Starting phenix.real_space_refine on Sun Mar 24 03:27:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/03_2024/7jl2_22370_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/03_2024/7jl2_22370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/03_2024/7jl2_22370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/03_2024/7jl2_22370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/03_2024/7jl2_22370_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jl2_22370/03_2024/7jl2_22370_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 17661 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 94 5.49 5 Mg 3 5.21 5 S 126 5.16 5 C 13691 2.51 5 N 3854 2.21 5 O 4342 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 370": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 824": "NH1" <-> "NH2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B ASP 454": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C ASP 526": "OD1" <-> "OD2" Residue "C PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 794": "OE1" <-> "OE2" Residue "C TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 824": "NH1" <-> "NH2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 937": "OE1" <-> "OE2" Residue "C TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "D PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 523": "OE1" <-> "OE2" Residue "E ASP 526": "OD1" <-> "OD2" Residue "E PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 572": "OD1" <-> "OD2" Residue "E TYR 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 794": "OE1" <-> "OE2" Residue "E TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 824": "NH1" <-> "NH2" Residue "E ASP 826": "OD1" <-> "OD2" Residue "E PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 937": "OE1" <-> "OE2" Residue "E TYR 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 336": "OD1" <-> "OD2" Residue "F PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F ASP 454": "OD1" <-> "OD2" Residue "F PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 465": "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: 22128 Number of models: 1 Model: "" Number of chains: 11 Chain: "X" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 944 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 25, 'rna3p_pyr': 18} Link IDs: {'rna2p': 1, 'rna3p': 42} Chain: "Y" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 26} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "C" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "E" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 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 6372 SG CYS A 907 84.451 54.137 76.421 1.00181.77 S ATOM 6395 SG CYS A 910 86.208 51.144 75.913 1.00194.53 S ATOM 6728 SG CYS A 962 84.298 52.526 72.877 1.00190.33 S ATOM 6743 SG CYS A 964 82.507 50.685 75.575 1.00196.45 S ATOM 13091 SG CYS C 907 109.597 83.124 123.362 1.00191.35 S ATOM 13114 SG CYS C 910 112.674 84.733 122.867 1.00198.31 S ATOM 13447 SG CYS C 962 111.206 82.904 119.821 1.00189.02 S ATOM 13462 SG CYS C 964 112.950 81.014 122.515 1.00195.39 S ATOM 19810 SG CYS E 907 54.307 77.760 29.630 1.00180.73 S ATOM 19833 SG CYS E 910 51.411 75.846 29.129 1.00197.41 S ATOM 20166 SG CYS E 962 52.686 77.823 26.089 1.00201.33 S ATOM 20181 SG CYS E 964 50.757 79.518 28.787 1.00210.14 S Time building chain proxies: 13.07, per 1000 atoms: 0.59 Number of scatterers: 22128 At special positions: 0 Unit cell: (134.672, 165.75, 163.679, 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 126 16.00 P 94 15.00 Al 3 13.00 Mg 3 11.99 F 12 9.00 O 4342 8.00 N 3854 7.00 C 13691 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: 10.65 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 910 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 962 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 907 " pdb=" ZN E1101 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 910 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 962 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 964 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 907 " Number of angles added : 18 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 24 sheets defined 39.3% alpha, 15.1% beta 28 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 10.50 Creating SS restraints... Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.861A pdb=" N GLU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 434 through 436 No H-bonds generated for 'chain 'A' and resid 434 through 436' Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 453 through 472 removed outlier: 3.721A pdb=" N ILE A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 549 through 564 Processing helix chain 'A' and resid 576 through 592 Processing helix chain 'A' and resid 598 through 616 Processing helix chain 'A' and resid 619 through 639 removed outlier: 3.594A pdb=" N ALA A 639 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 691 removed outlier: 4.551A pdb=" N LEU A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 715 Processing helix chain 'A' and resid 728 through 740 Processing helix chain 'A' and resid 742 through 747 removed outlier: 4.101A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 814 through 822 removed outlier: 4.151A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 863 removed outlier: 3.719A pdb=" N