Starting phenix.real_space_refine on Fri Mar 22 11:32:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl3_22371/03_2024/7jl3_22371_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl3_22371/03_2024/7jl3_22371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl3_22371/03_2024/7jl3_22371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl3_22371/03_2024/7jl3_22371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl3_22371/03_2024/7jl3_22371_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl3_22371/03_2024/7jl3_22371_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12144 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 3 6.06 5 Al 3 5.89 5 P 90 5.49 5 Mg 3 5.21 5 S 120 5.16 5 C 13251 2.51 5 N 3633 2.21 5 O 4104 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C ASP 585": "OD1" <-> "OD2" Residue "C PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 730": "NH1" <-> "NH2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 890": "OE1" <-> "OE2" Residue "C ASP 910": "OD1" <-> "OD2" Residue "D PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ASP 425": "OD1" <-> "OD2" Residue "E GLU 483": "OE1" <-> "OE2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "E ASP 585": "OD1" <-> "OD2" Residue "E PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 730": "NH1" <-> "NH2" Residue "E GLU 773": "OE1" <-> "OE2" Residue "E TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 890": "OE1" <-> "OE2" Residue "E ASP 910": "OD1" <-> "OD2" Residue "F PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "F ARG 342": "NH1" <-> "NH2" Residue "F TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21219 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5145 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 624} Chain breaks: 7 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1299 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5145 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 624} Chain breaks: 7 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1299 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5145 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 25, 'TRANS': 624} Chain breaks: 7 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "F" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1299 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "X" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 900 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 23, 'rna3p_pyr': 18} Link IDs: {'rna2p': 1, 'rna3p': 40} Chain: "Y" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 885 Classifications: {'RNA': 42} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 24} Link IDs: {'rna3p': 41} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4323 SG CYS A 810 96.252 96.843 76.846 1.00136.66 S ATOM 4349 SG CYS A 813 99.463 98.927 77.236 1.00133.12 S ATOM 4693 SG CYS A 864 98.588 97.784 73.898 1.00142.99 S ATOM 4732 SG CYS A 869 99.736 95.267 76.581 1.00150.16 S ATOM 10767 SG CYS C 810 95.090 66.122 30.617 1.00134.83 S ATOM 10793 SG CYS C 813 97.879 63.500 31.014 1.00134.18 S ATOM 11137 SG CYS C 864 96.564 64.072 27.674 1.00153.89 S ATOM 11176 SG CYS C 869 94.390 62.362 30.359 1.00148.92 S ATOM 17211 SG CYS E 810 66.936 105.513 123.134 1.00135.45 S ATOM 17237 SG CYS E 813 65.696 109.134 123.531 1.00139.28 S ATOM 17581 SG CYS E 864 66.583 108.011 120.190 1.00148.20 S ATOM 17620 SG CYS E 869 69.311 108.510 122.868 1.00148.98 S Time building chain proxies: 11.31, per 1000 atoms: 0.53 Number of scatterers: 21219 At special positions: 0 Unit cell: (161.515, 131.296, 160.473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 S 120 16.00 P 90 15.00 Al 3 13.00 Mg 3 11.99 F 12 9.00 O 4104 8.00 N 3633 7.00 C 13251 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: 9.19 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 813 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 864 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 869 " pdb="ZN ZN A2004 " - pdb=" SG CYS A 810 " pdb=" ZN C2004 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 813 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 864 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 869 " pdb="ZN ZN C2004 " - pdb=" SG CYS C 810 " pdb=" ZN E2004 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 813 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 864 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 869 " pdb="ZN ZN E2004 " - pdb=" SG CYS E 810 " Number of angles added : 18 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 27 sheets defined 