Starting phenix.real_space_refine on Wed Feb 14 22:14:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hip_34825/02_2024/8hip_34825_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hip_34825/02_2024/8hip_34825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hip_34825/02_2024/8hip_34825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hip_34825/02_2024/8hip_34825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hip_34825/02_2024/8hip_34825_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hip_34825/02_2024/8hip_34825_updated.pdb" } resolution = 2.77 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= 0.001 sd= 0.132 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 66 5.16 5 C 6788 2.51 5 N 1684 2.21 5 O 1856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 39": "OE1" <-> "OE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 762": "OD1" <-> "OD2" Residue "B ASP 763": "OD1" <-> "OD2" Residue "B ASP 764": "OD1" <-> "OD2" Residue "B PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A ASP 764": "OD1" <-> "OD2" Residue "A PHE 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10396 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5099 Classifications: {'peptide': 647} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5099 Classifications: {'peptide': 647} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' ZN': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' ZN': 1, '6OU': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.22, per 1000 atoms: 0.60 Number of scatterers: 10396 At special positions: 0 Unit cell: (90.48, 86.32, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 66 16.00 O 1856 8.00 N 1684 7.00 C 6788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 542 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN B 205 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN B 234 " " NAG F 1 " - " ASN A 205 " Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 803 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 540 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 740 " pdb="ZN ZN A 803 " - pdb=" NE2 HIS A 744 " pdb=" ZN B 803 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 540 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 740 " pdb="ZN ZN B 803 " - pdb=" NE2 HIS B 744 " 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 10 sheets defined 43.9% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 81 through 84 Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 206 through 209 No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 315 through 343 Proline residue: B 328 - end of helix removed outlier: 5.040A pdb=" N LEU B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 333 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Proline residue: B 334 - end of helix removed outlier: 3.638A pdb=" N ILE B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 439 through 453 Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 481 through 502 removed outlier: 4.582A pdb=" N ASN B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 488 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 490 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 539 removed outlier: 3.629A pdb=" N SER B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 568 removed outlier: 3.539A pdb=" N MET B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 595 removed outlier: 3.507A pdb=" N ASN B 580 " --> pdb=" O ALA B 577 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 581 " --> pdb=" O TYR B 578 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 584 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 585 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 587 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 588 " --> pdb=" O GLY B 585 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 590 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 591 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 593 " --> pdb=" O ASN B 590 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 595 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 