Starting phenix.real_space_refine on Sun Apr 14 18:52:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nih_12359/04_2024/7nih_12359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nih_12359/04_2024/7nih_12359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nih_12359/04_2024/7nih_12359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nih_12359/04_2024/7nih_12359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nih_12359/04_2024/7nih_12359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nih_12359/04_2024/7nih_12359_updated.pdb" } resolution = 2.6 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= 0.006 sd= 0.107 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 P 16 5.49 5 Mg 8 5.21 5 S 104 5.16 5 C 20752 2.51 5 N 5456 2.21 5 O 6128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "B TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "C TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "D GLU 675": "OE1" <-> "OE2" Residue "D TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 669": "OE1" <-> "OE2" Residue "E GLU 675": "OE1" <-> "OE2" Residue "E TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 669": "OE1" <-> "OE2" Residue "F GLU 675": "OE1" <-> "OE2" Residue "F TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 669": "OE1" <-> "OE2" Residue "G GLU 675": "OE1" <-> "OE2" Residue "G TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 669": "OE1" <-> "OE2" Residue "H GLU 675": "OE1" <-> "OE2" Residue "H TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32464 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "B" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "C" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "D" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "E" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "F" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "G" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "H" Number of atoms: 4030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4030 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 499} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.60, per 1000 atoms: 0.51 Number of scatterers: 32464 At special positions: 0 Unit cell: (159.997, 159.997, 135.956, 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) S 104 16.00 P 16 15.00 Mg 8 11.99 O 6128 8.00 N 5456 7.00 C 20752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.31 Conformation dependent library (CDL) restraints added in 6.3 seconds 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 160 helices and 40 sheets defined 40.0% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 30 through 50 Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.768A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 241 through 259 removed outlier: 3.917A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 451 Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 497 through 500 No H-bonds generated for 'chain 'A' and resid 497 through 500' Processing helix chain 'A' and resid 505 through 520 removed outlier: 3.593A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 570 through 574 Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 592 through 595 No H-bonds generated for 'chain 'A' and resid 592 through 595' Processing helix chain 'A' and resid 616 through 619 No H-bonds generated for 'chain 'A' and resid 616 through 619' Processing helix chain 'A' and resid 623 through 635 removed outlier: 3.967A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 657 removed outlier: 3.981A pdb=" N ARG A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 686 removed outlier: 3.520A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 30 through 50 Processing helix chain 'B' and resid 87 through 93 removed outlier: 3.769A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 106 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 241 through 259 removed outlier: 3.916A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 451 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 497 through 500 No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 505 through 520 removed outlier: 3.593A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 552 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 582 through 586 Processing helix chain 'B' and resid 592 through 595 No H-bonds generated for 'chain 'B' and resid 592 through 595' Processing helix chain 'B' and resid 616 through 619 No H-bonds generated for 'chain 'B' and resid 616 through 619' Processing helix chain 'B' and resid 623 through 635 removed outlier: 3.967A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 657 removed outlier: 3.981A pdb=" N ARG B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 686 removed outlier: 3.519A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 707 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 30 through 50 Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.768A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 241 through 259 removed outlier: 3.916A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 451 Processing helix chain 'C' and resid 458 through 463 Processing helix chain 'C' and resid 497 through 500 No H-bonds generated for 'chain 'C' and resid 497 through 500' Processing helix chain 'C' and resid 505 through 520 removed outlier: 3.595A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 552 Processing helix chain 'C' and resid 570 through 574 Processing helix chain 'C' and resid 582 through 586 Processing helix chain 'C' and resid 592 through 595 No H-bonds generated for 'chain 'C' and resid 592 through 595' Processing helix chain 'C' and resid 616 through 619 No H-bonds generated for 'chain 'C' and resid 616 through 619' Processing helix chain 'C' and resid 623 through 635 removed outlier: 3.967A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 657 removed outlier: 3.982A pdb=" N ARG C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 686 removed outlier: 3.520A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 30 through 50 Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.769A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 241 through 259 removed outlier: 3.916A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 451 Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 497 through 500 No H-bonds generated for 'chain 'D' and resid 497 through 500' Processing helix chain 'D' and resid 505 through 520 removed outlier: 3.595A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 552 Processing helix chain 'D' and resid 570 through 574 Processing helix chain 'D' and resid 582 through 586 Processing helix chain 'D' and resid 592 through 595 No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 616 through 619 No H-bonds generated for 'chain 'D' and resid 616 through 619' Processing helix chain 'D' and resid 623 through 635 removed outlier: 3.966A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 657 removed outlier: 3.981A pdb=" N ARG D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 686 removed outlier: 3.520A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 707 Processing helix chain 'E' and resid 19 through 28 Processing helix chain 'E' and resid 30 through 50 Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.769A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 241 through 259 removed outlier: 3.916A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 451 Processing helix chain 'E' and resid 458 through 463 Processing helix chain 'E' and resid 497 through 500 No H-bonds generated for 'chain 'E' and resid 497 through 500' Processing helix chain 'E' and resid 505 through 520 removed outlier: 3.593A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 552 Processing helix chain 'E' and resid 570 through 574 Processing helix chain 'E' and resid 582 through 586 Processing helix chain 'E' and resid 592 through 595 No H-bonds generated for 'chain 'E' and resid 592 through 595' Processing helix chain 'E' and resid 616 through 619 No H-bonds generated for 'chain 'E' and resid 616 through 619' Processing helix chain 'E' and resid 623 through 635 removed outlier: 3.966A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 651 through 657 removed outlier: 3.980A pdb=" N ARG E 657 " --> pdb=" O ALA E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 686 removed outlier: 3.520A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 707 Processing helix chain 'F' and resid 19 through 28 Processing helix chain 'F' and resid 30 through 50 Processing helix chain 'F' and resid 87 through 93 removed outlier: 3.768A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 209 through 219 Processing helix chain 'F' and resid 241 through 259 removed outlier: 3.916A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 451 Processing helix chain 'F' and resid 458 through 463 Processing helix chain 'F' and resid 497 through 500 No H-bonds generated