ASN A 863 " --> pdb=" O HIS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 894 removed outlier: 3.532A pdb=" N ILE A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 919 No H-bonds generated for 'chain 'A' and resid 917 through 919' Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'B' and resid 322 through 329 removed outlier: 4.149A pdb=" N GLN B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN B 329 " --> pdb=" O LYS B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 366 through 376 removed outlier: 3.862A pdb=" N GLU C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 434 through 436 No H-bonds generated for 'chain 'C' and resid 434 through 436' Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 453 through 472 removed outlier: 3.722A pdb=" N ILE C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 513 Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 549 through 564 Processing helix chain 'C' and resid 576 through 592 Processing helix chain 'C' and resid 598 through 616 Processing helix chain 'C' and resid 619 through 639 removed outlier: 3.594A pdb=" N ALA C 639 " --> pdb=" O ASP C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 691 removed outlier: 4.552A pdb=" N LEU C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C 682 " --> pdb=" O THR C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 Processing helix chain 'C' and resid 728 through 740 Processing helix chain 'C' and resid 742 through 747 removed outlier: 4.101A pdb=" N VAL C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 792 No H-bonds generated for 'chain 'C' and resid 790 through 792' Processing helix chain 'C' and resid 814 through 822 removed outlier: 4.151A pdb=" N ALA C 819 " --> pdb=" O ALA C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 863 removed outlier: 3.718A pdb=" N ASN C 863 " --> pdb=" O HIS C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 894 removed outlier: 3.533A pdb=" N ILE C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 919 No H-bonds generated for 'chain 'C' and resid 917 through 919' Processing helix chain 'C' and resid 933 through 938 Processing helix chain 'C' and resid 984 through 986 No H-bonds generated for 'chain 'C' and resid 984 through 986' Processing helix chain 'D' and resid 322 through 329 removed outlier: 4.297A pdb=" N GLN D 328 " --> pdb=" O ARG D 324 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASN D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 316 Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 366 through 376 removed outlier: 3.861A pdb=" N GLU E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 381 No H-bonds generated for 'chain 'E' and resid 378 through 381' Processing helix chain 'E' and resid 400 through 406 Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 434 through 436 No H-bonds generated for 'chain 'E' and resid 434 through 436' Processing helix chain 'E' and resid 445 through 447 No H-bonds generated for 'chain 'E' and resid 445 through 447' Processing helix chain 'E' and resid 453 through 472 removed outlier: 3.721A pdb=" N ILE E 457 " --> pdb=" O VAL E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 513 Processing helix chain 'E' and resid 525 through 531 Processing helix chain 'E' and resid 549 through 564 Processing helix chain 'E' and resid 576 through 592 Processing helix chain 'E' and resid 598 through 616 Processing helix chain 'E' and resid 619 through 639 removed outlier: 3.595A pdb=" N ALA E 639 " --> pdb=" O ASP E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 691 removed outlier: 4.552A pdb=" N LEU E 679 " --> pdb=" O PHE E 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 682 " --> pdb=" O THR E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 715 Processing helix chain 'E' and resid 728 through 740 Processing helix chain 'E' and resid 742 through 747 removed outlier: 4.100A pdb=" N VAL E 747 " --> pdb=" O LYS E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 768 through 780 Processing helix chain 'E' and resid 790 through 792 No H-bonds generated for 'chain 'E' and resid 790 through 792' Processing helix chain 'E' and resid 814 through 822 removed outlier: 4.151A pdb=" N ALA E 819 " --> pdb=" O ALA E 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 841 through 863 removed outlier: 3.719A pdb=" N ASN E 863 " --> pdb=" O HIS E 859 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 894 removed outlier: 3.532A pdb=" N ILE E 881 " --> pdb=" O GLN E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 917 through 919 No H-bonds generated for 'chain 'E' and resid 917 through 919' Processing helix chain 'E' and resid 933 through 938 Processing helix chain 'E' and resid 984 through 986 No H-bonds generated for 'chain 'E' and resid 984 through 986' Processing helix chain 'F' and resid 322 through 329 removed outlier: 4.315A pdb=" N GLN F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.755A pdb=" N GLY A 486 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 536 through 542 Processing sheet with id= C, first strand: chain 'A' and resid 987 through 990 removed outlier: 3.686A pdb=" N CYS A 915 " --> pdb=" O PHE A 905 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS A 907 " --> pdb=" O LEU A 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 913 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 