625 removed outlier: 3.547A pdb=" N GLU B 622 " --> pdb=" O CYS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 650 removed outlier: 3.638A pdb=" N MET B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 683 removed outlier: 4.369A pdb=" N ALA B 662 " --> pdb=" O LEU B 658 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 663 " --> pdb=" O ASN B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 712 removed outlier: 4.085A pdb=" N GLN B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 739 through 767 removed outlier: 3.617A pdb=" N ALA B 748 " --> pdb=" O HIS B 744 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP B 764 " --> pdb=" O PHE B 760 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B 765 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ILE B 766 " --> pdb=" O ASP B 762 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASN B 767 " --> pdb=" O ASP B 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 81 through 84 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 206 through 209 No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 315 through 343 Proline residue: A 328 - end of helix removed outlier: 5.041A pdb=" N LEU A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.638A pdb=" N ILE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 439 through 453 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 481 through 502 removed outlier: 4.582A pdb=" N ASN A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 539 removed outlier: 3.629A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 568 removed outlier: 3.538A pdb=" N MET A 563 " --> pdb=" O CYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 595 removed outlier: 3.507A pdb=" N ASN A 580 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 581 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 584 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 585 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 587 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 588 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN A 590 " --> pdb=" O VAL A 587 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE A 591 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 593 " --> pdb=" O ASN A 590 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 595 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 625 removed outlier: 3.547A pdb=" N GLU A 622 " --> pdb=" O CYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.638A pdb=" N MET A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 removed outlier: 4.369A pdb=" N ALA A 662 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 663 " --> pdb=" O ASN A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 712 removed outlier: 4.085A pdb=" N GLN A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 739 through 767 removed outlier: 3.617A pdb=" N ALA A 748 " --> pdb=" O HIS A 744 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 762 " --> pdb=" O VAL A 758 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASP A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 765 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE A 766 " --> pdb=" O ASP A 762 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.371A pdb=" N VAL B 56 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE B 38 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 58 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.686A pdb=" N THR B 72 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 186 through 189 removed outlier: 3.516A pdb=" N GLN B 213 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 192 through 194 Processing sheet with id= E, first strand: chain 'B' and resid 200 through 205 Processing sheet with id= F, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.371A pdb=" N VAL A 56 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 38 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 58 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 46 through 51 removed outlier: 3.686A pdb=" N THR A 72 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 186 through 189 removed outlier: 3.516A pdb=" N GLN A 213 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 192 through 194 Processing sheet with id= J, first strand: chain 'A' and resid 200 through 205 486 hydrogen bonds defined for protein. 