for 'chain 'F' and resid 497 through 500' Processing helix chain 'F' and resid 505 through 520 removed outlier: 3.593A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 552 Processing helix chain 'F' and resid 570 through 574 Processing helix chain 'F' and resid 582 through 586 Processing helix chain 'F' and resid 592 through 595 No H-bonds generated for 'chain 'F' and resid 592 through 595' Processing helix chain 'F' and resid 616 through 619 No H-bonds generated for 'chain 'F' and resid 616 through 619' Processing helix chain 'F' and resid 623 through 635 removed outlier: 3.967A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 651 through 657 removed outlier: 3.981A pdb=" N ARG F 657 " --> pdb=" O ALA F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 686 removed outlier: 3.520A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 707 Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 30 through 50 Processing helix chain 'G' and resid 87 through 93 removed outlier: 3.769A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 209 through 219 Processing helix chain 'G' and resid 241 through 259 removed outlier: 3.917A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 426 through 451 Processing helix chain 'G' and resid 458 through 463 Processing helix chain 'G' and resid 497 through 500 No H-bonds generated for 'chain 'G' and resid 497 through 500' Processing helix chain 'G' and resid 505 through 520 removed outlier: 3.593A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 552 Processing helix chain 'G' and resid 570 through 574 Processing helix chain 'G' and resid 582 through 586 Processing helix chain 'G' and resid 592 through 595 No H-bonds generated for 'chain 'G' and resid 592 through 595' Processing helix chain 'G' and resid 616 through 619 No H-bonds generated for 'chain 'G' and resid 616 through 619' Processing helix chain 'G' and resid 623 through 635 removed outlier: 3.966A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 651 through 657 removed outlier: 3.981A pdb=" N ARG G 657 " --> pdb=" O ALA G 653 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 686 removed outlier: 3.519A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 702 through 707 Processing helix chain 'H' and resid 19 through 28 Processing helix chain 'H' and resid 30 through 50 Processing helix chain 'H' and resid 87 through 93 removed outlier: 3.769A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 209 through 219 Processing helix chain 'H' and resid 241 through 259 removed outlier: 3.916A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 451 Processing helix chain 'H' and resid 458 through 463 Processing helix chain 'H' and resid 497 through 500 No H-bonds generated for 'chain 'H' and resid 497 through 500' Processing helix chain 'H' and resid 505 through 520 removed outlier: 3.594A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 552 Processing helix chain 'H' and resid 570 through 574 Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 592 through 595 No H-bonds generated for 'chain 'H' and resid 592 through 595' Processing helix chain 'H' and resid 616 through 619 No H-bonds generated for 'chain 'H' and resid 616 through 619' Processing helix chain 'H' and resid 623 through 635 removed outlier: 3.967A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 657 removed outlier: 3.982A pdb=" N ARG H 657 " --> pdb=" O ALA H 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 673 through 686 removed outlier: 3.520A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 702 through 707 Processing sheet with id= A, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.514A pdb=" N GLU A 56 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 110 through 114 Processing sheet with id= C, first strand: chain 'A' and resid 182 through 184 removed outlier: 3.809A pdb=" N ARG A 139 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 192 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE A 137 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS A 693 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A 471 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 695 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY A 692 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 639 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 531 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 641 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY A 533 " --> pdb=" O ILE A 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP A 605 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP A 562 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE A 607 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN A 62 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE A 411 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 416 through 418 removed outlier: 4.514A pdb=" N GLU B 56 " --> pdb=" O ASP B 418 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 110 through 114 Processing sheet with id= H, first strand: chain 'B' and resid 182 through 184 removed outlier: 3.810A pdb=" N ARG B 139 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN B 192 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE B 137 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS B 693 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER B 471 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 695 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 692 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE B 639 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 531 " --> pdb=" O ILE B 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE B 641 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY B 533 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 605 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP B 562 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE B 607 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN B 62 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 411 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 416 through 418 removed outlier: 4.515A pdb=" N GLU C 56 " --> pdb=" O ASP C 418 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 110 through 114 Processing sheet with id= M, first strand: chain 'C' and resid 182 through 184 removed outlier: 3.808A pdb=" N ARG C 139 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN C 192 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE C 137 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS C 693 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER C 471 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 695 " --> pdb=" O SER C 471 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY C 692 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE C 639 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE C 531 " --> pdb=" O ILE C 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 641 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY C 533 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP C 605 " --> pdb=" O PHE C 560 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP C 562 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE C 607 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN C 62 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE C 411 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 416 through 418 removed outlier: 4.514A pdb=" N GLU D 56 " --> pdb=" O ASP D 418 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 110 through 114 Processing sheet with id= R, first strand: chain 'D' and resid 182 through 184 removed outlier: 3.808A pdb=" N ARG D 139 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN D 192 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE D 137 " --> pdb=" O ASN D 192 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS D 693 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER D 471 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 695 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY D 692 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE D 639 " --> pdb=" O LEU D 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE D 531 " --> pdb=" O ILE D 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE D 641 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY D 533 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP D 605 " --> pdb=" O PHE D 560 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP D 562 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 607 " --> pdb=" O ASP D 562 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.577A pdb=" N GLN D 62 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE D 411 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 416 through 418 removed outlier: 4.514A pdb=" N GLU E 56 " --> pdb=" O ASP E 418 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 110 through 114 Processing sheet with id= W, first strand: chain 'E' and resid 182 through 184 removed outlier: 3.809A pdb=" N ARG E 139 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 192 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE E 137 " --> pdb=" O ASN E 192 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 468 through 472 removed outlier: 7.920A pdb=" N CYS E 693 " --> pdb=" O TYR E 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER E 471 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 695 " --> pdb=" O SER E 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY E 692 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE E 639 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE E 531 " --> pdb=" O ILE E 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 641 " --> pdb=" O ILE E 531 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY E 533 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP E 605 " --> pdb=" O PHE E 560 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP E 562 " --> pdb=" O ASP E 605 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE E 607 " --> pdb=" O ASP E 562 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN E 62 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE E 411 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 416 through 418 removed outlier: 4.515A pdb=" N GLU F 56 " --> pdb=" O ASP F 418 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 110 through 114 Processing sheet with id= AB, first strand: chain 'F' and resid 182 through 184 removed outlier: 3.809A pdb=" N ARG F 139 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN F 192 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE F 137 " --> pdb=" O ASN F 192 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS F 693 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER F 471 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU F 695 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY F 692 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE F 639 " --> pdb=" O LEU F 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE F 531 " --> pdb=" O ILE F 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE F 641 " --> pdb=" O ILE F 531 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY F 533 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP F 605 " --> pdb=" O PHE F 560 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP F 562 " --> pdb=" O ASP F 605 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE F 607 " --> pdb=" O ASP F 562 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN F 62 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE F 411 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 416 through 418 removed outlier: 4.514A pdb=" N GLU G 56 " --> pdb=" O ASP G 418 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 110 through 114 Processing sheet with id= AG, first strand: chain 'G' and resid 182 through 184 removed outlier: 3.809A pdb=" N ARG G 139 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN G 192 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE G 137 " --> pdb=" O ASN G 192 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS G 693 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER G 471 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU G 695 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY G 692 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE G 639 " --> pdb=" O LEU G 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE G 531 " --> pdb=" O ILE G 639 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE G 641 " --> pdb=" O ILE G 531 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY G 533 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP G 605 " --> pdb=" O PHE G 560 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP G 562 " --> pdb=" O ASP G 605 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE G 607 " --> pdb=" O ASP G 562 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN G 62 " --> pdb=" O ILE G 411 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE G 411 " --> pdb=" O GLN G 62 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 416 through 418 removed outlier: 4.515A pdb=" N GLU H 56 " --> pdb=" O ASP H 418 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 110 through 114 Processing sheet with id= AL, first strand: chain 'H' and resid 182 through 184 removed outlier: 3.809A pdb=" N ARG H 139 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN H 192 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE H 137 " --> pdb=" O ASN H 192 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 468 through 472 removed outlier: 7.919A pdb=" N CYS H 693 " --> pdb=" O TYR H 469 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER H 471 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU H 695 " --> pdb=" O SER H 471 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY H 692 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE H 639 " --> pdb=" O LEU H 529 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE H 531 " --> pdb=" O ILE H 639 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE H 641 " --> pdb=" O ILE H 531 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY H 533 " --> pdb=" O ILE H 641 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP H 605 " --> pdb=" O PHE H 560 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP H 562 " --> pdb=" O ASP H 605 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE H 607 " --> pdb=" O ASP H 562 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 60 through 62 removed outlier: 6.576A pdb=" N GLN H 62 " --> pdb=" O ILE H 411 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE H 411 " --> pdb=" O GLN H 62 " (cutoff:3.500A) 1424 hydrogen bonds defined for protein. 4128 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: 12.88 Time building geometry restraints manager: 13.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10514 1.34 - 1.45: 4378 1.45 - 1.57: 17876 1.57 - 1.69: 24 1.69 - 1.81: 192 Bond restraints: 32984 Sorted by residual: bond pdb=" C6 ADP A1000 " pdb=" N6 ADP A1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C6 ADP D1000 " pdb=" N6 ADP D1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C6 ADP C1000 " pdb=" N6 ADP C1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 ADP B1000 " pdb=" N6 ADP B1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C6 ADP H1000 " pdb=" N6 ADP H1000 " ideal model delta sigma weight residual 1.355 1.460 -0.105 2.00e-02 2.50e+03 2.74e+01 ... (remaining 32979 not shown) Histogram of bond angle deviations from ideal: 99.64 - 107.14: 982 107.14 - 114.64: 20306 114.64 - 122.14: 17677 122.14 - 129.64: 5635 129.64 - 137.15: 136 Bond angle restraints: 44736 Sorted by residual: angle pdb=" PA ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " ideal model delta sigma weight residual 120.50 132.15 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" PA ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " ideal model delta sigma weight residual 120.50 132.13 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" PA ADP G1000 " pdb=" O3A ADP G1000 " pdb=" PB ADP G1000 " ideal model delta sigma weight residual 120.50 132.12 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" PA ADP B1000 " pdb=" O3A ADP B1000 " pdb=" PB ADP B1000 " ideal model delta sigma weight residual 120.50 132.11 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" PA ADP F1000 " pdb=" O3A ADP F1000 " pdb=" PB ADP F1000 " ideal model delta sigma weight residual 120.50 132.10 -11.60 3.00e+00 1.11e-01 1.50e+01 ... (remaining 44731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.87: 19680 32.87 - 65.74: 272 65.74 - 98.61: 24 98.61 - 131.48: 8 131.48 - 164.35: 16 Dihedral angle restraints: 20000 sinusoidal: 8000 harmonic: 12000 Sorted by residual: dihedral pdb=" O1B ADP G1000 " pdb=" O3A ADP G1000 " pdb=" PB ADP G1000 " pdb=" PA ADP G1000 " ideal model delta sinusoidal sigma weight residual 300.00 135.65 164.35 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1B ADP H1000 " pdb=" O3A ADP H1000 " pdb=" PB ADP H1000 " pdb=" PA ADP H1000 " ideal model delta sinusoidal sigma weight residual 300.00 135.67 164.33 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 135.68 164.32 1 2.00e+01 2.50e-03 4.71e+01 ... (remaining 19997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2582 0.030 - 0.060: 1713 0.060 - 0.090: 647 0.090 - 0.120: 324 0.120 - 0.149: 62 Chirality restraints: 5328 Sorted by residual: chirality pdb=" CA HIS H 712 " pdb=" N HIS H 712 " pdb=" C HIS H 712 " pdb=" CB HIS H 712 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA HIS B 712 " pdb=" N HIS B 712 " pdb=" C HIS B 712 " pdb=" CB HIS B 712 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA HIS C 712 " pdb=" N HIS C 712 " pdb=" C HIS C 712 " pdb=" CB HIS C 712 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 5325 not shown) Planarity restraints: 