: 231 average time/residue: 0.7008 time to fit residues: 254.1737 Evaluate side-chains 224 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain B residue 557 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19544 Z= 0.193 Angle : 0.593 12.907 26488 Z= 0.297 Chirality : 0.043 0.523 3036 Planarity : 0.004 0.054 3276 Dihedral : 8.320 112.799 2644 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.66 % Favored : 90.16 % Rotamer: Outliers : 0.67 % Allowed : 10.67 % Favored : 88.65 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.30 (0.18), residues: 2308 helix: 0.14 (0.14), residues: 1324 sheet: -3.45 (0.53), residues: 84 loop : -2.10 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 409 HIS 0.003 0.001 HIS D 309 PHE 0.018 0.001 PHE C 707 TYR 0.015 0.001 TYR C 553 ARG 0.003 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 244 time to evaluate : 3.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 ASP cc_start: 0.6557 (t0) cc_final: 0.6194 (t0) REVERT: B 743 ASP cc_start: 0.6624 (t0) cc_final: 0.6246 (t0) REVERT: C 743 ASP cc_start: 0.6564 (t0) cc_final: 0.6215 (t0) REVERT: D 743 ASP cc_start: 0.6576 (t0) cc_final: 0.6225 (t0) outliers start: 14 outliers final: 6 residues processed: 252 average time/residue: 0.6714 time to fit residues: 266.5478 Evaluate side-chains 239 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19544 Z= 0.194 Angle : 0.588 12.606 26488 Z= 0.292 Chirality : 0.043 0.517 3036 Planarity : 0.004 0.049 3276 Dihedral : 8.244 112.279 2644 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.84 % Favored : 90.99 % Rotamer: Outliers : 0.29 % Allowed : 11.54 % Favored : 88.17 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.12 (0.18), residues: 2308 helix: 0.32 (0.14), residues: 1320 sheet: -3.42 (0.54), residues: 84 loop : -2.05 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 409 HIS 0.002 0.001 HIS A 326 PHE 0.015 0.001 PHE D 756 TYR 0.016 0.001 TYR C 602 ARG 0.001 0.000 ARG A 757 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 TYR cc_start: 0.7914 (t80) cc_final: 0.7368 (t80) REVERT: A 743 ASP cc_start: 0.6605 (t0) cc_final: 0.6174 (t0) REVERT: B 621 TYR cc_start: 0.7896 (t80) cc_final: 0.7315 (t80) REVERT: B 743 ASP cc_start: 0.6581 (t0) cc_final: 0.6142 (t0) REVERT: C 621 TYR cc_start: 0.7886 (t80) cc_final: 0.7310 (t80) REVERT: C 743 ASP cc_start: 0.6588 (t0) cc_final: 0.6163 (t0) REVERT: D 621 TYR cc_start: 0.7896 (t80) cc_final: 0.7321 (t80) REVERT: D 743 ASP cc_start: 0.6599 (t0) cc_final: 0.6173 (t0) outliers start: 6 outliers final: 6 residues processed: 236 average time/residue: 0.6890 time to fit residues: 252.6758 Evaluate side-chains 230 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 117 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19544 Z= 0.214 Angle : 0.593 12.676 26488 Z= 0.293 Chirality : 0.043 0.511 3036 Planarity : 0.004 0.047 3276 Dihedral : 8.168 111.283 2644 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.14 % Favored : 89.69 % Rotamer: Outliers : 0.67 % Allowed : 11.25 % Favored : 88.08 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.18), residues: 2308 helix: 0.34 (0.14), residues: 1328 sheet: -3.46 (0.55), residues: 84 loop : -2.00 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 409 HIS 0.002 0.001 HIS B 243 PHE 0.017 0.001 PHE C 756 TYR 0.016 0.001 TYR D 602 ARG 0.002 0.000 ARG B 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 743 ASP cc_start: 0.6606 (t0) cc_final: 0.6162 (t0) REVERT: B 743 ASP cc_start: 0.6605 (t0) cc_final: 0.6156 (t0) REVERT: C 621 TYR cc_start: 0.7640 (t80) cc_final: 0.7217 (t80) REVERT: C 743 ASP cc_start: 0.6612 (t0) cc_final: 0.6161 (t0) REVERT: D 743 ASP cc_start: 0.6622 (t0) cc_final: 0.6171 (t0) outliers start: 14 outliers final: 10 residues processed: 232 average time/residue: 0.6823 time to fit residues: 251.4955 Evaluate side-chains 