1356 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: 3.42 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1626 1.32 - 1.44: 2944 1.44 - 1.56: 5954 1.56 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 10622 Sorted by residual: bond pdb=" C31 6OU B 802 " pdb=" O30 6OU B 802 " ideal model delta sigma weight residual 1.331 1.202 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C31 6OU A 802 " pdb=" O30 6OU A 802 " ideal model delta sigma weight residual 1.331 1.203 0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C ILE B 229 " pdb=" O ILE B 229 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.11e-02 8.12e+03 1.33e+01 bond pdb=" C ILE A 229 " pdb=" O ILE A 229 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.11e-02 8.12e+03 1.33e+01 bond pdb=" C HIS A 740 " pdb=" O HIS A 740 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.19e-02 7.06e+03 8.68e+00 ... (remaining 10617 not shown) Histogram of bond angle deviations from ideal: 88.22 - 97.40: 2 97.40 - 106.57: 225 106.57 - 115.74: 6731 115.74 - 124.91: 7290 124.91 - 134.09: 130 Bond angle restraints: 14378 Sorted by residual: angle pdb=" N TYR A 175 " pdb=" CA TYR A 175 " pdb=" C TYR A 175 " ideal model delta sigma weight residual 109.41 88.22 21.19 1.52e+00 4.33e-01 1.94e+02 angle pdb=" N TYR B 175 " pdb=" CA TYR B 175 " pdb=" C TYR B 175 " ideal model delta sigma weight residual 109.50 88.76 20.74 1.58e+00 4.01e-01 1.72e+02 angle pdb=" C ILE A 237 " pdb=" CA ILE A 237 " pdb=" CB ILE A 237 " ideal model delta sigma weight residual 112.14 99.12 13.02 1.35e+00 5.49e-01 9.30e+01 angle pdb=" C ILE B 237 " pdb=" CA ILE B 237 " pdb=" CB ILE B 237 " ideal model delta sigma weight residual 112.14 99.16 12.98 1.35e+00 5.49e-01 9.25e+01 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 113.88 106.53 7.35 1.23e+00 6.61e-01 3.57e+01 ... (remaining 14373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 6092 23.07 - 46.14: 252 46.14 - 69.21: 37 69.21 - 92.28: 12 92.28 - 115.35: 3 Dihedral angle restraints: 6396 sinusoidal: 2582 harmonic: 3814 Sorted by residual: dihedral pdb=" CB CYS B 225 " pdb=" SG CYS B 225 " pdb=" SG CYS B 287 " pdb=" CB CYS B 287 " ideal model delta sinusoidal sigma weight residual -86.00 -131.13 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" CB CYS A 225 " pdb=" SG CYS A 225 " pdb=" SG CYS A 287 " pdb=" CB CYS A 287 " ideal model delta sinusoidal sigma weight residual -86.00 -131.13 45.13 1 1.00e+01 1.00e-02 2.83e+01 dihedral pdb=" C ASN A 234 " pdb=" N ASN A 234 " pdb=" CA ASN A 234 " pdb=" CB ASN A 234 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 6393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.405: 1707 0.405 - 0.811: 5 0.811 - 1.216: 0 1.216 - 1.621: 0 1.621 - 2.027: 2 Chirality restraints: 1714 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.03e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.37 -2.03 2.00e-01 2.50e+01 1.03e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.41 -1.99 2.00e-01 2.50e+01 9.87e+01 ... (remaining 1711 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 205 " 0.161 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" CG ASN B 205 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 205 " -0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN B 205 " -0.258 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 205 " -0.159 2.00e-02 2.50e+03 1.63e-01 3.31e+02 pdb=" CG ASN A 205 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 205 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 205 " 0.254 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.130 2.00e-02 2.50e+03 1.07e-01 1.42e+02 pdb=" C7 NAG E 2 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.169 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.022 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.09: 6886 