920 through 923 Processing sheet with id= E, first strand: chain 'A' and resid 940 through 942 Processing sheet with id= F, first strand: chain 'A' and resid 971 through 974 Processing sheet with id= G, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.556A pdb=" N TYR B 475 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER B 466 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 372 through 374 Processing sheet with id= I, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.754A pdb=" N GLY C 486 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 536 through 542 Processing sheet with id= K, first strand: chain 'C' and resid 987 through 990 removed outlier: 3.685A pdb=" N CYS C 915 " --> pdb=" O PHE C 905 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS C 907 " --> pdb=" O LEU C 913 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C 913 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 920 through 923 Processing sheet with id= M, first strand: chain 'C' and resid 940 through 942 Processing sheet with id= N, first strand: chain 'C' and resid 971 through 974 Processing sheet with id= O, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.730A pdb=" N TRP D 386 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET D 453 " --> pdb=" O TRP D 386 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 475 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER D 466 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 372 through 374 Processing sheet with id= Q, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.754A pdb=" N GLY E 486 " --> pdb=" O ILE E 325 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 536 through 542 Processing sheet with id= S, first strand: chain 'E' and resid 987 through 990 removed outlier: 3.686A pdb=" N CYS E 915 " --> pdb=" O PHE E 905 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS E 907 " --> pdb=" O LEU E 913 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU E 913 " --> pdb=" O CYS E 907 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 920 through 923 Processing sheet with id= U, first strand: chain 'E' and resid 940 through 942 Processing sheet with id= V, first strand: chain 'E' and resid 971 through 974 Processing sheet with id= W, first strand: chain 'F' and resid 344 through 347 removed outlier: 3.680A pdb=" N TRP F 386 " --> pdb=" O MET F 453 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 453 " --> pdb=" O TRP F 386 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 475 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER F 466 " --> pdb=" O PRO F 473 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 372 through 374 914 hydrogen bonds defined for protein. 2637 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 8.53 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6190 1.33 - 1.46: 4853 1.46 - 1.58: 11300 1.58 - 1.70: 186 1.70 - 1.82: 207 Bond restraints: 22736 Sorted by residual: bond pdb=" CA LYS A 782 " pdb=" C LYS A 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.64e+01 bond pdb=" CA LYS E 782 " pdb=" C LYS E 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.62e+01 bond pdb=" CA LYS C 782 " pdb=" C LYS C 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.62e+01 bond pdb=" F1 ALF E1103 " pdb="AL ALF E1103 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" F1 ALF C1103 " pdb="AL ALF C1103 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 22731 not shown) Histogram of bond angle deviations from ideal: 89.52 - 107.52: 1428 107.52 - 125.52: 29087 125.52 - 143.53: 604 143.53 - 161.53: 0 161.53 - 179.53: 6 Bond angle restraints: 31125 Sorted by residual: angle pdb=" F1 ALF E1103 " pdb="AL ALF E1103 " pdb=" F2 ALF E1103 " ideal model delta sigma weight residual 108.68 179.46 -70.78 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 179.44 -70.76 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F1 ALF C1103 " pdb="AL ALF C1103 " pdb=" F2 ALF C1103 " ideal model delta sigma weight residual 108.68 179.42 -70.74 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F3 ALF C1103 " pdb="AL ALF C1103 " pdb=" F4 ALF C1103 " ideal model delta sigma weight residual 109.63 179.53 -69.90 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 179.52 -69.89 3.00e+00 1.11e-01 5.43e+02 ... (remaining 31120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 13472 34.56 - 69.13: 398 69.13 - 103.69: 51 103.69 - 138.25: 3 138.25 - 172.82: 4 Dihedral angle restraints: 13928 sinusoidal: 6539 harmonic: 7389 Sorted by residual: dihedral pdb=" C5' ADP A1102 " pdb=" O5' ADP A1102 " pdb=" PA ADP A1102 " pdb=" O2A ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.47 -143.47 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP E1102 " pdb=" O5' ADP E1102 " pdb=" PA ADP E1102 " pdb=" O2A ADP E1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.43 -143.43 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP C1102 " pdb=" O5' ADP C1102 " pdb=" PA ADP C1102 " pdb=" O2A ADP C1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.40 -143.40 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 13925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3110 0.066 - 0.132: 416 0.132 - 0.198: 19 0.198 - 0.265: 3 0.265 - 0.331: 3 Chirality restraints: 3551 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS E 782 " pdb=" N