5648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 602 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLY B 602 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY B 602 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 603 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 602 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.91e+00 pdb=" C GLY A 602 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY A 602 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 603 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 602 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C GLY E 602 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY E 602 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY E 603 " -0.008 2.00e-02 2.50e+03 ... (remaining 5645 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 283 2.58 - 3.16: 27809 3.16 - 3.74: 50510 3.74 - 4.32: 76804 4.32 - 4.90: 121410 Nonbonded interactions: 276816 Sorted by model distance: nonbonded pdb=" O2B ADP D1000 " pdb="MG MG D1001 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP C1000 " pdb="MG MG C1001 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP F1000 " pdb="MG MG F1001 " model vdw 1.999 2.170 nonbonded pdb=" O2B ADP B1000 " pdb="MG MG B1001 " model vdw 2.000 2.170 nonbonded pdb=" O2B ADP A1000 " pdb="MG MG A1001 " model vdw 2.000 2.170 ... (remaining 276811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.370 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: 0.040 Extract box with map and model: 12.300 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 87.230 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 : 0.008 0.105 32984 Z= 0.553 Angle : 0.734 11.647 44736 Z= 0.362 Chirality : 0.047 0.149 5328 Planarity : 0.004 0.033 5648 Dihedral : 12.987 164.350 12288 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.10), residues: 4112 helix: -2.17 (0.09), residues: 1808 sheet: -0.52 (0.17), residues: 616 loop : -2.19 (0.12), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP G 477 HIS 0.005 0.001 HIS E 710 PHE 0.012 0.002 PHE F 604 TYR 0.015 0.002 TYR A 708 ARG 0.004 0.001 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 3.778 Fit side-chains revert: symmetry clash REVERT: A 621 MET cc_start: 0.8832 (mtp) cc_final: 0.8490 (mtp) REVERT: A 680 MET cc_start: 0.8183 (mtp) cc_final: 0.7711 (mtt) REVERT: B 231 MET cc_start: 0.7532 (mmt) cc_final: 0.6804 (mmt) REVERT: B 621 MET cc_start: 0.8979 (mtp) cc_final: 0.8669 (mtp) REVERT: B 680 MET cc_start: 0.8195 (mtp) cc_final: 0.7895 (mtp) REVERT: C 680 MET cc_start: 0.8215 (mtp) cc_final: 0.7725 (mtt) REVERT: D 621 MET cc_start: 0.8885 (mtp) cc_final: 0.8369 (mtp) REVERT: D 680 MET cc_start: 0.8127 (mtp) cc_final: 0.7875 (mtp) REVERT: E 243 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7603 (ttt180) REVERT: E 680 MET cc_start: 0.8187 (mtp) cc_final: 0.7714 (mtt) REVERT: F 621 MET cc_start: 0.8796 (mtp) cc_final: 0.8449 (mtp) REVERT: F 680 MET cc_start: 0.8188 (mtp) cc_final: 0.7917 (mtp) REVERT: G 255 TYR cc_start: 0.8332 (t80) cc_final: 0.8131 (t80) REVERT: G 680 MET cc_start: 0.8226 (mtp) cc_final: 0.7726 (mtt) REVERT: H 231 MET cc_start: 0.7740 (mmt) cc_final: 0.7096 (mmt) REVERT: H 255 TYR cc_start: 0.8330 (t80) cc_final: 0.8107 (t80) REVERT: H 621 MET cc_start: 0.8965 (mtp) cc_final: 0.8631 (mtp) REVERT: H 680 MET cc_start: 0.8223 (mtp) cc_final: 0.7931 (mtp) outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 1.3690 time to fit residues: 1026.0789 Evaluate side-chains 445 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 326 optimal weight: 30.0000 chunk 126 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 377 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 173 GLN A 254 ASN A 571 HIS A 576 HIS A 611 GLN A 671 ASN B 29 HIS B 111 GLN B 173 GLN B 254 ASN B 518 HIS B 571 HIS B 576 HIS B 671 ASN C 29 HIS C 111 GLN C 173 GLN C 206 GLN C 254 ASN C 518 HIS C 571 HIS C 576 HIS C 611 GLN C 671 ASN D 29 HIS D 111 GLN D 173 GLN D 206 GLN D 254 ASN D 571 HIS D 576 HIS D 589 GLN D 611 GLN D 671 ASN E 29 HIS E 173 GLN E 254 ASN E 571 HIS E 576 HIS E 611 GLN E 671 ASN F 29 HIS F 111 GLN F 173 GLN F 246 HIS F 254 ASN F 571 HIS F 576 HIS F 589 GLN F 611 GLN F 671 ASN G 29 HIS G 111 GLN G 173 GLN G 254 ASN G 571 HIS G 576 HIS G 611 GLN G 671 ASN H 29 HIS H 111 GLN H 173 GLN H 254 ASN H 518 HIS H 571 HIS H 576 HIS H 671 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32984 Z= 0.325 Angle : 0.653 9.799 44736 Z= 0.317 Chirality : 0.047 0.163 5328 Planarity : 0.004 0.036 5648 Dihedral : 9.266 122.970 4544 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.31 % Allowed : 10.67 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.34 (0.11), residues: 4112 helix: -0.47 (0.11), residues: 1848 sheet: -0.12 (0.16), residues: 680 loop : -1.62 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 631 HIS 0.008 0.001 HIS C 518 PHE 0.011 0.002 PHE E 202 TYR 0.013 0.002 TYR B 708 ARG 0.005 0.001 ARG F 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 492 time to evaluate : 3.645 Fit side-chains revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8750 (mm) REVERT: A 459 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 621 MET cc_start: 0.8847 (mtp) cc_final: 0.8545 (mtp) REVERT: A 680 MET cc_start: 0.8206 (mtp) cc_final: 0.7722 (mtt) REVERT: B 31 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7318 (mptt) REVERT: B 231 MET cc_start: 0.7738 (mmt) cc_final: 0.7139 (mmt) REVERT: B 418 ASP cc_start: 0.7638 (t0) cc_final: 0.7387 (t0) REVERT: B 459 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: B 523 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6461 (mp0) REVERT: B 621 MET cc_start: 0.8888 (mtp) cc_final: 0.8498 (mtp) REVERT: B 680 MET cc_start: 0.8212 (mtp) cc_final: 0.7912 (mtp) REVERT: B 684 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: C 31 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7489 (mptt) REVERT: C 680 MET cc_start: 0.8197 (mtp) cc_final: 0.7691 (mtt) REVERT: D 31 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7382 (mptt) REVERT: D 54 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8231 (mp) REVERT: D 231 MET cc_start: 0.7708 (mmt) cc_final: 0.6945 (mmt) REVERT: D 459 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: D 621 MET cc_start: 0.8848 (mtp) cc_final: 0.8397 (mtp) REVERT: D 680 MET cc_start: 0.8195 (mtp) cc_final: 0.7941 (mtp) REVERT: D 684 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: E 31 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7416 (mptt) REVERT: E 243 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7502 (ttt180) REVERT: E 680 MET cc_start: 0.8189 (mtp) cc_final: 0.7686 (mtt) REVERT: F 31 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7390 (mptt) REVERT: F 231 MET cc_start: 0.7805 (mmt) cc_final: 0.7165 (mmt) REVERT: F 459 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: F 621 MET cc_start: 0.8849 (mtp) cc_final: 0.8426 (mtp) REVERT: F 680 MET cc_start: 0.8219 (mtp) cc_final: 0.7951 (mtp) REVERT: F 684 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: G 31 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7431 (mptt) REVERT: G 54 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8147 (mp) REVERT: G 680 MET cc_start: 0.8190 (mtp) cc_final: 0.7682 (mtt) REVERT: H 31 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7291 (mptt) REVERT: H 231 MET cc_start: 0.7758 (mmt) cc_final: 0.7197 (mmt) REVERT: H 459 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: H 523 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: H 621 MET cc_start: 0.8848 (mtp) cc_final: 0.8502 (mtp) REVERT: H 680 MET cc_start: 0.8218 (mtp) cc_final: 0.7923 (mtp) REVERT: H 684 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7313 (mt-10) outliers start: 153 outliers final: 42 residues processed: 570 average time/residue: 1.3090 time to fit residues: 898.8165 Evaluate side-chains 505 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 442 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 459 GLU Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 523 GLU Chi-restraints excluded: chain H residue 684 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 314 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 408 optimal weight: 0.0670 chunk 337 optimal weight: 2.9990 chunk 375 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 611 GLN C 206 GLN D 206 GLN E 518 HIS H 253 GLN H 611 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32984 Z= 0.347 Angle : 0.650 10.380 44736 Z= 0.316 Chirality : 0.047 0.165 5328 Planarity : 0.004 0.041 5648 Dihedral : 9.028 123.542 4544 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.45 % Allowed : 11.66 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 4112 helix: 0.21 (0.12), residues: 1840 sheet: 0.38 (0.19), residues: 592 loop : -1.43 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 631 HIS 0.009 0.001 HIS E 518 PHE 0.011 0.002 PHE D 604 TYR 0.014 