3.09 - 3.69: 15325 3.69 - 4.30: 25250 4.30 - 4.90: 40934 Nonbonded interactions: 88460 Sorted by model distance: nonbonded pdb=" OG SER B 244 " pdb=" CE1 HIS A 248 " model vdw 1.885 3.260 nonbonded pdb=" CE1 HIS B 248 " pdb=" OG SER A 244 " model vdw 1.889 3.260 nonbonded pdb=" N TYR A 175 " pdb=" O TYR A 175 " model vdw 2.080 2.496 nonbonded pdb=" N TYR B 175 " pdb=" O TYR B 175 " model vdw 2.145 2.496 nonbonded pdb=" O VAL B 648 " pdb=" OG1 THR B 652 " model vdw 2.240 2.440 ... (remaining 88455 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' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.710 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: 0.000 Extract box with map and model: 7.390 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 34.240 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.129 10622 Z= 0.376 Angle : 0.805 21.187 14378 Z= 0.466 Chirality : 0.089 2.027 1714 Planarity : 0.008 0.107 1762 Dihedral : 13.364 115.353 3896 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.20), residues: 1278 helix: -3.54 (0.12), residues: 550 sheet: 0.84 (0.31), residues: 266 loop : -1.42 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 717 HIS 0.003 0.001 HIS A 540 PHE 0.014 0.001 PHE B 639 TYR 0.018 0.002 TYR B 650 ARG 0.005 0.000 ARG B 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.188 Fit side-chains REVERT: B 52 GLU cc_start: 0.7505 (mp0) cc_final: 0.7211 (mp0) REVERT: B 312 GLN cc_start: 0.8158 (pt0) cc_final: 0.7954 (pt0) REVERT: B 449 PHE cc_start: 0.7552 (m-80) cc_final: 0.7086 (t80) REVERT: B 451 LYS cc_start: 0.8341 (tmmt) cc_final: 0.7955 (tmmt) REVERT: B 522 ASP cc_start: 0.8179 (m-30) cc_final: 0.7859 (m-30) REVERT: B 634 PHE cc_start: 0.7374 (m-80) cc_final: 0.6129 (p90) REVERT: B 641 MET cc_start: 0.7236 (mmp) cc_final: 0.6979 (mmt) REVERT: B 675 MET cc_start: 0.8527 (mtm) cc_final: 0.8311 (mtp) REVERT: B 729 LYS cc_start: 0.7659 (mtmm) cc_final: 0.7041 (mmtt) REVERT: A 52 GLU cc_start: 0.7525 (mp0) cc_final: 0.7218 (mp0) REVERT: A 312 GLN cc_start: 0.8161 (pt0) cc_final: 0.7908 (pt0) REVERT: A 449 PHE cc_start: 0.7551 (m-80) cc_final: 0.7073 (t80) REVERT: A 451 LYS cc_start: 0.8355 (tmmt) cc_final: 0.7973 (tmmt) REVERT: A 522 ASP cc_start: 0.8127 (m-30) cc_final: 0.7843 (m-30) REVERT: A 634 PHE cc_start: 0.7339 (m-80) cc_final: 0.6130 (p90) REVERT: A 675 MET cc_start: 0.8518 (mtm) cc_final: 0.8290 (mtp) REVERT: A 729 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7047 (mmtt) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 1.0598 time to fit residues: 240.6411 Evaluate side-chains 146 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 ASN B 57 HIS B 248 HIS B 342 ASN B 432 GLN B 468 HIS B 482 ASN B 566 GLN B 728 ASN A 57 HIS A 248 HIS A 342 ASN A 432 GLN A 450 HIS A 468 HIS A 482 ASN A 566 GLN A 728 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 10622 Z= 0.589 Angle : 0.766 8.594 14378 Z= 0.397 Chirality : 0.053 0.174 1714 Planarity : 0.006 0.077 1762 Dihedral : 9.154 91.274 1610 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.12 % Allowed : 10.43 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.22), residues: 1278 helix: -0.92 (0.19), residues: 538 sheet: 1.25 (0.32), residues: 270 loop : -1.24 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 717 HIS 0.010 0.002 HIS A 248 PHE 0.019 0.003 PHE B 528 TYR 0.021 0.003 TYR A 673 ARG 0.004 0.001 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 1.147 Fit side-chains REVERT: B 45 LYS cc_start: 0.7945 (mmpt) cc_final: 0.6986 (tptp) REVERT: B 52 GLU cc_start: 0.7604 (mp0) cc_final: 0.7213 (mp0) REVERT: B 449 PHE cc_start: 0.7529 (m-80) cc_final: 0.6998 (t80) REVERT: B 451 LYS cc_start: 0.8401 (tmmt) cc_final: 0.7971 (tmmt) REVERT: B 634 PHE cc_start: 0.7307 (m-80) cc_final: 0.6072 (p90) REVERT: B 729 LYS cc_start: 0.7837 (mtmm) cc_final: 0.7092 (mmmt) REVERT: A 45 LYS cc_start: 0.7954 (mmpt) cc_final: 0.6998 (tptp) REVERT: A 52 GLU cc_start: 0.7631 (mp0) cc_final: 0.7234 (mp0) REVERT: A 449 PHE cc_start: 0.7489 (m-80) cc_final: 0.7006 (t80) REVERT: A 451 LYS cc_start: 0.8441 (tmmt) cc_final: 