Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 05:04:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/07_2023/8sey_40433_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/07_2023/8sey_40433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/07_2023/8sey_40433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/07_2023/8sey_40433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/07_2023/8sey_40433_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sey_40433/07_2023/8sey_40433_updated.pdb" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.003 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 160 5.16 5 C 13360 2.51 5 N 3280 2.21 5 O 3764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 3967": "OE1" <-> "OE2" Residue "A GLU 4224": "OE1" <-> "OE2" Residue "A GLU 4232": "OE1" <-> "OE2" Residue "A TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4726": "OD1" <-> "OD2" Residue "A ASP 4730": "OD1" <-> "OD2" Residue "A PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4878": "OD1" <-> "OD2" Residue "B GLU 3967": "OE1" <-> "OE2" Residue "B GLU 4050": "OE1" <-> "OE2" Residue "B GLU 4224": "OE1" <-> "OE2" Residue "B GLU 4232": "OE1" <-> "OE2" Residue "B TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4726": "OD1" <-> "OD2" Residue "B ASP 4730": "OD1" <-> "OD2" Residue "B PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4878": "OD1" <-> "OD2" Residue "C GLU 3967": "OE1" <-> "OE2" Residue "C GLU 4050": "OE1" <-> "OE2" Residue "C GLU 4224": "OE1" <-> "OE2" Residue "C GLU 4232": "OE1" <-> "OE2" Residue "C TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4726": "OD1" <-> "OD2" Residue "C ASP 4730": "OD1" <-> "OD2" Residue "C PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4878": "OD1" <-> "OD2" Residue "D GLU 3967": "OE1" <-> "OE2" Residue "D GLU 4050": "OE1" <-> "OE2" Residue "D GLU 4224": "OE1" <-> "OE2" Residue "D GLU 4232": "OE1" <-> "OE2" Residue "D TYR 4580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4726": "OD1" <-> "OD2" Residue "D ASP 4730": "OD1" <-> "OD2" Residue "D PHE 4780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4878": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "C" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "D" Number of atoms: 5122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5122 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {' ZN': 1, 'ADN%rna2p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A4958 56.002 81.276 88.845 1.00 44.66 S ATOM 4473 SG CYS A4961 58.248 82.388 91.794 1.00 41.54 S ATOM 9570 SG CYS B4958 60.404 56.002 88.845 1.00 44.78 S ATOM 9595 SG CYS B4961 59.292 58.248 91.794 1.00 41.58 S ATOM 14692 SG CYS C4958 85.678 60.404 88.845 1.00 44.43 S ATOM 14717 SG CYS C4961 83.432 59.292 91.794 1.00 41.45 S ATOM 19814 SG CYS D4958 81.277 85.678 88.845 1.00 44.61 S ATOM 19839 SG CYS D4961 82.388 83.432 91.794 1.00 41.80 S Time building chain proxies: 9.75, per 1000 atoms: 0.47 Number of scatterers: 20568 At special positions: 0 Unit cell: (142.968, 142.968, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 160 16.00 O 3764 8.00 N 3280 7.00 C 13360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.97 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 8 sheets defined 71.3% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 3951 through 3969 removed outlier: 3.532A pdb=" N VAL A3957 " --> pdb=" O LYS A3953 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3974 through 3982 removed outlier: 3.603A pdb=" N ALA A3981 " --> pdb=" O GLN A3977 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4005 removed outlier: 4.015A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4010 through 4031 removed outlier: 3.951A pdb=" N GLU A4015 " --> pdb=" O GLU A4011 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4050 removed outlier: 3.548A pdb=" N GLN A4043 " --> pdb=" O MET A4039 " (cutoff:3.500A) Processing helix chain 'A' and resid 4052 through 4058 removed outlier: 4.076A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A4058 " --> pdb=" O ASN A4054 " (cutoff:3.500A) Processing helix chain 'A' and resid 4199 through 4206 Processing helix chain 'A' and resid 4208 through 4223 Processing helix chain 'A' and resid 4230 through 4251 Processing helix chain 'A' and resid 4544 through 4557 Processing helix chain 'A' and resid 4559 through 4579 removed outlier: 4.408A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4639 through 4664 Processing helix chain 'A' and resid 4666 through 4683 Processing helix chain 'A' and resid 4686 through 4689 No H-bonds generated for 'chain 'A' and resid 4686 through 4689' Processing helix chain 'A' and resid 4697 through 4707 removed outlier: 4.443A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASN A4707 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4720 through 4732 removed outlier: 5.207A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4734 through 4741 Processing