37.7% alpha, 14.4% beta 32 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 9.10 Creating SS restraints... Processing helix chain 'A' and resid 245 through 256 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 334 through 340 removed outlier: 4.572A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.517A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 3.543A pdb=" N GLN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.646A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 520 Processing helix chain 'A' and resid 529 through 557 Processing helix chain 'A' and resid 560 through 573 removed outlier: 4.037A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.744A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 675 through 685 removed outlier: 3.673A pdb=" N PHE A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 700 No H-bonds generated for 'chain 'A' and resid 698 through 700' Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.922A pdb=" N ARG A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 removed outlier: 3.655A pdb=" N LEU A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 794 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 836 through 841 removed outlier: 3.518A pdb=" N CYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'C' and resid 245 through 256 Proline residue: C 253 - end of helix Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.573A pdb=" N GLU C 339 " --> pdb=" O GLU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 357 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 382 through 395 Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.517A pdb=" N LEU C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 452 removed outlier: 3.543A pdb=" N GLN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 489 removed outlier: 3.646A pdb=" N ILE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 529 through 557 Processing helix chain 'C' and resid 560 through 573 removed outlier: 4.037A pdb=" N LEU C 564 " --> pdb=" O MET C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 601 removed outlier: 3.745A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 606 No H-bonds generated for 'chain 'C' and resid 604 through 606' Processing helix chain 'C' and resid 609 through 624 Processing helix chain 'C' and resid 637 through 648 Processing helix chain 'C' and resid 675 through 685 removed outlier: 3.672A pdb=" N PHE C 685 " --> pdb=" O ILE C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 700 No H-bonds generated for 'chain 'C' and resid 698 through 700' Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.922A pdb=" N ARG C 730 " --> pdb=" O GLN C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 770 removed outlier: 3.656A pdb=" N LEU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 794 Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 836 through 841 removed outlier: 3.517A pdb=" N CYS C 841 " --> pdb=" O ALA C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 889 through 891 No H-bonds generated for 'chain 'C' and resid 889 through 891' Processing helix chain 'E' and resid 245 through 256 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 270 through 283 Processing helix chain 'E' and resid 300 through 314 Processing helix chain 'E' and resid 334 through 340 removed outlier: 4.572A pdb=" N GLU E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 357 Processing helix chain 'E' and resid 363 through 365 No H-bonds generated for 'chain 'E' and resid 363 through 365' Processing helix chain 'E' and resid 374 through 376 No H-bonds generated for 'chain 'E' and resid 374 through 376' Processing helix chain 'E' and resid 382 through 395 Processing helix chain 'E' and resid 420 through 434 removed outlier: 3.518A pdb=" N LEU E 434 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 452 removed outlier: 3.543A pdb=" N GLN E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 489 removed outlier: 3.647A pdb=" N ILE E 489 " --> pdb=" O LEU E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 520 Processing helix chain 'E' and resid 529 through 557 Processing helix chain 'E' and resid 560 through 573 removed outlier: 4.037A pdb=" N LEU E 564 " --> pdb=" O MET E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 582 through 601 removed outlier: 3.745A pdb=" N LYS E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLN E 595 " --> pdb=" O GLU E 591 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU E 596 " --> pdb=" O GLU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 606 No H-bonds generated