0.002 TYR H 708 ARG 0.005 0.001 ARG H 682 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 462 time to evaluate : 3.563 Fit side-chains REVERT: A 31 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7253 (mptt) REVERT: A 459 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: A 621 MET cc_start: 0.8856 (mtp) cc_final: 0.8580 (mtp) REVERT: A 680 MET cc_start: 0.8213 (mtp) cc_final: 0.7712 (mtt) REVERT: B 31 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7227 (mptt) REVERT: B 231 MET cc_start: 0.7755 (mmt) cc_final: 0.7274 (mmt) REVERT: B 418 ASP cc_start: 0.7807 (t0) cc_final: 0.7540 (t0) REVERT: B 459 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 522 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6590 (ptp) REVERT: B 523 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: B 621 MET cc_start: 0.8800 (mtp) cc_final: 0.8428 (mtp) REVERT: B 680 MET cc_start: 0.8186 (mtp) cc_final: 0.7893 (mtp) REVERT: B 684 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: C 31 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7380 (mptt) REVERT: C 418 ASP cc_start: 0.7620 (t0) cc_final: 0.7416 (t70) REVERT: C 459 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: C 523 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: C 680 MET cc_start: 0.8192 (mtp) cc_final: 0.7695 (mtt) REVERT: D 31 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7318 (mptt) REVERT: D 54 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8265 (mp) REVERT: D 418 ASP cc_start: 0.7756 (t0) cc_final: 0.7488 (t0) REVERT: D 459 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: D 523 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: D 621 MET cc_start: 0.8811 (mtp) cc_final: 0.8453 (mtp) REVERT: D 680 MET cc_start: 0.8183 (mtp) cc_final: 0.7916 (mtp) REVERT: D 684 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: E 31 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7339 (mptt) REVERT: E 98 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8556 (mt) REVERT: E 459 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: E 525 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7785 (ptmt) REVERT: E 680 MET cc_start: 0.8186 (mtp) cc_final: 0.7693 (mtt) REVERT: F 31 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7334 (mptt) REVERT: F 231 MET cc_start: 0.7793 (mmt) cc_final: 0.7129 (mmt) REVERT: F 418 ASP cc_start: 0.7822 (t0) cc_final: 0.7537 (t0) REVERT: F 459 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: F 523 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: F 680 MET cc_start: 0.8205 (mtp) cc_final: 0.7937 (mtp) REVERT: F 684 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: G 31 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7360 (mptt) REVERT: G 459 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: G 680 MET cc_start: 0.8169 (mtp) cc_final: 0.7669 (mtt) REVERT: H 31 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7228 (mptt) REVERT: H 231 MET cc_start: 0.7705 (mmt) cc_final: 0.7176 (mmt) REVERT: H 459 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: H 523 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: H 621 MET cc_start: 0.8798 (mtp) cc_final: 0.8431 (mtp) REVERT: H 680 MET cc_start: 0.8198 (mtp) cc_final: 0.7907 (mtp) REVERT: H 684 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7288 (mt-10) outliers start: 158 outliers final: 71 residues processed: 540 average time/residue: 1.3863 time to fit residues: 894.5899 Evaluate side-chains 554 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 454 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 716 SER Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 525 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 523 GLU Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 716 SER Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 459 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 192 ASN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 459 GLU Chi-restraints excluded: chain H residue 523 GLU Chi-restraints excluded: chain H residue 684 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 379 optimal weight: 9.9990 chunk 402 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN C 114 GLN C 206 GLN D 114 GLN D 206 GLN E 114 GLN F 114 GLN G 114 GLN H 114 GLN H 253 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32984 Z= 0.414 Angle : 0.691 11.720 44736 Z= 0.336 Chirality : 0.049 0.164 5328 Planarity : 0.004 0.045 5648 Dihedral : 9.253 124.254 4544 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.48 % Allowed : 12.92 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.44 (0.12), residues: 4112 helix: 0.36 (0.12), residues: 1840 sheet: 0.64 (0.20), residues: 592 loop : -1.33 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 631 HIS 0.008 0.002 HIS G 712 PHE 0.012 0.002 PHE H 604 TYR 0.019 0.002 TYR B 255 ARG 0.006 0.001 ARG F 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 459 time to evaluate : 3.633 Fit side-chains REVERT: A 31 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7229 (mptt) REVERT: A 459 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 621 MET cc_start: 0.8841 (mtp) cc_final: 0.8574 (mtp) REVERT: A 680 MET cc_start: 0.8203 (mtp) cc_final: 0.7702 (mtt) REVERT: B 31 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7183 (mptt) REVERT: B 231 MET cc_start: 0.7680 (mmt) cc_final: 0.7116 (mmt) REVERT: B 418 ASP cc_start: 0.7825 (t0) cc_final: 0.7536 (t0) REVERT: B 459 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: B 462 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: B 523 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: B 680 MET cc_start: 0.8187 (mtp) cc_final: 0.7899 (mtp) REVERT: B 684 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 31 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7336 (mptt) REVERT: C 418 ASP cc_start: 0.7665 (t0) cc_final: 0.7446 (t70) REVERT: C 459 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7178 (mp0) REVERT: C 523 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: C 680 MET cc_start: 0.8187 (mtp) cc_final: 0.7687 (mtt) REVERT: D 31 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7263 (mptt) REVERT: D 54 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8323 (mp) REVERT: D 231 MET cc_start: 0.7756 (mmt) cc_final: 0.7278 (mmt) REVERT: D 418 ASP cc_start: 0.7798 (t0) cc_final: 0.7525 (t0) REVERT: D 459 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: D 462 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: D 523 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: D 680 MET cc_start: 0.8189 (mtp) cc_final: 0.7898 (mtp) REVERT: D 684 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: E 31 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7339 (mptt) REVERT: E 98 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8538 (mt) REVERT: E 113 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: E 459 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: E 523 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: E 680 MET cc_start: 0.8183 (mtp) cc_final: 0.7687 (mtt) REVERT: F 31 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7279 (mptt) REVERT: F 231 MET cc_start: 0.7792 (mmt) cc_final: 0.7170 (mmt) REVERT: F 418 ASP cc_start: 0.7858 (t0) cc_final: 0.7575 (t0) REVERT: F 459 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: F 523 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6572 (mp0) REVERT: F 680 MET cc_start: 0.8207 (mtp) cc_final: 0.7912 (mtp) REVERT: F 684 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: G 31 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7341 (mptt) REVERT: G 54 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8288 (mp) REVERT: G 459 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: G 523 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: G 680 MET cc_start: 0.8168 (mtp) cc_final: 0.7671 (mtt) REVERT: H 31 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7148 (mptt) REVERT: H 459 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: H 462 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: H 523 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: H 680 MET cc_start: 0.8202 (mtp) cc_final: 0.7913 (mtp) REVERT: H 684 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7374 (mt-10) outliers start: 159 outliers final: 78 residues processed: 532 average time/residue: 1.4284 time to fit residues: 904.8062 Evaluate side-chains 565 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 453 time to evaluate : 5.