helix chain 'A' and resid 4745 through 4748 Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.775A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 removed outlier: 3.581A pdb=" N LEU A4814 " --> pdb=" O ALA A4811 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.697A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4834 through 4858 Processing helix chain 'A' and resid 4860 through 4862 No H-bonds generated for 'chain 'A' and resid 4860 through 4862' Processing helix chain 'A' and resid 4879 through 4892 removed outlier: 4.562A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) Processing helix chain 'A' and resid 4897 through 4899 No H-bonds generated for 'chain 'A' and resid 4897 through 4899' Processing helix chain 'A' and resid 4910 through 4923 Processing helix chain 'A' and resid 4927 through 4956 removed outlier: 4.025A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4965 through 4970 removed outlier: 3.944A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4980 Processing helix chain 'A' and resid 4985 through 4997 Processing helix chain 'A' and resid 5005 through 5015 Processing helix chain 'A' and resid 5028 through 5036 removed outlier: 6.525A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3969 removed outlier: 3.534A pdb=" N VAL B3957 " --> pdb=" O LYS B3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3974 through 3982 removed outlier: 3.587A pdb=" N ALA B3981 " --> pdb=" O GLN B3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4005 removed outlier: 4.001A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4010 through 4030 removed outlier: 3.942A pdb=" N GLU B4015 " --> pdb=" O GLU B4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN B4020 " --> pdb=" O LEU B4016 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4050 Processing helix chain 'B' and resid 4052 through 4058 removed outlier: 4.077A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B4058 " --> pdb=" O ASN B4054 " (cutoff:3.500A) Processing helix chain 'B' and resid 4199 through 4206 Processing helix chain 'B' and resid 4208 through 4223 Processing helix chain 'B' and resid 4230 through 4251 Processing helix chain 'B' and resid 4544 through 4557 Processing helix chain 'B' and resid 4559 through 4579 removed outlier: 4.408A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4639 through 4664 Processing helix chain 'B' and resid 4666 through 4683 Processing helix chain 'B' and resid 4686 through 4689 No H-bonds generated for 'chain 'B' and resid 4686 through 4689' Processing helix chain 'B' and resid 4697 through 4707 removed outlier: 4.442A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B4707 " --> pdb=" O ARG B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4720 through 4732 removed outlier: 5.207A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4734 through 4741 Processing helix chain 'B' and resid 4745 through 4748 Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.775A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4819 removed outlier: 3.580A pdb=" N LEU B4814 " --> pdb=" O ALA B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.696A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4834 through 4858 Processing helix chain 'B' and resid 4860 through 4862 No H-bonds generated for 'chain 'B' and resid 4860 through 4862' Processing helix chain 'B' and resid 4879 through 4892 removed outlier: 4.563A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) Processing helix chain 'B' and resid 4897 through 4899 No H-bonds generated for 'chain 'B' and resid 4897 through 4899' Processing helix chain 'B' and resid 4910 through 4923 Processing helix chain 'B' and resid 4927 through 4956 removed outlier: 4.024A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4965 through 4970 removed outlier: 3.945A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4974 through 4980 Processing helix chain 'B' and resid 4985 through 4997 Processing helix chain 'B' and resid 5005 through 5015 Processing helix chain 'B' and resid 5028 through 5036 removed outlier: 6.524A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3969 removed outlier: 3.534A pdb=" N VAL C3957 " --> pdb=" O LYS C3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3974 through 3982 removed outlier: 3.587A pdb=" N ALA C3981 " --> pdb=" O GLN C3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4005 removed outlier: 4.002A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4010 through 4030 removed outlier: 3.942A pdb=" N GLU C4015 " --> pdb=" O GLU C4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C4020 " --> pdb=" O LEU C4016 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4050 Processing helix chain 'C' and resid 4052 through 4058 removed outlier: 4.077A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C4058 " --> pdb=" O ASN C4054 " (cutoff:3.500A) Processing helix chain 'C' and resid 4199 through 4206 Processing helix chain 