0.8014 (tmmt) REVERT: A 634 PHE cc_start: 0.7324 (m-80) cc_final: 0.6160 (p90) REVERT: A 641 MET cc_start: 0.7182 (mmt) cc_final: 0.6823 (mmt) REVERT: A 675 MET cc_start: 0.8615 (mtm) cc_final: 0.8415 (mtp) REVERT: A 729 LYS cc_start: 0.7834 (mtmm) cc_final: 0.7098 (mmmt) outliers start: 35 outliers final: 14 residues processed: 158 average time/residue: 1.0769 time to fit residues: 186.3534 Evaluate side-chains 133 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 116 optimal weight: 0.0020 chunk 125 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 GLN B 450 HIS B 466 HIS B 660 GLN B 728 ASN A 54 ASN A 450 HIS A 466 HIS A 660 GLN A 728 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10622 Z= 0.188 Angle : 0.530 6.525 14378 Z= 0.282 Chirality : 0.042 0.167 1714 Planarity : 0.004 0.062 1762 Dihedral : 8.127 74.595 1610 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 12.12 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1278 helix: 0.63 (0.22), residues: 534 sheet: 1.43 (0.32), residues: 270 loop : -0.74 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 567 HIS 0.003 0.001 HIS A 740 PHE 0.010 0.001 PHE A 528 TYR 0.015 0.001 TYR B 650 ARG 0.002 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.210 Fit side-chains REVERT: B 45 LYS cc_start: 0.7859 (mmpt) cc_final: 0.6910 (tptp) REVERT: B 52 GLU cc_start: 0.7600 (mp0) cc_final: 0.7139 (mp0) REVERT: B 449 PHE cc_start: 0.7406 (m-80) cc_final: 0.6937 (t80) REVERT: B 463 MET cc_start: 0.7991 (ttp) cc_final: 0.7771 (ptt) REVERT: B 634 PHE cc_start: 0.7289 (m-80) cc_final: 0.6045 (p90) REVERT: B 729 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7026 (mmmt) REVERT: B 766 ILE cc_start: 0.7974 (tp) cc_final: 0.7351 (pp) REVERT: A 45 LYS cc_start: 0.7869 (mmpt) cc_final: 0.6924 (tptp) REVERT: A 52 GLU cc_start: 0.7605 (mp0) cc_final: 0.7135 (mp0) REVERT: A 449 PHE cc_start: 0.7427 (m-80) cc_final: 0.6948 (t80) REVERT: A 463 MET cc_start: 0.8007 (ttp) cc_final: 0.7782 (ptt) REVERT: A 634 PHE cc_start: 0.7280 (m-80) cc_final: 0.6045 (p90) REVERT: A 675 MET cc_start: 0.8479 (mtm) cc_final: 0.8154 (mtp) REVERT: A 729 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7024 (mmmt) outliers start: 29 outliers final: 19 residues processed: 153 average time/residue: 0.9559 time to fit residues: 160.7854 Evaluate side-chains 136 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 728 ASN ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS A 728 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10622 Z= 0.277 Angle : 0.560 6.923 14378 Z= 0.293 Chirality : 0.044 0.160 1714 Planarity : 0.004 0.062 1762 Dihedral : 7.870 65.753 1610 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.57 % Allowed : 12.75 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1278 helix: 1.23 (0.23), residues: 534 sheet: 1.47 (0.32), residues: 270 loop : -0.62 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 567 HIS 0.003 0.001 HIS B 450 PHE 0.013 0.001 PHE B 528 TYR 0.017 0.001 TYR A 650 ARG 0.002 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.096 Fit side-chains REVERT: B 45 LYS cc_start: 0.7920 (mmtt) cc_final: 0.6929 (tptp) REVERT: B 52 GLU cc_start: 0.7596 (mp0) cc_final: 0.7099 (mp0) REVERT: B 287 CYS cc_start: 0.7032 (p) cc_final: 0.6580 (p) REVERT: B 449 PHE cc_start: 0.7428 (m-80) cc_final: 0.6976 (t80) REVERT: B 451 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7614 (tttm) REVERT: B 634 PHE cc_start: 0.7275 (m-80) cc_final: 0.6057 (p90) REVERT: B 659 ASN cc_start: 0.7297 (m110) cc_final: 0.6973 (OUTLIER) REVERT: B 729 LYS cc_start: 0.7774 (mtmm) cc_final: 0.7022 (mmmt) REVERT: B 766 ILE cc_start: 0.7974 (tp) cc_final: 0.7380 (pp) REVERT: A 45 LYS cc_start: 0.7906 (mmtt) cc_final: 0.6933 (tptp) REVERT: A 52 GLU cc_start: 0.7599 (mp0) cc_final: 0.7092 (mp0) REVERT: A 287 CYS cc_start: 0.7043 (p) cc_final: 0.6583 (p) REVERT: A 449 PHE cc_start: 0.7452 (m-80) cc_final: 0.6983 (t80) REVERT: A 451 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7616 (tttm) REVERT: A 634 PHE cc_start: 0.7264 (m-80) cc_final: 0.6053 (p90) REVERT: A 