LYS E 782 " pdb=" C LYS E 782 " pdb=" CB LYS E 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA LYS C 782 " pdb=" N LYS C 782 " pdb=" C LYS C 782 " pdb=" CB LYS C 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3548 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 15 " 0.042 2.00e-02 2.50e+03 1.88e-02 9.73e+00 pdb=" N9 A X 15 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A X 15 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A X 15 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A X 15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A X 15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 15 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A X 15 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A X 15 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 790 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C THR A 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 791 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 790 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR C 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR C 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL C 791 " -0.011 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 209 2.49 - 3.09: 16865 3.09 - 3.70: 35244 3.70 - 4.30: 48625 4.30 - 4.90: 75117 Nonbonded interactions: 176060 Sorted by model distance: nonbonded pdb=" F4 ALF C1103 " pdb="MG MG C1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF E1103 " pdb="MG MG E1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF A1103 " pdb="MG MG A1104 " model vdw 1.889 2.120 nonbonded pdb=" F1 ALF E1103 " pdb="MG MG E1104 " model vdw 1.891 2.120 nonbonded pdb=" F1 ALF A1103 " pdb="MG MG A1104 " model vdw 1.892 2.120 ... (remaining 176055 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' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'D' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'F' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.010 Extract box with map and model: 4.830 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 73.660 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 22736 Z= 0.412 Angle : 1.348 70.785 31125 Z= 0.577 Chirality : 0.045 0.331 3551 Planarity : 0.004 0.034 3631 Dihedral : 16.275 172.817 9122 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.55 % Allowed : 0.87 % Favored : 98.59 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.17), residues: 2466 helix: 0.45 (0.16), residues: 927 sheet: 0.18 (0.23), residues: 501 loop : -1.38 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 386 HIS 0.013 0.002 HIS D 343 PHE 0.020 0.002 PHE A 724 TYR 0.030 0.002 TYR E 732 ARG 0.019 0.001 ARG D 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7620 (tpp) cc_final: 0.7337 (tpp) REVERT: A 854 MET cc_start: 0.9086 (tmm) cc_final: 0.8605 (tmm) REVERT: A 968 TRP cc_start: 0.6673 (m-10) cc_final: 0.6388 (m-10) REVERT: A 972 MET cc_start: 0.6772 (ptp) cc_final: 0.6359 (ptm) REVERT: B 368 PHE cc_start: 0.8094 (m-10) cc_final: 0.7869 (m-10) REVERT: C 313 MET cc_start: 0.7721 (tpp) cc_final: 0.7276 (tpp) REVERT: C 567 MET cc_start: 0.5579 (mmp) cc_final: 0.5298 (mmp) REVERT: C 683 ASN cc_start: 0.8047 (m110) cc_final: 0.7780 (m-40) REVERT: C 878 MET cc_start: 0.9219 (mtp) cc_final: 0.8976 (mtp) REVERT: C 968 TRP cc_start: 0.6761 (m-10) cc_final: 0.6286 (m-10) REVERT: D 368 PHE cc_start: 0.8003 (m-10) cc_final: 0.7802 (m-10) REVERT: D 415 ASN cc_start: 0.7213 (m-40) cc_final: 0.6875 (m-40) REVERT: D 478 HIS cc_start: 0.8080 (m-70) cc_final: 0.7667 (m90) REVERT: E 313 MET cc_start: 0.7451 (tpp) cc_final: 0.6993 (tpp) REVERT: E 683 ASN cc_start: 0.7768 (m110) cc_final: 0.7388 (m-40) REVERT: F 368 PHE cc_start: 0.7941 (m-10) cc_final: 0.7689 (m-80) outliers start: 12 outliers final: 6 residues processed: 208 average time/residue: 0.3396 time to fit residues: 113.5175 Evaluate side-chains 156 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 HIS ** A 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN ** C 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22736 Z= 0.173 Angle : 0.587 7.591 31125 Z= 0.300 Chirality : 0.041 0.143 3551 Planarity : 0.003 0.029 3631 Dihedral : 14.479 171.643 4076 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.24 (0.17), residues: 2466 helix: 1.47 (0.17), residues: 939 sheet: 0.29 (0.24), residues: 510 loop : -1.15 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 386 HIS 0.006 0.001 HIS B 383 PHE 0.015 0.002 PHE A 681 TYR 0.013 0.001 TYR A 311 ARG 0.002 0.000 ARG C 822 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7513 (tpp) cc_final: 0.7051 (tpt) REVERT: A 854 MET cc_start: 0.9160 (tmm) cc_final: 0.8433 (tmm) REVERT: A 968 TRP cc_start: 0.6475 (m-10) cc_final: 0.6146 (m-10) REVERT: B 368 PHE cc_start: 0.8109 (m-10) cc_final: 0.7875 (m-10) REVERT: B 415 ASN cc_start: 0.7290 (m-40) cc_final: 0.7059 (m-40) REVERT: B 453 MET cc_start: 0.7361 (ppp) cc_final: 0.6714 (ppp) REVERT: C 306 LEU cc_start: 0.7954 (mp) cc_final: 0.7332 (tp) REVERT: C 313 MET cc_start: 0.7443 (tpp) cc_final: 0.7207 (tpt) REVERT: C 567 MET cc_start: 0.5538 (mmp) cc_final: 0.5270 (mmp) REVERT: C 854 MET cc_start: 0.9150 (tmm) cc_final: 0.8882 (tmm) REVERT: C 864 MET cc_start: 0.7608 (mtp) cc_final: 0.6838 (ttm) REVERT: C 878 MET cc_start: 0.8995 (mtp) cc_final: 0.8591 (mtp) REVERT: C 968 TRP