'C' and resid 4208 through 4223 Processing helix chain 'C' and resid 4230 through 4251 Processing helix chain 'C' and resid 4544 through 4557 Processing helix chain 'C' and resid 4559 through 4579 removed outlier: 4.408A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4639 through 4664 Processing helix chain 'C' and resid 4666 through 4683 Processing helix chain 'C' and resid 4686 through 4689 No H-bonds generated for 'chain 'C' and resid 4686 through 4689' Processing helix chain 'C' and resid 4697 through 4707 removed outlier: 4.442A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN C4707 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4720 through 4732 removed outlier: 5.207A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4734 through 4741 Processing helix chain 'C' and resid 4745 through 4748 Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.775A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4819 removed outlier: 3.580A pdb=" N LEU C4814 " --> pdb=" O ALA C4811 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.695A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4834 through 4858 Processing helix chain 'C' and resid 4860 through 4862 No H-bonds generated for 'chain 'C' and resid 4860 through 4862' Processing helix chain 'C' and resid 4879 through 4892 removed outlier: 4.562A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) Processing helix chain 'C' and resid 4897 through 4899 No H-bonds generated for 'chain 'C' and resid 4897 through 4899' Processing helix chain 'C' and resid 4910 through 4923 Processing helix chain 'C' and resid 4927 through 4956 removed outlier: 4.023A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4965 through 4970 removed outlier: 3.945A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4980 Processing helix chain 'C' and resid 4985 through 4997 Processing helix chain 'C' and resid 5005 through 5015 Processing helix chain 'C' and resid 5028 through 5036 removed outlier: 6.524A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3969 removed outlier: 3.534A pdb=" N VAL D3957 " --> pdb=" O LYS D3953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3974 through 3982 removed outlier: 3.587A pdb=" N ALA D3981 " --> pdb=" O GLN D3977 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4005 removed outlier: 4.001A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4010 through 4030 removed outlier: 3.942A pdb=" N GLU D4015 " --> pdb=" O GLU D4011 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D4020 " --> pdb=" O LEU D4016 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4050 Processing helix chain 'D' and resid 4052 through 4058 removed outlier: 4.077A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE D4058 " --> pdb=" O ASN D4054 " (cutoff:3.500A) Processing helix chain 'D' and resid 4199 through 4206 Processing helix chain 'D' and resid 4208 through 4223 Processing helix chain 'D' and resid 4230 through 4251 Processing helix chain 'D' and resid 4544 through 4557 Processing helix chain 'D' and resid 4559 through 4579 removed outlier: 4.408A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4639 through 4664 Processing helix chain 'D' and resid 4666 through 4683 Processing helix chain 'D' and resid 4686 through 4689 No H-bonds generated for 'chain 'D' and resid 4686 through 4689' Processing helix chain 'D' and resid 4697 through 4707 removed outlier: 4.442A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN D4707 " --> pdb=" O ARG D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4720 through 4732 removed outlier: 5.207A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4734 through 4741 Processing helix chain 'D' and resid 4745 through 4748 Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.775A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 removed outlier: 3.580A pdb=" N LEU D4814 " --> pdb=" O ALA D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.695A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4834 through 4858 Processing helix chain 'D' and resid 4860 through 4862 No H-bonds generated for 'chain 'D' and resid 4860 through 4862' Processing helix chain 'D' and resid 4879 through 4892 removed outlier: 4.563A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) Processing helix chain 'D' and resid 4897 through 4899 No H-bonds generated for 'chain 'D' and resid 4897 through 4899' Processing helix chain 'D' and resid 4910 through 4923 Processing helix chain 'D' and resid 4927 through 4956 removed outlier: 4.023A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4965 through 4970 removed outlier: 3.944A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4974 through 4980 Processing helix chain 'D' and resid 4985 through 4997 Processing helix chain 'D' and resid 5005 through 5015 Processing helix chain 'D' and resid 5028 through 5036 removed outlier: 6.524A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4178 through 4184 removed outlier: 3.565A pdb=" N PHE A4195 " --> pdb=" O GLY A4179 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id= C, first strand: chain 'B' and resid 4178 through 4184 removed outlier: 3.564A pdb=" N PHE B4195 " --> pdb=" O GLY B4179 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id= E, first strand: chain 'C' and resid 4178 through 4184 removed outlier: 3.564A pdb=" N PHE C4195 " --> pdb=" O GLY C4179 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id= G, first strand: chain 'D' and resid 4178 through 4184 removed outlier: 3.563A pdb=" N PHE D4195 " --> pdb=" O GLY D4179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 4580 through 4583 1192 hydrogen bonds defined for protein. 