675 MET cc_start: 0.8519 (mtm) cc_final: 0.8234 (mtp) REVERT: A 729 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7034 (mmmt) outliers start: 40 outliers final: 25 residues processed: 156 average time/residue: 0.9283 time to fit residues: 159.6575 Evaluate side-chains 145 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 663 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 HIS B 728 ASN A 192 GLN A 450 HIS A 728 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10622 Z= 0.314 Angle : 0.582 6.933 14378 Z= 0.302 Chirality : 0.045 0.156 1714 Planarity : 0.004 0.064 1762 Dihedral : 7.767 57.517 1608 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.39 % Allowed : 13.55 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1278 helix: 1.41 (0.22), residues: 534 sheet: 1.47 (0.33), residues: 270 loop : -0.50 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 567 HIS 0.004 0.001 HIS B 450 PHE 0.012 0.002 PHE B 746 TYR 0.017 0.002 TYR A 650 ARG 0.002 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 1.494 Fit side-chains REVERT: B 45 LYS cc_start: 0.7916 (mmtt) cc_final: 0.6955 (tptp) REVERT: B 52 GLU cc_start: 0.7609 (mp0) cc_final: 0.7107 (mp0) REVERT: B 449 PHE cc_start: 0.7437 (m-80) cc_final: 0.6982 (t80) REVERT: B 451 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7603 (tttm) REVERT: B 634 PHE cc_start: 0.7253 (m-80) cc_final: 0.6048 (p90) REVERT: B 659 ASN cc_start: 0.7372 (m110) cc_final: 0.7088 (OUTLIER) REVERT: B 712 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7575 (mm110) REVERT: B 729 LYS cc_start: 0.7779 (mtmm) cc_final: 0.7017 (mmmt) REVERT: B 766 ILE cc_start: 0.7957 (tp) cc_final: 0.7389 (pp) REVERT: A 45 LYS cc_start: 0.7928 (mmtt) cc_final: 0.6951 (tptp) REVERT: A 52 GLU cc_start: 0.7639 (mp0) cc_final: 0.7124 (mp0) REVERT: A 449 PHE cc_start: 0.7403 (m-80) cc_final: 0.6993 (t80) REVERT: A 451 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7602 (tttm) REVERT: A 634 PHE cc_start: 0.7241 (m-80) cc_final: 0.6036 (p90) REVERT: A 675 MET cc_start: 0.8526 (mtm) cc_final: 0.8229 (mtp) REVERT: A 729 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7030 (mmmt) outliers start: 38 outliers final: 28 residues processed: 154 average time/residue: 1.0777 time to fit residues: 181.5732 Evaluate side-chains 147 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 659 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 GLN B 450 HIS B 728 ASN A 450 HIS A 728 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10622 Z= 0.393 Angle : 0.625 7.138 14378 Z= 0.324 Chirality : 0.047 0.159 1714 Planarity : 0.004 0.067 1762 Dihedral : 7.976 58.403 1608 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.65 % Allowed : 14.71 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1278 helix: 1.43 (0.23), residues: 522 sheet: 1.65 (0.32), residues: 266 loop : -0.72 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 717 HIS 0.005 0.001 HIS B 450 PHE 0.015 0.002 PHE A 528 TYR 0.018 0.002 TYR A 673 ARG 0.003 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7988 (mmtt) cc_final: 0.6962 (tptp) REVERT: B 52 GLU cc_start: 0.7694 (mp0) cc_final: 0.7177 (mp0) REVERT: B 449 PHE cc_start: 0.7403 (m-80) cc_final: 0.6996 (t80) REVERT: B 451 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7618 (tttm) REVERT: B 712 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7868 (mm-40) REVERT: B 729 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7000 (mmmt) REVERT: A 45 LYS cc_start: 0.7980 (mmtt) cc_final: 0.6963 (tptp) REVERT: A 52 GLU cc_start: 0.7699 (mp0) cc_final: 0.7162 (mp0) REVERT: A 449 PHE cc_start: 0.7441 (m-80) cc_final: 0.7024 (t80) REVERT: A 451 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7619 (tttm) REVERT: A 675 MET cc_start: 0.8524 (mtm) cc_final: 0.8212 (mtp) REVERT: A 729 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7073 (mmmt) outliers start: 41 outliers final: 28 residues processed: 152 average time/residue: 0.9892 time to fit residues: 165.0023 Evaluate side-chains 151 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain B residue 712 