cc_start: 0.6855 (m-10) cc_final: 0.6202 (m100) REVERT: D 343 HIS cc_start: 0.8639 (m170) cc_final: 0.8434 (m-70) REVERT: D 415 ASN cc_start: 0.7365 (m-40) cc_final: 0.7038 (m-40) REVERT: D 478 HIS cc_start: 0.8074 (m-70) cc_final: 0.7546 (m90) REVERT: D 497 LEU cc_start: 0.9160 (tp) cc_final: 0.8946 (tp) REVERT: E 313 MET cc_start: 0.7310 (tpp) cc_final: 0.6950 (tpp) REVERT: E 854 MET cc_start: 0.9086 (tmm) cc_final: 0.8378 (tmm) REVERT: E 878 MET cc_start: 0.8933 (mtp) cc_final: 0.8447 (mtp) REVERT: E 968 TRP cc_start: 0.6594 (m-10) cc_final: 0.5929 (m-10) REVERT: F 343 HIS cc_start: 0.8233 (m170) cc_final: 0.7900 (m170) REVERT: F 354 LYS cc_start: 0.7544 (pttt) cc_final: 0.7321 (pttm) REVERT: F 368 PHE cc_start: 0.7923 (m-10) cc_final: 0.7658 (m-80) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3040 time to fit residues: 109.6811 Evaluate side-chains 164 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 255 optimal weight: 40.0000 chunk 210 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 189 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN A 835 HIS ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 428 GLN B 478 HIS ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 GLN C 835 HIS ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS D 383 HIS ** D 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 GLN E 835 HIS ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 HIS ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22736 Z= 0.282 Angle : 0.661 6.395 31125 Z= 0.347 Chirality : 0.044 0.165 3551 Planarity : 0.004 0.034 3631 Dihedral : 14.389 171.554 4076 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.14 (0.17), residues: 2466 helix: 1.22 (0.17), residues: 942 sheet: 0.02 (0.23), residues: 510 loop : -1.41 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 386 HIS 0.009 0.001 HIS D 383 PHE 0.018 0.002 PHE A 681 TYR 0.017 0.002 TYR C 461 ARG 0.004 0.001 ARG C 822 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7516 (tpp) cc_final: 0.7081 (tpt) REVERT: A 854 MET cc_start: 0.9211 (tmm) cc_final: 0.8488 (tmm) REVERT: A 968 TRP cc_start: 0.6581 (m-10) cc_final: 0.6235 (m-10) REVERT: B 343 HIS cc_start: 0.8063 (m-70) cc_final: 0.7857 (m170) REVERT: B 368 PHE cc_start: 0.7932 (m-10) cc_final: 0.7699 (m-80) REVERT: B 415 ASN cc_start: 0.7344 (m-40) cc_final: 0.7092 (m-40) REVERT: B 453 MET cc_start: 0.7352 (ppp) cc_final: 0.6438 (ppp) REVERT: C 306 LEU cc_start: 0.7893 (mp) cc_final: 0.7378 (tp) REVERT: C 854 MET cc_start: 0.9091 (tmm) cc_final: 0.8778 (ppp) REVERT: C 878 MET cc_start: 0.8871 (mtp) cc_final: 0.8641 (mtp) REVERT: C 968 TRP cc_start: 0.6633 (m-10) cc_final: 0.5908 (m100) REVERT: D 386 TRP cc_start: 0.6513 (p90) cc_final: 0.5993 (p90) REVERT: D 415 ASN cc_start: 0.7407 (m-40) cc_final: 0.6932 (m-40) REVERT: D 453 MET cc_start: 0.7093 (ppp) cc_final: 0.6880 (ppp) REVERT: D 461 CYS cc_start: 0.6229 (m) cc_final: 0.5982 (m) REVERT: E 313 MET cc_start: 0.7394 (tpp) cc_final: 0.7116 (tpp) REVERT: E 854 MET cc_start: 0.9120 (tmm) cc_final: 0.8609 (tmm) REVERT: E 878 MET cc_start: 0.9087 (mtp) cc_final: 0.8596 (mtp) REVERT: E 968 TRP cc_start: 0.6715 (m-10) cc_final: 0.5858 (m-10) REVERT: F 345 TYR cc_start: 0.7880 (m-10) cc_final: 0.7395 (m-80) REVERT: F 368 PHE cc_start: 0.7863 (m-10) cc_final: 0.7512 (m-80) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.3108 time to fit residues: 105.5513 Evaluate side-chains 161 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 8.9990 chunk 177 optimal weight: 0.4980 chunk 122 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 158 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 251 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 531 GLN A 862 GLN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 446 HIS C 512 ASN C 531 GLN C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN E 512 ASN E 531 GLN E 862 GLN ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 974 HIS F 343 HIS ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22736 Z= 0.207 Angle : 0.591 5.937 31125 Z= 0.303 Chirality : 0.042 0.174 3551 Planarity : 0.004 0.031 3631 Dihedral : 14.328 173.036 4076 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.14 % Allowed : 3.01 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.17), residues: 2466 helix: 1.62 (0.17), residues: 936 sheet: -0.08 (0.23), residues: 525 loop : -1.33 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 386 HIS 0.004 0.001 HIS E 835 PHE 0.020 0.002 PHE F 379 TYR 0.029 0.002 TYR B 475 ARG 0.002 0.000 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 224 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7476 (tpp) cc_final: 0.7053 (tpt) REVERT: A 567 MET cc_start: 0.6349 (mmp) cc_final: 0.5305 (mmm) REVERT: A 854 MET cc_start: 0.9163 (tmm) cc_final: 0.8947 (tmm) REVERT: A 878 MET cc_start: 0.8928 (mtm) cc_final: 0.8367 (mtp) REVERT: A 968 TRP cc_start: 0.6518 (m-10) cc_final: 0.6155 (m-10) REVERT: B 344 PHE cc_start: 0.8054 (m-10) cc_final: 0.7825 (m-10) REVERT: B 368 PHE cc_start: 0.7982 (m-10) cc_final: 0.7627 (m-10) REVERT: B 386 TRP cc_start: 0.6903 (p90) cc_final: 0.6566 (p90) REVERT: B 415 ASN cc_start: 0.7316 (m-40) cc_final: 0.7024 (m-40) REVERT: B 497 LEU cc_start: 0.9102 (tp) cc_final: 0.8845 (tp) REVERT: C 306 LEU cc_start: 0.7959 (mp) cc_final: 0.7386 (tp) REVERT: C 864 MET