for 'chain 'E' and resid 604 through 606' Processing helix chain 'E' and resid 609 through 624 Processing helix chain 'E' and resid 637 through 648 Processing helix chain 'E' and resid 675 through 685 removed outlier: 3.673A pdb=" N PHE E 685 " --> pdb=" O ILE E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 700 No H-bonds generated for 'chain 'E' and resid 698 through 700' Processing helix chain 'E' and resid 721 through 730 removed outlier: 3.923A pdb=" N ARG E 730 " --> pdb=" O GLN E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 745 through 770 removed outlier: 3.656A pdb=" N LEU E 766 " --> pdb=" O ASN E 762 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 770 " --> pdb=" O LEU E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 776 through 794 Processing helix chain 'E' and resid 820 through 822 No H-bonds generated for 'chain 'E' and resid 820 through 822' Processing helix chain 'E' and resid 836 through 841 removed outlier: 3.517A pdb=" N CYS E 841 " --> pdb=" O ALA E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 889 through 891 No H-bonds generated for 'chain 'E' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 438 through 440 Processing sheet with id= B, first strand: chain 'A' and resid 457 through 462 Processing sheet with id= C, first strand: chain 'A' and resid 892 through 895 removed outlier: 6.317A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 826 Processing sheet with id= E, first strand: chain 'A' and resid 842 through 844 Processing sheet with id= F, first strand: chain 'A' and resid 874 through 878 Processing sheet with id= G, first strand: chain 'B' and resid 272 through 274 Processing sheet with id= H, first strand: chain 'B' and resid 301 through 303 removed outlier: 4.209A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 348 " --> pdb=" O TRP B 360 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 357 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 313 through 317 removed outlier: 4.588A pdb=" N VAL B 375 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 438 through 440 Processing sheet with id= K, first strand: chain 'C' and resid 457 through 462 Processing sheet with id= L, first strand: chain 'C' and resid 892 through 895 removed outlier: 6.317A pdb=" N CYS C 810 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 816 " --> pdb=" O CYS C 810 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 823 through 826 Processing sheet with id= N, first strand: chain 'C' and resid 842 through 844 Processing sheet with id= O, first strand: chain 'C' and resid 874 through 878 Processing sheet with id= P, first strand: chain 'D' and resid 272 through 274 Processing sheet with id= Q, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.209A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 356 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 357 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 313 through 317 removed outlier: 4.586A pdb=" N VAL D 375 " --> pdb=" O VAL D 392 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 438 through 440 Processing sheet with id= T, first strand: chain 'E' and resid 457 through 462 Processing sheet with id= U, first strand: chain 'E' and resid 892 through 895 removed outlier: 6.317A pdb=" N CYS E 810 " --> pdb=" O LEU E 816 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU E 816 " --> pdb=" O CYS E 810 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 823 through 826 Processing sheet with id= W, first strand: chain 'E' and resid 842 through 844 Processing sheet with id= X, first strand: chain 'E' and resid 874 through 878 Processing sheet with id= Y, first strand: chain 'F' and resid 272 through 274 Processing sheet with id= Z, first strand: chain 'F' and resid 301 through 303 removed outlier: 4.209A pdb=" N TRP F 325 " --> pdb=" O TRP F 351 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS F 348 " --> pdb=" O TRP F 360 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN F 356 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 357 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 313 through 317 removed outlier: 4.587A pdb=" N VAL F 375 " --> pdb=" O VAL F 392 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2502 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 8.31 Time building geometry restraints manager: 9.89 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: 6169 1.34 - 1.45: 3796 1.45 - 1.57: 11509 1.57 - 1.69: 178 1.69 - 1.81: 174 Bond restraints: 21826 Sorted by residual: bond pdb=" CA LEU E 493 " pdb=" C LEU E 493 " ideal model delta sigma weight residual 1.523 1.623 -0.100 1.34e-02 5.57e+03 5.58e+01 bond pdb=" F2 ALF E2002 " pdb="AL ALF E2002 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" F2 ALF C2002 " pdb="AL ALF C2002 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" F2 ALF A2002 " pdb="AL ALF A2002 " ideal model delta sigma weight residual 1.685 1.805 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CA LEU C 493 " pdb=" C LEU C 493 " ideal model delta sigma weight residual 1.520 1.596 -0.076 1.37e-02 5.33e+03 3.05e+01 ... (remaining 21821 not shown) Histogram of bond angle deviations from ideal: 89.37 - 107.41: 1265 107.41 - 125.45: 28059 125.45 - 143.50: 602 143.50 - 161.54: 0 161.54 - 179.58: 6 Bond angle restraints: 29932 Sorted by residual: angle pdb=" F3 ALF C2002 " pdb="AL ALF C2002 " pdb=" F4 ALF C2002 " ideal model delta sigma weight residual 109.63 179.58 -69.95 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F3 ALF A2002 " pdb="AL ALF A2002 " pdb=" F4 ALF A2002 " ideal model delta sigma weight residual 109.63 179.58 -69.95 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F3 ALF E2002 " pdb="AL ALF E2002 " pdb=" F4 ALF E2002 " ideal model delta sigma weight residual 109.63 179.57 -69.94 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F1 ALF A2002 " pdb="AL ALF A2002 " pdb=" F2 ALF A2002 " ideal model delta sigma weight residual 108.68 178.43 -69.75 3.00e+00 1.11e-01 5.41e+02 angle pdb=" F1 ALF C2002 " pdb="AL ALF C2002 " pdb=" F2 ALF C2002 " ideal model delta sigma weight residual 108.68 178.41 -69.73 3.00e+00 1.11e-01 5.40e+02 ... (remaining 29927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 12620 32.54 - 65.08: 517 65.08 - 97.61: 44 97.61 - 130.15: 3 130.15 - 162.69: 10 Dihedral angle restraints: 13194 sinusoidal: 6015 harmonic: 7179 Sorted by residual: dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 91.72 -151.72 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP C2001 " pdb=" O5' ADP C2001 " pdb=" PA ADP C2001 " pdb=" O2A ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 91.71 -151.71 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" C5' ADP E2001 " pdb=" O5' ADP E2001 " pdb=" PA ADP E2001 " pdb=" O2A ADP E2001 " ideal model delta sinusoidal sigma weight residual -60.00 91.69 -151.69 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 13191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3092 0.071 - 0.143: 339 0.143 - 0.214: 27 0.214 - 0.286: 3 0.286 - 0.357: 1 Chirality restraints: 3462 Sorted by residual: chirality pdb=" CA ASP E 492 " pdb=" N ASP E 492 " pdb=" C ASP E 492 " pdb=" CB ASP E 492 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP C 492 " pdb=" N ASP C 492 " pdb=" C ASP C 492 " pdb=" CB ASP C 492 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' A X 2 " pdb=" C4' A X 2 " pdb=" O3' A X 2 " pdb=" C2' A X 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 3459 not shown) Planarity restraints: 3435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 2 " 0.039 2.00e-02 2.50e+03 1.79e-02 8.82e+00 pdb=" N9 A X 2 " -0.042 2.00e-02 2.50e+03 pdb=" C8 A X 2 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A X 2 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A X 2 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A X 2 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A X 2 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A X 2 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A X 2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A X 2 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A X 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 408 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO D 409 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 409 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 409 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 408 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO F 409 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 409 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 409 " -0.037 5.00e-02 4.00e+02 ... (remaining 3432 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 238 2.58 - 3.16: 17856 3.16 - 3.74: 33796 3.74 - 4.32: 43686 4.32 - 4.90: 70352 Nonbonded interactions: 165928 Sorted by model distance: nonbonded pdb=" O1B ADP C2001 " pdb="MG MG C2003 " model vdw 1.999 2.170 nonbonded pdb=" O1B ADP E2001 " pdb="MG MG E2003 " model vdw 2.000 2.170 nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2003 " model vdw 2.000 2.170 nonbonded pdb=" F4 ALF C2002 " pdb="MG MG C2003 " model vdw 2.015 2.120 nonbonded pdb=" F4 ALF A2002 " pdb="MG MG A2003 " model vdw 2.016 2.120 ... (remaining 165923 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 7.240 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 67.780 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.004 0.120 21826 Z= 0.267 Angle : 1.316 69.949 29932 Z= 0.553 Chirality : 0.045 0.357 3462 Planarity : 0.004 0.067 3435 Dihedral : 17.306 162.689 8514 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.45 % Allowed : 0.39 % Favored : 98.