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 192 ASN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 522 MET Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 523 GLU Chi-restraints excluded: chain F residue 594 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 459 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 192 ASN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 459 GLU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 523 GLU Chi-restraints excluded: chain H residue 594 MET Chi-restraints excluded: chain H residue 684 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.0070 chunk 228 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 chunk 343 optimal weight: 0.6980 chunk 277 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 0.5980 chunk 360 optimal weight: 0.2980 chunk 101 optimal weight: 0.5980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN B 62 GLN B 114 GLN C 114 GLN C 206 GLN D 114 GLN D 206 GLN E 114 GLN E 253 GLN F 114 GLN G 114 GLN H 114 GLN H 253 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32984 Z= 0.139 Angle : 0.536 7.720 44736 Z= 0.256 Chirality : 0.043 0.143 5328 Planarity : 0.003 0.030 5648 Dihedral : 8.152 109.755 4544 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.39 % Allowed : 14.61 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.12 (0.12), residues: 4112 helix: 1.05 (0.12), residues: 1832 sheet: 0.66 (0.20), residues: 592 loop : -1.22 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 631 HIS 0.002 0.000 HIS B 710 PHE 0.011 0.001 PHE B 542 TYR 0.016 0.001 TYR H 255 ARG 0.001 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 521 time to evaluate : 3.528 Fit side-chains REVERT: A 31 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7245 (mptt) REVERT: A 522 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6471 (ptp) REVERT: A 523 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: A 680 MET cc_start: 0.8163 (mtp) cc_final: 0.7686 (mtt) REVERT: B 418 ASP cc_start: 0.7740 (t0) cc_final: 0.7465 (t0) REVERT: B 523 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: B 680 MET cc_start: 0.8145 (mtp) cc_final: 0.7908 (mtp) REVERT: B 684 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: C 31 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7266 (mptt) REVERT: C 522 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6414 (ptp) REVERT: C 523 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6268 (mp0) REVERT: C 680 MET cc_start: 0.8135 (mtp) cc_final: 0.7706 (mtt) REVERT: C 707 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7826 (ttt-90) REVERT: D 231 MET cc_start: 0.7675 (mmt) cc_final: 0.7332 (mmt) REVERT: D 418 ASP cc_start: 0.7744 (t0) cc_final: 0.7478 (t70) REVERT: D 523 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: D 680 MET cc_start: 0.8143 (mtp) cc_final: 0.7883 (mtp) REVERT: D 684 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: E 31 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7268 (mptt) REVERT: E 462 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: E 523 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: E 680 MET cc_start: 0.8130 (mtp) cc_final: 0.7648 (mtt) REVERT: E 707 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7790 (ttt-90) REVERT: F 231 MET cc_start: 0.7681 (mmt) cc_final: 0.7273 (mmt) REVERT: F 418 ASP cc_start: 0.7828 (t0) cc_final: 0.7533 (t0) REVERT: F 523 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: F 680 MET cc_start: 0.8174 (mtp) cc_final: 0.7908 (mtp) REVERT: G 31 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7268 (mptt) REVERT: G 522 MET cc_start: 0.6826 (ptp) cc_final: 0.6489 (ptp) REVERT: G 523 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: G 680 MET cc_start: 0.8125 (mtp) cc_final: 0.7651 (mtt) REVERT: H 231 MET cc_start: 0.7777 (mmt) cc_final: 0.7558 (mmt) REVERT: H 523 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: H 680 MET cc_start: 0.8167 (mtp) cc_final: 0.7928 (mtp) outliers start: 85 outliers final: 19 residues processed: 557 average time/residue: 1.4939 time to fit residues: 983.7620 Evaluate side-chains 500 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 462 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 523 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 523 GLU Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 523 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 1.9990 chunk 362 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 402 optimal weight: 2.9990 chunk 334 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 133 optimal weight: 0.0030 chunk 211 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 253 GLN B 114 GLN C 114 GLN C 206 GLN D 114 GLN D 206 GLN E 114 GLN E 253 GLN F 114 GLN G 114 GLN G 164 ASN H 114 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32984 Z= 0.205 Angle : 0.564 8.559 44736 Z= 0.269 Chirality : 0.044 0.154 5328 Planarity : 0.003 0.029 5648 Dihedral : 8.478 119.604 4544 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.01 % Allowed : 15.15 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.31 (0.13), residues: 4112 helix: 1.23 (0.12), residues: 1824 sheet: 0.75 (0.20), residues: 592 loop : -1.13 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 631 HIS 0.003 0.001 HIS H 710 PHE 0.009 0.001 PHE D 542 TYR 0.013 0.001 TYR H 255 ARG 0.002 0.000 ARG E 682 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 453 time to evaluate : 3.825 Fit side-chains REVERT: A 31 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7254 (mptt) REVERT: A 462 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: A 523 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6372 (mp0) REVERT: A 680 MET cc_start: 0.8160 (mtp) cc_final: 0.7727 (mtt) REVERT: B 31 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7153 (mptt) REVERT: B 231 MET cc_start: 0.7615 (mmt) cc_final: 0.6685 (mmt) REVERT: B 462 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: B 523 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: B 680 MET cc_start: 0.8162 (mtp) cc_final: 0.7896 (mtp) REVERT: B 684 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: C 31 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7296 (mptt) REVERT: C 462 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: C 523 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: C 680 MET cc_start: 0.8126 (mtp) cc_final: 0.7689 (mtt) REVERT: C 707 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7877 (ttt-90) REVERT: D 31 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7172 (mptt) REVERT: D 54 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8236 (mp) REVERT: D 231 MET cc_start: 0.7722 (mmt) cc_final: 0.7194 (mmt) REVERT: D 418 ASP cc_start: 0.7837 (t0) cc_final: 0.7556 (t70) REVERT: D 680 MET cc_start: 0.8145 (mtp) cc_final: 0.7871 (mtp) REVERT: D 684 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: E 31 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7300 (mptt) REVERT: E 462 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: E 523 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: E 680 MET cc_start: 0.8138 (mtp) cc_final: 0.7708 (mtt) REVERT: E 707 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7860 (ttt-90) REVERT: F 31 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7186 (mptt) REVERT: F 231 MET cc_start: 0.7738 (mmt) cc_final: 0.7233 (mmt) REVERT: F 462 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: F 680 MET cc_start: 0.8169 (mtp) cc_final: 0.7883 (mtp) REVERT: F 684 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: F 707 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7792 (ttt-90) REVERT: G 31 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7300 (mptt) REVERT: G 462 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: G 522 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6431 (ptp) REVERT: G 523 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: G 680 MET cc_start: 0.8126 (mtp) cc_final: 0.7680 (mtt) REVERT: H 31 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7163 (mptt) REVERT: H 231 MET cc_start: 0.7823 (mmt) cc_final: 0.7246 (mmt) REVERT: H 462 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: H 523 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: H 680 MET cc_start: 0.8180 (mtp) cc_final: 0.7917 (mtp) REVERT: H 684 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7322 (mt-10) outliers start: 107 outliers final: 41 residues processed: 506 average time/residue: 1.5233 time to fit residues: 909.1785 Evaluate side-chains 522 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 451 time to evaluate : 3.