GLN Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 728 ASN A 450 HIS A 728 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10622 Z= 0.245 Angle : 0.548 6.556 14378 Z= 0.288 Chirality : 0.044 0.154 1714 Planarity : 0.004 0.064 1762 Dihedral : 7.716 59.481 1608 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.30 % Allowed : 15.15 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1278 helix: 1.74 (0.23), residues: 522 sheet: 1.63 (0.33), residues: 266 loop : -0.60 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 567 HIS 0.002 0.001 HIS B 450 PHE 0.011 0.001 PHE B 528 TYR 0.016 0.001 TYR A 650 ARG 0.003 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.078 Fit side-chains REVERT: B 45 LYS cc_start: 0.7973 (mmtt) cc_final: 0.6968 (tptp) REVERT: B 52 GLU cc_start: 0.7654 (mp0) cc_final: 0.7127 (mp0) REVERT: B 287 CYS cc_start: 0.7017 (p) cc_final: 0.6442 (p) REVERT: B 449 PHE cc_start: 0.7372 (m-80) cc_final: 0.6976 (t80) REVERT: B 451 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: A 45 LYS cc_start: 0.7963 (mmtt) cc_final: 0.6969 (tptp) REVERT: A 287 CYS cc_start: 0.7033 (p) cc_final: 0.6448 (p) REVERT: A 449 PHE cc_start: 0.7396 (m-80) cc_final: 0.6986 (t80) REVERT: A 451 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7563 (tttm) REVERT: A 675 MET cc_start: 0.8524 (mtm) cc_final: 0.8215 (mtp) REVERT: A 729 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7000 (mmmt) outliers start: 37 outliers final: 29 residues processed: 146 average time/residue: 0.9459 time to fit residues: 151.9714 Evaluate side-chains 147 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 728 ASN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 728 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS A 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10622 Z= 0.397 Angle : 0.616 6.961 14378 Z= 0.320 Chirality : 0.047 0.158 1714 Planarity : 0.004 0.066 1762 Dihedral : 7.892 64.734 1608 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.30 % Allowed : 15.24 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1278 helix: 1.59 (0.23), residues: 522 sheet: 1.66 (0.33), residues: 266 loop : -0.67 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 717 HIS 0.004 0.001 HIS B 450 PHE 0.015 0.002 PHE B 528 TYR 0.018 0.002 TYR A 673 ARG 0.003 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.290 Fit side-chains REVERT: B 45 LYS cc_start: 0.7997 (mmtt) cc_final: 0.6961 (tptp) REVERT: B 52 GLU cc_start: 0.7695 (mp0) cc_final: 0.7166 (mp0) REVERT: B 287 CYS cc_start: 0.7118 (p) cc_final: 0.6582 (p) REVERT: B 307 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7879 (mtpt) REVERT: B 449 PHE cc_start: 0.7422 (m-80) cc_final: 0.7013 (t80) REVERT: B 451 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7585 (tttm) REVERT: B 729 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7028 (mmmt) REVERT: A 45 LYS cc_start: 0.7990 (mmtt) cc_final: 0.6963 (tptp) REVERT: A 287 CYS cc_start: 0.7116 (p) cc_final: 0.6576 (p) REVERT: A 449 PHE cc_start: 0.7448 (m-80) cc_final: 0.7024 (t80) REVERT: A 451 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7587 (tttm) REVERT: A 675 MET cc_start: 0.8533 (mtm) cc_final: 0.8222 (mtp) REVERT: A 729 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7057 (mmmt) outliers start: 37 outliers final: 30 residues processed: 145 average time/residue: 1.0005 time to fit residues: 159.0538 Evaluate side-chains 150 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 772 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS A 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10622 Z= 0.223 Angle : 0.532 6.885 14378 Z= 0.281 Chirality : 0.043 0.154 1714 Planarity : 0.004 0.064 1762 Dihedral : 7.607 65.824 1608 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.94 % Allowed : 15.24 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1278 helix: 1.88 (0.23), residues: 522 sheet: 1.74 (0.33), residues: 260 loop : -0.56 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 567 HIS 0.003 0.001 HIS A 450 PHE 0.011 0.001 PHE B 528 TYR 0.015 0.001 TYR B 650 ARG 0.004 