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2379 helix: 1.47 (0.17), residues: 909 sheet: -0.42 (0.25), residues: 411 loop : -0.45 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 512 HIS 0.011 0.001 HIS C 444 PHE 0.010 0.001 PHE B 389 TYR 0.035 0.002 TYR E 756 ARG 0.010 0.001 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 303 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 TRP cc_start: 0.8752 (m-90) cc_final: 0.8430 (m-90) REVERT: B 352 LYS cc_start: 0.8964 (ptmt) cc_final: 0.8585 (pttm) REVERT: B 381 ASN cc_start: 0.7676 (p0) cc_final: 0.5907 (p0) REVERT: B 428 LYS cc_start: 0.9068 (tptt) cc_final: 0.8712 (tptp) REVERT: D 352 LYS cc_start: 0.8921 (ptmt) cc_final: 0.8593 (pttm) REVERT: D 417 TYR cc_start: 0.8565 (t80) cc_final: 0.8193 (t80) REVERT: D 428 LYS cc_start: 0.9077 (tptt) cc_final: 0.8714 (tptp) REVERT: E 881 THR cc_start: 0.7416 (t) cc_final: 0.7190 (p) REVERT: F 352 LYS cc_start: 0.9022 (ptmt) cc_final: 0.8650 (pttm) REVERT: F 381 ASN cc_start: 0.7690 (p0) cc_final: 0.6164 (p0) REVERT: F 414 PHE cc_start: 0.8946 (m-10) cc_final: 0.8659 (m-10) REVERT: F 428 LYS cc_start: 0.9099 (tptt) cc_final: 0.8840 (tptp) outliers start: 30 outliers final: 5 residues processed: 321 average time/residue: 0.3252 time to fit residues: 159.9703 Evaluate side-chains 169 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 164 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 105 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 623 HIS A 784 GLN B 260 HIS C 623 HIS C 784 GLN D 260 HIS ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN E 623 HIS E 784 GLN ** F 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21826 Z= 0.280 Angle : 0.949 32.580 29932 Z= 0.412 Chirality : 0.042 0.223 3462 Planarity : 0.004 0.043 3435 Dihedral : 16.900 179.552 3927 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2379 helix: 1.52 (0.16), residues: 921 sheet: -0.18 (0.25), residues: 447 loop : -0.45 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 360 HIS 0.006 0.001 HIS C 375 PHE 0.020 0.002 PHE F 263 TYR 0.033 0.002 TYR A 756 ARG 0.003 0.001 ARG D 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 THR cc_start: 0.8541 (m) cc_final: 0.8323 (p) REVERT: C 680 CYS cc_start: 0.8371 (m) cc_final: 0.8021 (t) REVERT: D 360 TRP cc_start: 0.7543 (m100) cc_final: 0.6849 (m100) REVERT: D 428 LYS cc_start: 0.9047 (tptt) cc_final: 0.8745 (tptp) REVERT: F 389 PHE cc_start: 0.7348 (m-10) cc_final: 0.7105 (m-10) REVERT: F 414 PHE cc_start: 0.8889 (m-10) cc_final: 0.8622 (m-10) REVERT: F 428 LYS cc_start: 0.9093 (tptt) cc_final: 0.8822 (tptp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3478 time to fit residues: 102.4785 Evaluate side-chains 128 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS B 423 ASN C 623 HIS D 423 ASN ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 ASN ** F 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21826 Z= 0.282 Angle : 0.945 29.878 29932 Z= 0.411 Chirality : 0.042 0.220 3462 Planarity : 0.004 0.047 3435 Dihedral : 16.869 179.337 3927 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2379 helix: 1.71 (0.16), residues: 903 sheet: -0.29 (0.25), residues: 432 loop : -0.24 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 360 HIS 0.006 0.001 HIS C 375 PHE 0.024 0.002 PHE D 263 TYR 0.028 0.002 TYR E 622 ARG 0.005 0.000 ARG C 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 366 THR cc_start: 0.8509 (m) cc_final: 0.8290 (p) REVERT: C 680 CYS cc_start: 0.8358 (m) cc_final: 0.8074 (t) REVERT: C 755 MET cc_start: 0.8808 (ptp) cc_final: 0.8577 (ptp) REVERT: D 350 GLU cc_start: 0.7862 (tp30) cc_final: 0.7295 (tp30) REVERT: D 360 TRP cc_start: 0.7683 (m100) cc_final: 0.6876 (m100) REVERT: D 381 ASN cc_start: 0.7950 (p0) cc_final: 0.7493 (p0) REVERT: D 386 LYS cc_start: 0.7733 (mmmt) cc_final: 0.7334 (mmmt) REVERT: E 387 MET cc_start: 0.8544 (mmm) cc_final: 0.8219 (mmp) REVERT: F 288 GLN cc_start: 0.9205 (tp40) cc_final: 0.8977 (tp40) REVERT: F 401 GLU cc_start: 0.8490 (mp0) cc_final: 0.8228 (mp0) REVERT: F 414 PHE