231 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 221 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 188 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19544 Z= 0.224 Angle : 0.593 12.987 26488 Z= 0.295 Chirality : 0.043 0.515 3036 Planarity : 0.004 0.045 3276 Dihedral : 8.134 110.992 2644 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.71 % Favored : 90.12 % Rotamer: Outliers : 0.87 % Allowed : 11.39 % Favored : 87.74 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.18), residues: 2308 helix: 0.40 (0.14), residues: 1324 sheet: -3.51 (0.55), residues: 84 loop : -2.01 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 409 HIS 0.002 0.001 HIS B 243 PHE 0.018 0.001 PHE A 756 TYR 0.018 0.002 TYR B 602 ARG 0.002 0.000 ARG C 315 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 TYR cc_start: 0.7564 (t80) cc_final: 0.7121 (t80) REVERT: A 743 ASP cc_start: 0.6690 (t0) cc_final: 0.6216 (t0) REVERT: B 621 TYR cc_start: 0.7574 (t80) cc_final: 0.7133 (t80) REVERT: B 743 ASP cc_start: 0.6685 (t0) cc_final: 0.6208 (t0) REVERT: C 621 TYR cc_start: 0.7559 (t80) cc_final: 0.7121 (t80) REVERT: C 743 ASP cc_start: 0.6699 (t0) cc_final: 0.6217 (t0) REVERT: D 621 TYR cc_start: 0.7561 (t80) cc_final: 0.7127 (t80) REVERT: D 743 ASP cc_start: 0.6690 (t0) cc_final: 0.6204 (t0) outliers start: 18 outliers final: 18 residues processed: 226 average time/residue: 0.6668 time to fit residues: 237.3189 Evaluate side-chains 243 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 225 time to evaluate : 3.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN C 588 ASN D 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19544 Z= 0.340 Angle : 0.654 12.983 26488 Z= 0.330 Chirality : 0.044 0.521 3036 Planarity : 0.004 0.046 3276 Dihedral : 8.118 107.846 2644 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.96 % Favored : 87.91 % Rotamer: Outliers : 1.25 % Allowed : 11.73 % Favored : 87.02 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.18), residues: 2308 helix: 0.09 (0.14), residues: 1320 sheet: -3.72 (0.54), residues: 84 loop : -2.09 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 463 HIS 0.005 0.001 HIS B 243 PHE 0.026 0.002 PHE C 756 TYR 0.033 0.002 TYR B 621 ARG 0.003 0.000 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 2.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 TYR cc_start: 0.7294 (t80) cc_final: 0.7080 (t80) REVERT: A 621 TYR cc_start: 0.7738 (t80) cc_final: 0.7370 (t80) REVERT: A 743 ASP cc_start: 0.6682 (t0) cc_final: 0.6224 (t0) REVERT: B 346 TYR cc_start: 0.7273 (t80) cc_final: 0.7062 (t80) REVERT: B 621 TYR cc_start: 0.7801 (t80) cc_final: 0.7546 (t80) REVERT: B 743 ASP cc_start: 0.6679 (t0) cc_final: 0.6218 (t0) REVERT: C 346 TYR cc_start: 0.7288 (t80) cc_final: 0.7067 (t80) REVERT: C 621 TYR cc_start: 0.7782 (t80) cc_final: 0.7528 (t80) REVERT: C 743 ASP cc_start: 0.6691 (t0) cc_final: 0.6229 (t0) REVERT: D 346 TYR cc_start: 0.7293 (t80) cc_final: 0.7071 (t80) REVERT: D 621 TYR cc_start: 0.7777 (t80) cc_final: 0.7519 (t80) REVERT: D 743 ASP cc_start: 0.6686 (t0) cc_final: 0.6220 (t0) outliers start: 26 outliers final: 17 residues processed: 224 average time/residue: 0.6957 time to fit residues: 246.6767 Evaluate side-chains 234 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 217 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 339 THR Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.1980 chunk 208 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19544 Z= 0.177 Angle : 0.590 12.866 26488 Z= 0.290 Chirality : 0.042 0.515 3036 Planarity : 0.004 0.044 3276 Dihedral : 8.210 112.683 2644 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.67 % Allowed : 12.16 % Favored : 87.16 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.18), residues: 2308 helix: 0.47 (0.14), residues: 1320 sheet: -3.62 (0.54), residues: 84 loop : -2.05 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 409 HIS 0.003 0.001 HIS C 326 PHE 0.016 0.001 PHE C 756 TYR 0.017 0.001 TYR C 602 ARG 0.001 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 223 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 TYR cc_start: 0.6852 (t80) cc_final: 0.6161 (t80) REVERT: A 621 TYR cc_start: 0.7571 (t80) cc_final: 0.7125 (t80) REVERT: A 743 ASP cc_start: 0.6458 (t0) cc_final: 0.5950 (t0) REVERT: B 553 TYR cc_start: 0.6793 (t80) cc_final: 0.6063 (t80) REVERT: B 621 TYR cc_start: 0.7634 (t80) cc_final: 0.7198 (t80) REVERT: B 743 ASP cc_start: 0.6463 (t0) cc_final: 0.5947 (t0) REVERT: C 621 TYR cc_start: 0.7604 (t80) cc_final: 0.7167 (t80) REVERT: C 743 ASP cc_start: 0.6473 (t0) cc_final: 0.5957 (t0) REVERT: D 553 TYR cc_start: 0.6739 (t80) cc_final: 0.6094 (t80) REVERT: D 621 TYR cc_start: 0.7601 (t80) cc_final: 0.7165 (t80) REVERT: D 743 ASP cc_start: 0.6471 (t0) cc_final: 0.5951 (t0) outliers start: 14 outliers final: 11 residues processed: 223 average time/residue: 0.6695 time to fit residues: 233.6778 Evaluate side-chains 232 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN ** B 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 ASN ** D 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19544 Z= 0.209 Angle : 0.594 13.016 26488 Z= 0.293 Chirality : 0.043 0.520 3036 Planarity : 0.004 0.043 3276 Dihedral : 8.071 110.966 2644 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 0.58 % Allowed : 11.83 % Favored : 87.60 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.18), residues: 2308 helix: 0.51 (0.14), residues: 1320 sheet: -3.67 (0.53), residues: 84 loop : -2.02 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.003 0.001 HIS B 243 PHE 0.017 0.001 PHE D 756 TYR 0.018 0.001 TYR A 621 ARG 0.005 0.000 ARG D 774 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 3.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 TYR cc_start: 0.7426 (t80) cc_final: 0.6944 (t80) REVERT: A 743 ASP cc_start: 0.6587 (t0) cc_final: 0.6039 (t0) REVERT: B 621 TYR cc_start: 0.7408 (t80) cc_final: 0.6877 (t80) REVERT: B 743 ASP cc_start: 0.6571 (t0) cc_final: 0.6027 (t0) REVERT: C 621 TYR cc_start: 0.7424 (t80) cc_final: 0.6920 (t80) REVERT: C 743 ASP cc_start: 0.6599 (t0) cc_final: 0.6049 (t0) REVERT: D 621 TYR cc_start: 0.7410 (t80) cc_final: 0.6905 (t80) REVERT: D 743 ASP cc_start: 0.6604 (t0) cc_final: 0.6051 (t0) outliers start: 12 outliers final: 9 residues processed: 227 average time/residue: 0.6878 time to fit residues: 245.0998 Evaluate side-chains 232 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 632 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN ** A 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 712 ASN ** 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 = 0.4681 r_free = 0.4681 target = 0.180923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.147078 restraints weight = 127570.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.152799 restraints weight = 61577.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.156370 restraints weight = 39801.544| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19544 Z= 0.228 Angle : 0.599 12.974 26488 Z= 0.295 Chirality : 0.043 0.521 3036 Planarity : 0.004 0.043 3276 Dihedral : 8.041 109.989 2644 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 0.62 % Allowed : 11.92 % Favored : 87.45 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.18), residues: 2308 helix: 0.48 (0.14), residues: 1320 sheet: -3.66 (0.54), residues: 84 loop : -2.04 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.002 0.001 HIS B 243 PHE 0.019 0.001 PHE C 756 TYR 0.017 0.002 TYR A 602 ARG 0.002 0.000 ARG D 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6610.24 seconds wall clock time: 119 minutes 37.60 seconds (7177.60 seconds total)