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 693 CYS Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 92 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 522 MET Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 462 GLU Chi-restraints excluded: chain H residue 523 GLU Chi-restraints excluded: chain H residue 684 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 293 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 338 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 400 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 185 optimal weight: 0.0470 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 253 GLN B 114 GLN C 114 GLN D 107 ASN D 114 GLN D 206 GLN E 114 GLN E 253 GLN F 114 GLN G 114 GLN H 114 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32984 Z= 0.196 Angle : 0.557 8.713 44736 Z= 0.265 Chirality : 0.044 0.149 5328 Planarity : 0.003 0.028 5648 Dihedral : 8.419 118.252 4544 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.04 % Allowed : 15.15 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.46 (0.13), residues: 4112 helix: 1.36 (0.12), residues: 1840 sheet: 0.81 (0.19), residues: 592 loop : -1.08 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 631 HIS 0.003 0.001 HIS F 710 PHE 0.010 0.001 PHE B 542 TYR 0.011 0.001 TYR H 255 ARG 0.002 0.000 ARG E 682 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 455 time to evaluate : 3.596 Fit side-chains REVERT: A 31 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7290 (mptt) REVERT: A 446 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 462 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: A 523 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: A 680 MET cc_start: 0.8155 (mtp) cc_final: 0.7718 (mtt) REVERT: B 31 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7156 (mptt) REVERT: B 231 MET cc_start: 0.7595 (mmt) cc_final: 0.6557 (mmt) REVERT: B 459 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: B 523 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: B 680 MET cc_start: 0.8166 (mtp) cc_final: 0.7897 (mtp) REVERT: B 684 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: C 31 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7284 (mptt) REVERT: C 446 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8150 (tp) REVERT: C 462 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: C 523 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: C 680 MET cc_start: 0.8126 (mtp) cc_final: 0.7682 (mtt) REVERT: C 707 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7855 (ttt-90) REVERT: D 31 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7171 (mptt) REVERT: D 231 MET cc_start: 0.7691 (mmt) cc_final: 0.7225 (mmt) REVERT: D 459 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: D 462 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: D 680 MET cc_start: 0.8153 (mtp) cc_final: 0.7876 (mtp) REVERT: D 684 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: E 31 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7289 (mptt) REVERT: E 462 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: E 523 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: E 680 MET cc_start: 0.8139 (mtp) cc_final: 0.7697 (mtt) REVERT: E 707 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7815 (ttt-90) REVERT: F 31 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7186 (mptt) REVERT: F 231 MET cc_start: 0.7711 (mmt) cc_final: 0.7208 (mmt) REVERT: F 459 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: F 462 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: F 680 MET cc_start: 0.8171 (mtp) cc_final: 0.7891 (mtp) REVERT: F 684 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: F 707 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7764 (ttt-90) REVERT: G 31 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7284 (mptt) REVERT: G 462 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: G 523 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: G 680 MET cc_start: 0.8116 (mtp) cc_final: 0.7662 (mtt) REVERT: H 31 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7166 (mptt) REVERT: H 231 MET cc_start: 0.7794 (mmt) cc_final: 0.7289 (mmt) REVERT: H 459 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: H 523 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: H 680 MET cc_start: 0.8181 (mtp) cc_final: 0.7912 (mtp) REVERT: H 684 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7308 (mt-10) outliers start: 108 outliers final: 40 residues processed: 506 average time/residue: 1.5449 time to fit residues: 929.5476 Evaluate side-chains 518 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 445 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 693 CYS Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain C residue 716 SER Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 192 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 523 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 459 GLU Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 693 CYS Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 523 GLU Chi-restraints excluded: chain G residue 525 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 459 GLU Chi-restraints excluded: chain H residue 523 GLU Chi-restraints excluded: chain H residue 684 GLU Chi-restraints excluded: chain H residue 693 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 5.9990 chunk 160 optimal weight: 0.0070 chunk 239 optimal weight: 0.9980 chunk 120 optimal weight: 0.0010 chunk 78 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 315 optimal weight: 2.9990 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN D 114 GLN D 206 GLN E 114 GLN F 114 GLN G 114 GLN H 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32984 Z= 0.137 Angle : 0.522 7.592 44736 Z= 0.247 Chirality : 0.043 0.147 5328 Planarity : 0.003 0.028 5648 Dihedral : 8.033 111.791 4544 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.34 % Allowed : 15.96 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.69 (0.13), residues: 4112 helix: 1.60 (0.12), residues: 1840 sheet: 0.90 (0.20), residues: 592 loop : -1.00 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 631 HIS 0.003 0.000 HIS F 710 PHE 0.011 0.001 PHE D 542 TYR 0.011 0.001 TYR B 255 ARG 0.002 0.000 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 464 time to evaluate : 3.758 Fit side-chains REVERT: A 31 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7254 (mptt) REVERT: A 462 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: A 523 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: A 680 MET cc_start: 0.8111 (mtp) cc_final: 0.7698 (mtt) REVERT: A 707 ARG cc_start: 0.8172 (tpt-90) cc_final: 0.7868 (ttt180) REVERT: B 31 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.7152 (mptt) REVERT: B 231 MET cc_start: 0.7553 (mmt) cc_final: 0.6258 (mmt) REVERT: B 680 MET cc_start: 0.8150 (mtp) cc_final: 0.7874 (mtp) REVERT: B 684 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: C 31 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7308 (mptt) REVERT: C 462 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: C 523 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: C 680 MET cc_start: 0.8097 (mtp) cc_final: 0.7686 (mtt) REVERT: C 707 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7758 (ttt-90) REVERT: D 31 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7213 (mptt) REVERT: D 231 MET cc_start: 0.7615 (mmt) cc_final: 0.7338 (mmt) REVERT: D 680 MET cc_start: 0.8124 (mtp) cc_final: 0.7844 (mtp) REVERT: D 684 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: E 31 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7317 (mptt) REVERT: E 462 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: E 557 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7901 (tttt) REVERT: E 680 MET cc_start: 0.8095 (mtp) cc_final: 0.7677 (mtt) REVERT: E 707 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7801 (ttt-90) REVERT: F 31 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7192 (mptt) REVERT: F 680 MET cc_start: 0.8164 (mtp) cc_final: 0.7894 (mtp) REVERT: F 707 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7827 (ttt180) REVERT: G 31 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7311 (mptt) REVERT: G 462 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: G 680 MET cc_start: 0.8081 (mtp) cc_final: 0.7657 (mtt) REVERT: H 31 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7159 (mptt) REVERT: H 231 MET cc_start: 0.7729 (mmt) cc_final: 0.7334 (mmt) REVERT: H 680 MET cc_start: 0.8164 (mtp) cc_final: 0.7892 (mtp) outliers start: 83 outliers final: 28 residues processed: 506 average time/residue: 1.4699 time to fit residues: 879.8021 Evaluate side-chains 491 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 444 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 693 CYS Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 594 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 693 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 6.9990 chunk 384 optimal weight: 0.9990 chunk 350 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 337 optimal weight: 6.9990 chunk 353 optimal weight: 0.0040 chunk 372 optimal weight: 8.9990 overall best weight: 0.