cc_start: 0.8944 (m-10) cc_final: 0.8664 (m-10) REVERT: F 427 ILE cc_start: 0.9185 (pt) cc_final: 0.8872 (pt) outliers start: 2 outliers final: 2 residues processed: 183 average time/residue: 0.3321 time to fit residues: 94.9185 Evaluate side-chains 122 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 10.0000 chunk 171 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 0.1980 chunk 153 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 623 HIS ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 623 HIS ** C 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21826 Z= 0.229 Angle : 0.912 29.647 29932 Z= 0.389 Chirality : 0.041 0.212 3462 Planarity : 0.004 0.053 3435 Dihedral : 16.739 179.368 3927 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2379 helix: 1.90 (0.16), residues: 900 sheet: -0.30 (0.25), residues: 432 loop : -0.19 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 360 HIS 0.004 0.001 HIS C 375 PHE 0.016 0.001 PHE D 263 TYR 0.016 0.002 TYR A 756 ARG 0.004 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8365 (tp) cc_final: 0.7871 (tt) REVERT: B 288 GLN cc_start: 0.8843 (mt0) cc_final: 0.8541 (mp10) REVERT: B 366 THR cc_start: 0.8543 (m) cc_final: 0.8330 (p) REVERT: C 680 CYS cc_start: 0.8366 (m) cc_final: 0.8027 (t) REVERT: C 755 MET cc_start: 0.8731 (ptp) cc_final: 0.8459 (ptp) REVERT: D 360 TRP cc_start: 0.7710 (m100) cc_final: 0.6925 (m100) REVERT: D 381 ASN cc_start: 0.7842 (p0) cc_final: 0.7534 (p0) REVERT: D 386 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7271 (mmmt) REVERT: D 389 PHE cc_start: 0.7135 (m-10) cc_final: 0.6900 (m-10) REVERT: D 428 LYS cc_start: 0.9038 (tptt) cc_final: 0.8803 (tmtt) REVERT: F 288 GLN cc_start: 0.9224 (tp40) cc_final: 0.8965 (tp40) REVERT: F 401 GLU cc_start: 0.8587 (mp0) cc_final: 0.8337 (mp0) REVERT: F 414 PHE cc_start: 0.8958 (m-10) cc_final: 0.8540 (m-10) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3319 time to fit residues: 92.2066 Evaluate side-chains 123 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 180 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 217 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 GLN E 573 ASN ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 21826 Z= 0.158 Angle : 0.887 29.792 29932 Z= 0.368 Chirality : 0.041 0.203 3462 Planarity : 0.003 0.056 3435 Dihedral : 16.432 176.546 3927 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2379 helix: 2.27 (0.17), residues: 909 sheet: -0.17 (0.25), residues: 432 loop : -0.13 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 292 HIS 0.011 0.001 HIS E 557 PHE 0.015 0.001 PHE D 263 TYR 0.014 0.001 TYR A 756 ARG 0.005 0.000 ARG E 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 257 TRP cc_start: 0.8657 (m-90) cc_final: 0.8451 (m-90) REVERT: B 288 GLN cc_start: 0.8870 (mt0) cc_final: 0.8564 (mp10) REVERT: B 428 LYS cc_start: 0.9008 (tptt) cc_final: 0.8701 (tmtt) REVERT: C 346 LEU cc_start: 0.8770 (tp) cc_final: 0.8498 (tp) REVERT: C 680 CYS cc_start: 0.8360 (m) cc_final: 0.8014 (t) REVERT: D 360 TRP cc_start: 0.7666 (m100) cc_final: 0.6905 (m100) REVERT: D 381 ASN cc_start: 0.8000 (p0) cc_final: 0.7638 (p0) REVERT: D 386 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7468 (mmmt) REVERT: D 389 PHE cc_start: 0.7099 (m-10) cc_final: 0.6784 (m-10) REVERT: D 427 ILE cc_start: 0.9063 (pt) cc_final: 0.8751 (pt) REVERT: D 428 LYS cc_start: 0.8999 (tptt) cc_final: 0.8754 (tmtt) REVERT: F 288 GLN cc_start: 0.9214 (tp40) cc_final: 0.9005 (tp40) REVERT: F 401 GLU cc_start: 0.8679 (mp0) cc_final: 0.8382 (mp0) REVERT: F 414 PHE cc_start: 0.8876 (m-10) cc_final: 0.8510 (m-10) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3164 time to fit residues: 90.9566 Evaluate side-chains 131 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 242 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS E 678 GLN ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21826 Z= 0.345 Angle : 0.967 31.146 29932 Z= 0.431 Chirality : 0.043 0.221 3462 Planarity : 0.004 0.055 3435 Dihedral : 16.656 177.627 3927 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2379 helix: 1.45 (0.16), residues: 924 sheet: -0.32 (0.26), residues: 402 loop : -0.42 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 360 HIS 0.010 0.002 HIS A 557 PHE 0.021 0.002 PHE F 263 TYR 0.016 0.002 TYR A 313 ARG 0.007 0.001 ARG E 732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8392 (tp) cc_final: 0.7878 (tt) REVERT: B 257 TRP cc_start: 0.8840 (m-90) cc_final: 0.8519 (m-90) REVERT: B 288 GLN cc_start: 0.8894 (mt0) cc_final: 0.8585 (mp10) REVERT: B 427 ILE cc_start: 0.9199 (pt) cc_final: 0.8907 (pt) REVERT: B 428 LYS cc_start: 0.8940 (tptt) cc_final: 0.8659 (tmtt) REVERT: C 680 CYS cc_start: 0.8409 (m) cc_final: 0.8059 (t) REVERT: D 356 GLN cc_start: 0.9446 (mm-40) cc_final: 0.8917 (mm110) REVERT: D 360 TRP cc_start: 0.7792 (m100) cc_final: 0.7022 (m100) REVERT: D 381 ASN cc_start: 0.7957 (p0) cc_final: 0.7551 (p0) REVERT: D 386 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7530 (mmmt) REVERT: E 560 MET cc_start: 0.7158 (tpp) cc_final: 0.6869 (tpt) REVERT: F 280 THR cc_start: 0.8822 (p) cc_final: 0.8620 (p) REVERT: F 288 GLN cc_start: 0.9120 (tp40) cc_final: 0.8813 (tp40) REVERT: F 414 PHE cc_start: 0.8977 (m-10) cc_final: 0.8687 (m-10) REVERT: F 420 HIS cc_start: 0.9149 (t-90) cc_final: 0.8949 (t-90) REVERT: F 428 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8793 (tptp) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3360 time to fit residues: 83.1457 Evaluate side-chains 119 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 0.0060 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 241 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS ** C 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 678 GLN ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21826 Z= 0.173 Angle : 0.893 29.868 29932 Z= 0.376 Chirality : 0.041 0.203 3462 Planarity : 0.003 0.057 3435 Dihedral : 16.410 178.934 3927 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2379 helix: 2.04 (0.17), residues: 924 sheet: -0.18 (0.25), residues: 426 loop : -0.33 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 512 HIS 0.006 0.001 HIS A 557 PHE 0.017 0.001 PHE E 776 TYR 0.015 0.001 TYR A 756 ARG 0.003 0.000 ARG F 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 GLN cc_start: 0.8909 (mt0) cc_final: 0.8587 (mp10) REVERT: B 389 PHE cc_start: 0.6834 (m-10) cc_final: 0.6591 (m-10) REVERT: B 428 LYS cc_start: 0.8987 (tptt) cc_final: 0.8678 (tmtt) REVERT: C 680 CYS cc_start: 0.8383 (m) cc_final: 0.7975 (t) REVERT: D 360 TRP cc_start: 0.7727 (m100) cc_final: 0.7009 (m100) REVERT: D 381 ASN cc_start: 0.7978 (p0) cc_final: 0.7548 (p0) REVERT: D 386 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7579 (mmmt) REVERT: D 427 ILE cc_start: 0.9254 (pt) cc_final: 0.9041 (pt) REVERT: D 428 LYS cc_start: 0.9067 (tptt) cc_final: 0.8769 (tmtt) REVERT: F 288 GLN cc_start: 0.9203 (tp40) cc_final: 0.8882 (tp40) REVERT: F 389 PHE cc_start: 0.7741 (m-80) cc_final: 0.7447 (m-10) REVERT: F 414 PHE cc_start: 0.8942 (m-10) cc_final: 0.8620 (m-10) REVERT: F 428 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8790 (tptp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.3333 time to fit residues: 87.1016 Evaluate side-chains 118 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 153 optimal weight: 30.0000 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN C 445 ASN C 623 HIS E 445 ASN ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21826 Z= 0.323 Angle : 0.955 30.279 29932 Z= 0.423 Chirality : 0.043 0.217 3462 Planarity : 0.004 0.054 3435 Dihedral : 16.583 177.870 3927 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2379 helix: 1.51 (0.16), residues: 921 sheet: -0.30 (0.26), residues: 402 loop : -0.43 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 360 HIS 0.007 0.001 HIS A 375 PHE 0.018 0.002 PHE F 263 TYR 0.016 0.002 TYR E 313 ARG 0.006 0.001 ARG E 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 427 ILE cc_start: 0.9261 (pt) cc_final: 0.8920 (pt) REVERT: B 428 LYS cc_start: 0.8982 (tptt) cc_final: 0.8659 (tmtt) REVERT: C 680 CYS cc_start: 0.8370 (m) cc_final: 0.8024 (t) REVERT: D 360 TRP cc_start: 0.7722 (m100) cc_final: 0.6971 (m100) REVERT: D 381 ASN cc_start: 0.7870 (p0) cc_final: 0.7641 (p0) REVERT: D 427 ILE cc_start: 0.9283 (pt) cc_final: 0.9046 (pt) REVERT: D 428 LYS cc_start: 0.9038 (tptt) cc_final: 0.8738 (tmtt) REVERT: F 280 THR cc_start: 0.8854 (p) cc_final: 0.8645 (p) REVERT: F 389 PHE cc_start: 0.7999 (m-80) cc_final: 0.7747 (m-10) REVERT: F 414 PHE cc_start: 0.9005 (m-10) cc_final: 0.8765 (m-10) REVERT: F 420 HIS cc_start: 0.9157 (t-90) cc_final: 0.8925 (t-90) REVERT: F 424 TYR cc_start: 0.9244 (p90) cc_final: 0.8974 (p90) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3342 time to fit residues: 81.8953 Evaluate side-chains 115 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.0770 chunk 231 optimal weight: 8.9990 chunk 211 optimal weight: 0.7980 chunk 225 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 213 optimal weight: 0.0070 chunk 224 optimal weight: 9.