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.324 Fit side-chains REVERT: B 45 LYS cc_start: 0.7991 (mmtt) cc_final: 0.7018 (tptp) REVERT: B 52 GLU cc_start: 0.7647 (mp0) cc_final: 0.7118 (mp0) REVERT: B 287 CYS cc_start: 0.6935 (p) cc_final: 0.6416 (p) REVERT: B 449 PHE cc_start: 0.7369 (m-80) cc_final: 0.6971 (t80) REVERT: B 451 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7519 (tttm) REVERT: B 729 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7007 (mmmt) REVERT: A 45 LYS cc_start: 0.7973 (mmtt) cc_final: 0.6989 (tptp) REVERT: A 287 CYS cc_start: 0.6933 (p) cc_final: 0.6410 (p) REVERT: A 449 PHE cc_start: 0.7357 (m-80) cc_final: 0.6970 (t80) REVERT: A 451 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7521 (tttm) REVERT: A 675 MET cc_start: 0.8515 (mtm) cc_final: 0.8207 (mtp) REVERT: A 729 LYS cc_start: 0.7749 (mtmm) cc_final: 0.6999 (mmmt) outliers start: 33 outliers final: 28 residues processed: 146 average time/residue: 1.0017 time to fit residues: 160.6885 Evaluate side-chains 152 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 634 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 727 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS A 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10622 Z= 0.310 Angle : 0.573 6.761 14378 Z= 0.300 Chirality : 0.045 0.154 1714 Planarity : 0.004 0.064 1762 Dihedral : 7.684 69.644 1608 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.85 % Allowed : 15.42 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1278 helix: 1.79 (0.23), residues: 522 sheet: 1.64 (0.33), residues: 266 loop : -0.58 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 567 HIS 0.003 0.001 HIS A 450 PHE 0.014 0.002 PHE B 528 TYR 0.017 0.002 TYR A 673 ARG 0.004 0.000 ARG B 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.269 Fit side-chains REVERT: B 45 LYS cc_start: 0.8013 (mmtt) cc_final: 0.6984 (tptp) REVERT: B 52 GLU cc_start: 0.7667 (mp0) cc_final: 0.7136 (mp0) REVERT: B 287 CYS cc_start: 0.6990 (p) cc_final: 0.6481 (p) REVERT: B 449 PHE cc_start: 0.7388 (m-80) cc_final: 0.6988 (t80) REVERT: B 451 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7536 (tttm) REVERT: B 729 LYS cc_start: 0.7742 (mtmm) cc_final: 0.6990 (mmmt) REVERT: A 45 LYS cc_start: 0.7999 (mmtt) cc_final: 0.6982 (tptp) REVERT: A 449 PHE cc_start: 0.7375 (m-80) cc_final: 0.6984 (t80) REVERT: A 451 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7539 (tttm) REVERT: A 675 MET cc_start: 0.8527 (mtm) cc_final: 0.8215 (mtp) REVERT: A 712 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7557 (mm110) REVERT: A 729 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7043 (mmmt) outliers start: 32 outliers final: 28 residues processed: 145 average time/residue: 1.0062 time to fit residues: 159.9637 Evaluate side-chains 151 residues out of total 1162 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 634 PHE Chi-restraints excluded: chain B residue 659 ASN Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 451 LYS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 712 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 5 optimal weight: 0.0270 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 HIS B 728 ASN A 450 HIS A 728 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.112516 restraints weight = 10462.346| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.90 r_work: 0.3163 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10622 Z= 0.182 Angle : 0.505 6.741 14378 Z= 0.268 Chirality : 0.042 0.153 1714 Planarity : 0.004 0.062 1762 Dihedral : 7.330 71.211 1608 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.67 % Allowed : 16.04 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1278 helix: 1.98 (0.23), residues: 528 sheet: 1.72 (0.33), residues: 260 loop : -0.36 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 567 HIS 0.002 0.001 HIS B 740 PHE 0.010 0.001 PHE B 528 TYR 0.015 0.001 TYR B 650 ARG 0.004 0.000 ARG A 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3531.55 seconds wall clock time: 64 minutes 24.06 seconds (3864.06 seconds total)