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN C 114 GLN D 114 GLN D 206 GLN E 114 GLN F 114 GLN G 114 GLN H 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32984 Z= 0.166 Angle : 0.537 7.595 44736 Z= 0.255 Chirality : 0.043 0.155 5328 Planarity : 0.003 0.028 5648 Dihedral : 8.183 116.121 4544 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.00 % Allowed : 16.72 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.13), residues: 4112 helix: 1.66 (0.12), residues: 1840 sheet: 0.94 (0.20), residues: 592 loop : -0.99 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 631 HIS 0.003 0.001 HIS F 710 PHE 0.010 0.001 PHE B 542 TYR 0.010 0.001 TYR A 718 ARG 0.002 0.000 ARG D 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 445 time to evaluate : 3.791 Fit side-chains REVERT: A 31 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7280 (mptt) REVERT: A 462 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: A 680 MET cc_start: 0.8111 (mtp) cc_final: 0.7695 (mtt) REVERT: B 31 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7196 (mptt) REVERT: B 231 MET cc_start: 0.7614 (mmt) cc_final: 0.6318 (mmt) REVERT: B 680 MET cc_start: 0.8151 (mtp) cc_final: 0.7865 (mtp) REVERT: B 684 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: C 31 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7276 (mptt) REVERT: C 462 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: C 680 MET cc_start: 0.8097 (mtp) cc_final: 0.7684 (mtt) REVERT: C 707 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7828 (ttt-90) REVERT: D 31 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7200 (mptt) REVERT: D 54 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8241 (mp) REVERT: D 462 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: D 680 MET cc_start: 0.8137 (mtp) cc_final: 0.7852 (mtp) REVERT: D 684 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: E 31 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7284 (mptt) REVERT: E 462 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: E 680 MET cc_start: 0.8093 (mtp) cc_final: 0.7682 (mtt) REVERT: E 707 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7828 (ttt-90) REVERT: F 31 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7210 (mptt) REVERT: F 231 MET cc_start: 0.7779 (mmt) cc_final: 0.7220 (mmt) REVERT: F 462 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: F 680 MET cc_start: 0.8175 (mtp) cc_final: 0.7905 (mtp) REVERT: F 707 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7847 (ttt180) REVERT: G 31 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7280 (mptt) REVERT: G 103 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8742 (mp) REVERT: H 31 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7199 (mptt) REVERT: H 231 MET cc_start: 0.7723 (mmt) cc_final: 0.7304 (mmt) REVERT: H 680 MET cc_start: 0.8168 (mtp) cc_final: 0.7885 (mtp) outliers start: 71 outliers final: 37 residues processed: 487 average time/residue: 1.5144 time to fit residues: 875.5169 Evaluate side-chains 497 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 440 time to evaluate : 3.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 693 CYS Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 594 MET Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 525 LYS Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 693 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 6.9990 chunk 395 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 274 optimal weight: 9.9990 chunk 414 optimal weight: 0.8980 chunk 381 optimal weight: 0.8980 chunk 330 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 254 optimal weight: 1.9990 chunk 202 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 114 GLN B 246 HIS C 114 GLN D 114 GLN D 206 GLN E 114 GLN F 114 GLN G 114 GLN H 114 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32984 Z= 0.149 Angle : 0.528 7.379 44736 Z= 0.250 Chirality : 0.043 0.155 5328 Planarity : 0.003 0.029 5648 Dihedral : 8.099 113.753 4544 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.03 % Allowed : 16.78 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.81 (0.13), residues: 4112 helix: 1.71 (0.12), residues: 1840 sheet: 0.94 (0.20), residues: 592 loop : -0.95 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 631 HIS 0.003 0.001 HIS B 710 PHE 0.011 0.001 PHE D 542 TYR 0.010 0.001 TYR B 255 ARG 0.001 0.000 ARG D 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8224 Ramachandran restraints generated. 4112 Oldfield, 0 Emsley, 4112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 452 time to evaluate : 3.876 Fit side-chains REVERT: A 31 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7292 (mptt) REVERT: A 680 MET cc_start: 0.8106 (mtp) cc_final: 0.7687 (mtt) REVERT: A 707 ARG cc_start: 0.8213 (tpt-90) cc_final: 0.7909 (ttt180) REVERT: B 31 LYS cc_start: 0.7539 (OUTLIER) cc_final: 0.7178 (mptt) REVERT: B 231 MET cc_start: 0.7602 (mmt) cc_final: 0.6229 (mmt) REVERT: B 680 MET cc_start: 0.8144 (mtp) cc_final: 0.7864 (mtp) REVERT: B 684 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: C 31 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7301 (mptt) REVERT: C 680 MET cc_start: 0.8083 (mtp) cc_final: 0.7672 (mtt) REVERT: C 707 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7826 (ttt-90) REVERT: D 31 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7188 (mptt) REVERT: D 231 MET cc_start: 0.7762 (mmt) cc_final: 0.7088 (mmt) REVERT: D 462 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: D 680 MET cc_start: 0.8126 (mtp) cc_final: 0.7862 (mtp) REVERT: D 684 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: E 31 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7307 (mptt) REVERT: E 462 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: E 680 MET cc_start: 0.8090 (mtp) cc_final: 0.7680 (mtt) REVERT: E 707 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7815 (ttt-90) REVERT: F 31 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7197 (mptt) REVERT: F 231 MET cc_start: 0.7760 (mmt) cc_final: 0.6962 (mmt) REVERT: F 418 ASP cc_start: 0.7850 (t0) cc_final: 0.7552 (t0) REVERT: F 462 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: F 680 MET cc_start: 0.8165 (mtp) cc_final: 0.7889 (mtp) REVERT: F 684 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: F 707 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7835 (ttt180) REVERT: G 31 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7293 (mptt) REVERT: G 103 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8734 (mp) REVERT: G 680 MET cc_start: 0.8079 (mtp) cc_final: 0.7653 (mtt) REVERT: H 31 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7167 (mptt) REVERT: H 231 MET cc_start: 0.7712 (mmt) cc_final: 0.7290 (mmt) REVERT: H 459 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7210 (mp0) REVERT: H 680 MET cc_start: 0.8165 (mtp) cc_final: 0.7889 (mtp) REVERT: H 684 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7328 (mt-10) outliers start: 72 outliers final: 37 residues processed: 493 average time/residue: 1.4425 time to fit residues: 844.0279 Evaluate side-chains 502 residues out of total 3552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 445 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 716 SER Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 693 CYS Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 693 CYS Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 516 SER Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 446 LEU Chi-restraints excluded: chain F residue 462 GLU Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 516 SER Chi-restraints excluded: chain G residue 684 GLU Chi-restraints excluded: chain G residue 716 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 446 LEU Chi-restraints excluded: chain H residue 459 GLU Chi-restraints excluded: chain H residue 684 GLU Chi-restraints excluded: chain H residue 693 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 3.9990 chunk 351 optimal weight: 0.0770 chunk 101 optimal weight: 5.9990 chunk 304 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 330 optimal weight: 2.9990 chunk 138 optimal weight: 0.3980 chunk 339 optimal weight: 0.7980 chunk 41 optimal weight: 0.0570 chunk 60 optimal weight: 4.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 246 HIS C 114 GLN D 107 ASN D 114 GLN D 206 GLN E 114 GLN E 192 ASN F 107 ASN F 114 GLN G 114 GLN H 114 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.186413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3443 r_free = 0.3443 target = 0.134667 restraints weight = 32069.633| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.78 r_work: 0.3179 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 32984 Z= 0.125 Angle : 0.515 7.239 44736 Z= 0.244 Chirality : 0.043 0.152 5328 Planarity : 0.003 0.028 5648 Dihedral : 7.845 108.950 4544 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 17.12 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.13), residues: 4112 helix: 1.84 (0.12), residues: 1832 sheet: 0.98 (0.20), residues: 592 loop : -0.81 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 631 HIS 0.002 0.000 HIS F 710 PHE 0.011 0.001 PHE D 542 TYR 0.011 0.001 TYR B 255 ARG 0.002 0.000 ARG D 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14311.72 seconds wall clock time: 256 minutes 33.89 seconds (15393.89 seconds total)