cc_start: 0.7417 (mtp) cc_final: 0.6830 (ttm) REVERT: C 878 MET cc_start: 0.8756 (mtp) cc_final: 0.8505 (mtp) REVERT: C 882 MET cc_start: 0.4762 (mpp) cc_final: 0.4434 (mpp) REVERT: C 968 TRP cc_start: 0.6612 (m-10) cc_final: 0.5802 (m100) REVERT: D 343 HIS cc_start: 0.8343 (m90) cc_final: 0.7811 (m170) REVERT: D 368 PHE cc_start: 0.7797 (m-80) cc_final: 0.7243 (m-80) REVERT: D 415 ASN cc_start: 0.7350 (m-40) cc_final: 0.6937 (m-40) REVERT: D 461 CYS cc_start: 0.6239 (m) cc_final: 0.5954 (m) REVERT: D 497 LEU cc_start: 0.9212 (tp) cc_final: 0.8934 (tp) REVERT: E 313 MET cc_start: 0.7367 (tpp) cc_final: 0.7100 (tpp) REVERT: E 854 MET cc_start: 0.9044 (tmm) cc_final: 0.8808 (tmm) REVERT: E 878 MET cc_start: 0.8976 (mtp) cc_final: 0.8323 (mtp) REVERT: E 908 LYS cc_start: 0.7116 (mtpt) cc_final: 0.6887 (mttt) REVERT: F 343 HIS cc_start: 0.8044 (m-70) cc_final: 0.7642 (m90) REVERT: F 354 LYS cc_start: 0.7472 (pttt) cc_final: 0.7245 (pttm) REVERT: F 368 PHE cc_start: 0.7869 (m-10) cc_final: 0.7530 (m-80) REVERT: F 408 ARG cc_start: 0.7323 (ptm-80) cc_final: 0.7056 (ptm-80) outliers start: 3 outliers final: 0 residues processed: 227 average time/residue: 0.3170 time to fit residues: 115.5265 Evaluate side-chains 164 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22736 Z= 0.276 Angle : 0.645 6.671 31125 Z= 0.334 Chirality : 0.043 0.186 3551 Planarity : 0.004 0.035 3631 Dihedral : 14.390 175.704 4076 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.09 % Allowed : 2.23 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.14 (0.17), residues: 2466 helix: 1.38 (0.17), residues: 945 sheet: -0.30 (0.23), residues: 531 loop : -1.42 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 386 HIS 0.006 0.001 HIS A 974 PHE 0.019 0.002 PHE D 379 TYR 0.017 0.002 TYR C 461 ARG 0.004 0.000 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7458 (tpp) cc_final: 0.7078 (tpt) REVERT: A 854 MET cc_start: 0.9214 (tmm) cc_final: 0.8525 (tmm) REVERT: A 878 MET cc_start: 0.8977 (mtm) cc_final: 0.8627 (mtm) REVERT: A 968 TRP cc_start: 0.6537 (m-10) cc_final: 0.6109 (m-10) REVERT: B 344 PHE cc_start: 0.8189 (m-10) cc_final: 0.7984 (m-10) REVERT: B 368 PHE cc_start: 0.7941 (m-10) cc_final: 0.7585 (m-10) REVERT: B 415 ASN cc_start: 0.7211 (m-40) cc_final: 0.6936 (m-40) REVERT: B 453 MET cc_start: 0.6977 (ppp) cc_final: 0.6391 (ppp) REVERT: C 306 LEU cc_start: 0.7941 (mp) cc_final: 0.7318 (tp) REVERT: C 567 MET cc_start: 0.6294 (mmp) cc_final: 0.6083 (mmp) REVERT: C 854 MET cc_start: 0.9119 (tmm) cc_final: 0.8515 (tmm) REVERT: C 864 MET cc_start: 0.7523 (mtp) cc_final: 0.6951 (ttm) REVERT: C 968 TRP cc_start: 0.6686 (m-10) cc_final: 0.5773 (m100) REVERT: C 971 MET cc_start: 0.7583 (tpt) cc_final: 0.7286 (tpt) REVERT: D 343 HIS cc_start: 0.8388 (m90) cc_final: 0.7939 (m90) REVERT: D 374 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7468 (pp30) REVERT: D 415 ASN cc_start: 0.7355 (m-40) cc_final: 0.6987 (m-40) REVERT: E 313 MET cc_start: 0.7260 (tpp) cc_final: 0.7038 (tpp) REVERT: E 854 MET cc_start: 0.9097 (tmm) cc_final: 0.8353 (tmm) REVERT: E 878 MET cc_start: 0.9078 (mtp) cc_final: 0.8862 (mtp) REVERT: F 343 HIS cc_start: 0.8101 (m-70) cc_final: 0.7658 (m90) REVERT: F 408 ARG cc_start: 0.7791 (ptm-80) cc_final: 0.6397 (ttm-80) REVERT: F 475 TYR cc_start: 0.7141 (t80) cc_final: 0.6873 (t80) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.3125 time to fit residues: 105.1710 Evaluate side-chains 158 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 251 optimal weight: 30.0000 chunk 208 optimal weight: 0.0980 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 50.0000 chunk 132 optimal weight: 0.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 ASN C 862 GLN E 446 HIS ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22736 Z= 0.166 Angle : 0.562 6.813 31125 Z= 0.286 Chirality : 0.041 0.181 3551 Planarity : 0.003 0.033 3631 Dihedral : 14.146 177.067 4076 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.19 (0.17), residues: 2466 helix: 1.78 (0.17), residues: 945 sheet: -0.17 (0.23), residues: 525 loop : -1.34 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 386 HIS 0.004 0.001 HIS C 835 PHE 0.011 0.001 PHE B 489 TYR 0.025 0.001 TYR B 475 ARG 0.002 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7337 (tpp) cc_final: 0.6985 (tpt) REVERT: A 854 MET cc_start: 0.9139 (tmm) cc_final: 0.8900 (tmm) REVERT: A 878 MET cc_start: 0.8899 (mtm) cc_final: 0.8375 (mtp) REVERT: A 968 TRP cc_start: 0.6454 (m-10) cc_final: 0.6033 (m-10) REVERT: B 368 PHE cc_start: 0.7897 (m-10) cc_final: 0.7504 (m-10) REVERT: B 415 ASN cc_start: 0.7265 (m-40) cc_final: 0.6961 (m-40) REVERT: B 453 MET cc_start: 0.7021 (ppp) cc_final: 0.6313 (ppp) REVERT: C 567 MET cc_start: 0.6250 (mmp) cc_final: 0.6027 (mmp) REVERT: C 766 MET cc_start: 0.8371 (tmm) cc_final: 0.8101 (tmm) REVERT: C 864 MET cc_start: 0.7376 (mtp) cc_final: 0.6813 (ttm) REVERT: C 968 TRP cc_start: 0.6584 (m-10) cc_final: 0.5666 (m100) REVERT: C 971 MET cc_start: 0.7826 (tpt) cc_final: 0.7469 (tpt) REVERT: D 368 PHE cc_start: 0.7897 (m-80) cc_final: 0.7272 (m-80) REVERT: D 415 ASN cc_start: 0.7315 (m-40) cc_final: 0.6977 (m-40) REVERT: D 489 PHE cc_start: 0.9185 (m-80) cc_final: 0.8686 (m-80) REVERT: E 313 MET cc_start: 0.7258 (tpp) cc_final: 0.6902 (tpp) REVERT: E 683 ASN cc_start: 0.7592 (m110) cc_final: 0.7251 (m110) REVERT: E 854 MET cc_start: 0.9045 (tmm) cc_final: 0.8785 (tmm) REVERT: E 878 MET cc_start: 0.8954 (mtp) cc_final: 0.8326 (mtp) REVERT: E 968 TRP cc_start: 0.6989 (m-10) cc_final: 0.6571 (m-10) REVERT: F 343 HIS cc_start: 0.7955 (m-70) cc_final: 0.7587 (m90) REVERT: F 408 ARG cc_start: 0.7460 (ptm-80) cc_final: 0.6309 (ttm-80) REVERT: F 492 LEU cc_start: 0.7795 (tp) cc_final: 0.7581 (tp) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.3153 time to fit residues: 112.0964 Evaluate side-chains 165 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 250 optimal weight: 0.0370 chunk 156 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 overall best weight: 2.