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 HIS ** C 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 GLN D 313 HIS ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 21826 Z= 0.154 Angle : 0.899 29.797 29932 Z= 0.377 Chirality : 0.041 0.197 3462 Planarity : 0.004 0.059 3435 Dihedral : 16.377 177.644 3927 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2379 helix: 2.34 (0.17), residues: 894 sheet: -0.27 (0.24), residues: 444 loop : -0.11 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 360 HIS 0.006 0.001 HIS C 557 PHE 0.020 0.001 PHE C 776 TYR 0.016 0.001 TYR A 756 ARG 0.002 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.8401 (tp) cc_final: 0.7920 (tp) REVERT: B 427 ILE cc_start: 0.9287 (pt) cc_final: 0.9031 (pt) REVERT: B 428 LYS cc_start: 0.8966 (tptt) cc_final: 0.8685 (tmtt) REVERT: C 680 CYS cc_start: 0.8346 (m) cc_final: 0.7941 (t) REVERT: D 360 TRP cc_start: 0.7745 (m100) cc_final: 0.7025 (m100) REVERT: D 381 ASN cc_start: 0.7909 (p0) cc_final: 0.7676 (p0) REVERT: D 386 LYS cc_start: 0.6793 (mmmt) cc_final: 0.6505 (mmmt) REVERT: D 427 ILE cc_start: 0.9296 (pt) cc_final: 0.9035 (pt) REVERT: D 428 LYS cc_start: 0.9041 (tptt) cc_final: 0.8739 (tmtt) REVERT: E 346 LEU cc_start: 0.8653 (tp) cc_final: 0.8374 (tp) REVERT: F 288 GLN cc_start: 0.9162 (tp40) cc_final: 0.8903 (tp40) REVERT: F 360 TRP cc_start: 0.7278 (m100) cc_final: 0.6626 (m100) REVERT: F 389 PHE cc_start: 0.7857 (m-80) cc_final: 0.7620 (m-10) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3298 time to fit residues: 88.9098 Evaluate side-chains 121 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 165 optimal weight: 0.3980 chunk 250 optimal weight: 10.0000 chunk 230 optimal weight: 0.0020 chunk 199 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 122 optimal weight: 9.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN ** C 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21826 Z= 0.161 Angle : 0.890 29.843 29932 Z= 0.372 Chirality : 0.041 0.200 3462 Planarity : 0.004 0.061 3435 Dihedral : 16.276 176.451 3927 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2379 helix: 2.23 (0.17), residues: 918 sheet: -0.29 (0.25), residues: 429 loop : -0.06 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 360 HIS 0.010 0.001 HIS B 313 PHE 0.012 0.001 PHE D 389 TYR 0.013 0.001 TYR A 756 ARG 0.002 0.000 ARG B 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4758 Ramachandran restraints generated. 2379 Oldfield, 0 Emsley, 2379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LYS cc_start: 0.8743 (tmtt) cc_final: 0.8502 (tptt) REVERT: B 288 GLN cc_start: 0.9034 (tp40) cc_final: 0.8785 (tp40) REVERT: B 428 LYS cc_start: 0.8987 (tptt) cc_final: 0.8732 (tmtt) REVERT: C 680 CYS cc_start: 0.8347 (m) cc_final: 0.7935 (t) REVERT: D 266 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8627 (tptt) REVERT: D 360 TRP cc_start: 0.7909 (m100) cc_final: 0.7172 (m100) REVERT: D 381 ASN cc_start: 0.7900 (p0) cc_final: 0.7637 (p0) REVERT: D 386 LYS cc_start: 0.6872 (mmmt) cc_final: 0.6593 (mmmt) REVERT: D 428 LYS cc_start: 0.9021 (tptt) cc_final: 0.8732 (tmtt) REVERT: E 346 LEU cc_start: 0.8605 (tp) cc_final: 0.8365 (tp) REVERT: F 288 GLN cc_start: 0.9132 (tp40) cc_final: 0.8883 (tp40) REVERT: F 420 HIS cc_start: 0.9025 (t-90) cc_final: 0.8821 (t-90) REVERT: F 427 ILE cc_start: 0.9102 (pt) cc_final: 0.8874 (pt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.3291 time to fit residues: 87.7132 Evaluate side-chains 125 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 61 optimal weight: 0.0070 chunk 183 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 204 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.039937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.026964 restraints weight = 159553.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028442 restraints weight = 79386.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.029384 restraints weight = 49731.110| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21826 Z= 0.152 Angle : 0.890 29.845 29932 Z= 0.372 Chirality : 0.041 0.198 3462 Planarity : 0.003 0.062 3435 Dihedral : 16.206 176.092 3927 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2379 helix: 2.23 (0.17), residues: 921 sheet: -0.16 (0.25), residues: 453 loop : -0.06 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 360 HIS 0.010 0.001 HIS F 313 PHE 0.010 0.001 PHE C 616 TYR 0.015 0.001 TYR A 756 ARG 0.005 0.000 ARG E 767 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3397.73 seconds wall clock time: 63 minutes 31.82 seconds (3811.82 seconds total)