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22736 Z= 0.162 Angle : 0.561 7.734 31125 Z= 0.284 Chirality : 0.040 0.176 3551 Planarity : 0.004 0.037 3631 Dihedral : 14.030 177.827 4076 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.23 (0.17), residues: 2466 helix: 1.88 (0.17), residues: 948 sheet: -0.25 (0.24), residues: 501 loop : -1.32 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 386 HIS 0.006 0.001 HIS B 393 PHE 0.010 0.001 PHE B 489 TYR 0.018 0.001 TYR E 869 ARG 0.005 0.000 ARG C 689 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7344 (tpp) cc_final: 0.7000 (tpt) REVERT: A 526 ASP cc_start: 0.8252 (t0) cc_final: 0.7912 (p0) REVERT: A 854 MET cc_start: 0.9172 (tmm) cc_final: 0.8913 (tmm) REVERT: A 878 MET cc_start: 0.8926 (mtm) cc_final: 0.8356 (mtp) REVERT: A 968 TRP cc_start: 0.6464 (m-10) cc_final: 0.6017 (m-10) REVERT: B 368 PHE cc_start: 0.7899 (m-10) cc_final: 0.7486 (m-10) REVERT: B 415 ASN cc_start: 0.7265 (m-40) cc_final: 0.6960 (m-40) REVERT: B 453 MET cc_start: 0.7113 (ppp) cc_final: 0.6406 (ppp) REVERT: B 475 TYR cc_start: 0.6482 (t80) cc_final: 0.6226 (t80) REVERT: C 864 MET cc_start: 0.7427 (mtp) cc_final: 0.6765 (ttm) REVERT: C 908 LYS cc_start: 0.6843 (mtpt) cc_final: 0.6366 (mttt) REVERT: C 968 TRP cc_start: 0.6543 (m-10) cc_final: 0.5626 (m100) REVERT: C 971 MET cc_start: 0.7963 (tpt) cc_final: 0.7653 (tpt) REVERT: D 368 PHE cc_start: 0.7931 (m-80) cc_final: 0.7275 (m-80) REVERT: D 415 ASN cc_start: 0.7384 (m-40) cc_final: 0.7020 (m-40) REVERT: E 313 MET cc_start: 0.7234 (tpp) cc_final: 0.6886 (tpp) REVERT: E 567 MET cc_start: 0.5824 (mmt) cc_final: 0.5527 (mmp) REVERT: E 683 ASN cc_start: 0.7628 (m110) cc_final: 0.7314 (m110) REVERT: E 854 MET cc_start: 0.9056 (tmm) cc_final: 0.8799 (tmm) REVERT: E 908 LYS cc_start: 0.6739 (mtmt) cc_final: 0.6525 (mttt) REVERT: E 968 TRP cc_start: 0.6766 (m-10) cc_final: 0.6210 (m-10) REVERT: F 343 HIS cc_start: 0.7966 (m-70) cc_final: 0.7556 (m170) REVERT: F 354 LYS cc_start: 0.7569 (pttt) cc_final: 0.7356 (pttm) REVERT: F 408 ARG cc_start: 0.7538 (ptm-80) cc_final: 0.6373 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.3070 time to fit residues: 106.6670 Evaluate side-chains 159 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22736 Z= 0.223 Angle : 0.610 7.958 31125 Z= 0.312 Chirality : 0.042 0.166 3551 Planarity : 0.004 0.034 3631 Dihedral : 14.101 179.149 4076 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.05 % Allowed : 1.46 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2466 helix: 1.65 (0.17), residues: 948 sheet: -0.14 (0.24), residues: 504 loop : -1.40 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 386 HIS 0.006 0.001 HIS F 393 PHE 0.013 0.001 PHE A 681 TYR 0.016 0.002 TYR E 869 ARG 0.003 0.000 ARG C 689 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7395 (tpp) cc_final: 0.7052 (tpt) REVERT: A 854 MET cc_start: 0.9158 (tmm) cc_final: 0.8874 (tmm) REVERT: A 878 MET cc_start: 0.8986 (mtm) cc_final: 0.8484 (mtp) REVERT: A 968 TRP cc_start: 0.6543 (m-10) cc_final: 0.6089 (m-10) REVERT: B 368 PHE cc_start: 0.7898 (m-10) cc_final: 0.7514 (m-10) REVERT: B 415 ASN cc_start: 0.7266 (m-40) cc_final: 0.6989 (m-40) REVERT: B 453 MET cc_start: 0.6887 (ppp) cc_final: 0.6448 (ppp) REVERT: B 475 TYR cc_start: 0.6484 (t80) cc_final: 0.6278 (t80) REVERT: B 489 PHE cc_start: 0.9534 (m-10) cc_final: 0.9320 (m-10) REVERT: C 864 MET cc_start: 0.7515 (mtp) cc_final: 0.6907 (ttm) REVERT: C 968 TRP cc_start: 0.6584 (m-10) cc_final: 0.5668 (m100) REVERT: D 415 ASN cc_start: 0.7345 (m-40) cc_final: 0.6989 (m-40) REVERT: D 497 LEU cc_start: 0.9238 (tp) cc_final: 0.9019 (tp) REVERT: E 313 MET cc_start: 0.7281 (tpp) cc_final: 0.6940 (tpp) REVERT: E 567 MET cc_start: 0.5995 (mmt) cc_final: 0.5708 (mmp) REVERT: E 854 MET cc_start: 0.9041 (tmm) cc_final: 0.8740 (tmm) REVERT: E 878 MET cc_start: 0.8976 (mtp) cc_final: 0.8411 (mtp) REVERT: E 908 LYS cc_start: 0.6728 (mtmt) cc_final: 0.6461 (mttt) REVERT: E 968 TRP cc_start: 0.6729 (m-10) cc_final: 0.6139 (m-10) REVERT: F 343 HIS cc_start: 0.8005 (m-70) cc_final: 0.7541 (m90) REVERT: F 408 ARG cc_start: 0.7554 (ptm-80) cc_final: 0.6368 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.3225 time to fit residues: 109.6566 Evaluate side-chains 152 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN C 966 GLN D 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22736 Z= 0.187 Angle : 0.588 9.243 31125 Z= 0.298 Chirality : 0.041 0.184 3551 Planarity : 0.004 0.034 3631 Dihedral : 13.976 179.617 4076 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.05 % Allowed : 0.96 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.15 (0.17), residues: 2466 helix: 1.72 (0.17), residues: 948 sheet: -0.18 (0.24), residues: 507 loop : -1.34 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 386 HIS 0.006 0.001 HIS E 603 PHE 0.027 0.001 PHE A 629 TYR 0.012 0.001 TYR C 461 ARG 0.004 0.000 ARG E 598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7346 (tpp) cc_final: 0.6978 (tpt) REVERT: A 854 MET cc_start: 0.9167 (tmm) cc_final: 0.8893 (tmm) REVERT: A 878 MET cc_start: 0.8973 (mtm) cc_final: 0.8467 (mtp) REVERT: A 968 TRP cc_start: 0.6609 (m-10) cc_final: 0.6161 (m-10) REVERT: B 344 PHE cc_start: 0.8143 (m-10) cc_final: 0.7856 (m-10) REVERT: B 368 PHE cc_start: 0.7898 (m-10) cc_final: 0.7507 (m-10) REVERT: B 415 ASN cc_start: 0.7383 (m-40) cc_final: 0.7088 (m-40) REVERT: B 453 MET cc_start: 0.7214 (ppp) cc_final: 0.6392 (ppp) REVERT: B 475 TYR cc_start: 0.6402 (t80) cc_final: 0.6191 (t80) REVERT: C 632 GLU cc_start: 0.8768 (pt0) cc_final: 0.8549 (pt0) REVERT: C 864 MET cc_start: 0.7427 (mtp) cc_final: 0.6842 (ttm) REVERT: C 908 LYS cc_start: 0.7037 (mtpt) cc_final: 0.6510 (mttt) REVERT: C 968 TRP cc_start: 0.6592 (m-10) cc_final: 0.5693 (m100) REVERT: D 415 ASN cc_start: 0.7384 (m-40) cc_final: 0.7035 (m-40) REVERT: E 313 MET cc_start: 0.7255 (tpp) cc_final: 0.6908 (tpp) REVERT: E 567 MET cc_start: 0.5989 (mmt) cc_final: 0.5727 (mmp) REVERT: E 854 MET cc_start: 0.9115 (tmm) cc_final: 0.8841 (tmm) REVERT: E 908 LYS cc_start: 0.6612 (mtmt) cc_final: 0.6341 (mttt) REVERT: E 968 TRP cc_start: 0.6586 (m-10) cc_final: 0.5991 (m-10) REVERT: F 408 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.6324 (ttm-80) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.3106 time to fit residues: 105.2145 Evaluate side-chains 154 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 150 optimal weight: 8.9990 chunk 117 optimal weight: 0.0070 chunk 171 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 0.2980 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS C 862 GLN D 478 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 22736 Z= 0.159 Angle : 0.572 8.677 31125 Z= 0.286 Chirality : 0.041 0.169 3551 Planarity : 0.004 0.035 3631 Dihedral : 13.853 178.741 4076 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.05 % Allowed : 0.36 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.27 (0.18), residues: 2466 helix: 1.82 (0.17), residues: 951 sheet: -0.15 (0.24), residues: 507 loop : -1.26 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 386 HIS 0.004 0.001 HIS F 393 PHE 0.022 0.001 PHE A 629 TYR 0.015 0.001 TYR B 385 ARG 0.003 0.000 ARG E 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: A 313 MET cc_start: 0.7407 (tpp) cc_final: 0.7027 (tpt) REVERT: A 526 ASP cc_start: 0.8187 (t0) cc_final: 0.7701 (p0) REVERT: A 854 MET cc_start: 0.9147 (tmm) cc_final: 0.8897 (tmm) REVERT: A 878 MET cc_start: 0.8978 (mtm) cc_final: 0.8459 (mtp) REVERT: A 968 TRP cc_start: 0.6578 (m-10) cc_final: 0.6101 (m-10) REVERT: B 368 PHE cc_start: 0.7898 (m-10) cc_final: 0.7519 (m-10) REVERT: B 415 ASN cc_start: 0.7391 (m-40) cc_final: 0.7069 (m-40) REVERT: B 453 MET cc_start: 0.7364 (ppp) cc_final: 0.6407 (ppp) REVERT: B 475 TYR cc_start: 0.6356 (t80) cc_final: 0.6145 (t80) REVERT: C 632 GLU cc_start: 0.8748 (pt0) cc_final: 0.8521 (pt0) REVERT: C 864 MET cc_start: 0.7380 (mtp) cc_final: 0.6874 (ttm) REVERT: C 878 MET cc_start: 0.8930 (mtp) cc_final: 0.8599 (mtp) REVERT: C 908 LYS cc_start: 0.6997 (mtpt) cc_final: 0.6539 (mttt) REVERT: C 968 TRP cc_start: 0.6687 (m-10) cc_final: 0.5737 (m100) REVERT: D 368 PHE cc_start: 0.7993 (m-80) cc_final: 0.7730 (m-80) REVERT: D 415 ASN cc_start: 0.7361 (m-40) cc_final: 0.6967 (m-40) REVERT: E 313 MET cc_start: 0.7262 (tpp) cc_final: 0.6892 (tpp) REVERT: E 567 MET cc_start: 0.5917 (mmt) cc_final: 0.5671 (mmp) REVERT: E 854 MET cc_start: 0.9108 (tmm) cc_final: 0.8860 (tmm) REVERT: E 878 MET cc_start: 0.9044 (mtp) cc_final: 0.8827 (mtp) REVERT: E 908 LYS cc_start: 0.6626 (mtmt) cc_final: 0.6408 (mttt) REVERT: E 968 TRP cc_start: 0.6512 (m-10) cc_final: 0.5989 (m-10) REVERT: F 343 HIS cc_start: 0.7881 (m-70) cc_final: 0.7456 (m170) REVERT: F 408 ARG cc_start: 0.7558 (ptm-80) cc_final: 0.6228 (ttm-80) outliers start: 1 outliers final: 1 residues processed: 215 average time/residue: 0.3211 time to fit residues: 111.6464 Evaluate side-chains 155 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 212 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 478 HIS ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045043 restraints weight = 281647.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046817 restraints weight = 135442.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048013 restraints weight = 69653.276| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22736 Z= 0.188 Angle : 0.584 8.677 31125 Z= 0.295 Chirality : 0.041 0.162 3551 Planarity : 0.004 0.035 3631 Dihedral : 13.854 177.729 4076 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.22 (0.17), residues: 2466 helix: 1.79 (0.17), residues: 948 sheet: -0.18 (0.24), residues: 507 loop : -1.29 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 386 HIS 0.005 0.001 HIS F 393 PHE 0.022 0.001 PHE A 629 TYR 0.014 0.001 TYR E 869 ARG 0.004 0.000 ARG E 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3555.34 seconds wall clock time: 66 minutes 33.40 seconds (3993.40 seconds total)