3432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6489 1.34 - 1.46: 4662 1.46 - 1.58: 9621 1.58 - 1.69: 0 1.69 - 1.81: 276 Bond restraints: 21048 Sorted by residual: bond pdb=" C5 ADN D5101 " pdb=" N7 ADN D5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C5 ADN C5101 " pdb=" N7 ADN C5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C5 ADN B5101 " pdb=" N7 ADN B5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C5 ADN A5101 " pdb=" N7 ADN A5101 " ideal model delta sigma weight residual 1.371 1.387 -0.016 2.00e-02 2.50e+03 6.31e-01 bond pdb=" C GLY D4225 " pdb=" O GLY D4225 " ideal model delta sigma weight residual 1.237 1.230 0.007 9.70e-03 1.06e+04 5.97e-01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.35: 456 106.35 - 113.27: 10946 113.27 - 120.19: 7955 120.19 - 127.11: 8875 127.11 - 134.02: 180 Bond angle restraints: 28412 Sorted by residual: angle pdb=" C GLU C4900 " pdb=" N ILE C4901 " pdb=" CA ILE C4901 " ideal model delta sigma weight residual 122.48 119.40 3.08 1.13e+00 7.83e-01 7.44e+00 angle pdb=" C GLU A4900 " pdb=" N ILE A4901 " pdb=" CA ILE A4901 " ideal model delta sigma weight residual 122.48 119.40 3.08 1.13e+00 7.83e-01 7.44e+00 angle pdb=" C GLU D4900 " pdb=" N ILE D4901 " pdb=" CA ILE D4901 " ideal model delta sigma weight residual 122.48 119.45 3.03 1.13e+00 7.83e-01 7.20e+00 angle pdb=" C GLU B4900 " pdb=" N ILE B4901 " pdb=" CA ILE B4901 " ideal model delta sigma weight residual 122.48 119.50 2.98 1.13e+00 7.83e-01 6.96e+00 angle pdb=" C ASN B4857 " pdb=" N PHE B4858 " pdb=" CA PHE B4858 " ideal model delta sigma weight residual 122.58 118.33 4.25 2.07e+00 2.33e-01 4.22e+00 ... (remaining 28407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 11290 16.69 - 33.37: 906 33.37 - 50.06: 113 50.06 - 66.75: 40 66.75 - 83.44: 23 Dihedral angle restraints: 12372 sinusoidal: 5052 harmonic: 7320 Sorted by residual: dihedral pdb=" CA GLY D3971 " pdb=" C GLY D3971 " pdb=" N PRO D3972 " pdb=" CA PRO D3972 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY A3971 " pdb=" C GLY A3971 " pdb=" N PRO A3972 " pdb=" CA PRO A3972 " ideal model delta harmonic sigma weight residual -180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY C3971 " pdb=" C GLY C3971 " pdb=" N PRO C3972 " pdb=" CA PRO C3972 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 12369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1946 0.029 - 0.058: 850 0.058 - 0.088: 230 0.088 - 0.117: 50 0.117 - 0.146: 12 Chirality restraints: 3088 Sorted by residual: chirality pdb=" CA MET D5013 " pdb=" N MET D5013 " pdb=" C MET D5013 " pdb=" CB MET D5013 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA MET A5013 " pdb=" N MET A5013 " pdb=" C MET A5013 " pdb=" CB MET A5013 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA MET C5013 " pdb=" N MET C5013 " pdb=" C MET C5013 " pdb=" CB MET C5013 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 3085 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B4666 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B4667 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B4667 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B4667 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C4666 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO C4667 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C4667 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C4667 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A4666 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO A4667 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A4667 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A4667 " 0.018 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3636 2.76 - 3.29: 20156 3.29 - 3.83: 34938 3.83 - 4.36: 40304 4.36 - 4.90: 69659 Nonbonded interactions: 168693 Sorted by model distance: nonbonded pdb=" OD2 ASP A4917 " pdb=" OH TYR D4888 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR C4888 " pdb=" OD2 ASP D4917 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR B4888 " pdb=" OD2 ASP C4917 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR A4888 " pdb=" OD2 ASP B4917 " model vdw 2.224 2.440 nonbonded pdb=" O THR A4825 " pdb=" OG SER A4828 " model vdw 2.235 2.440 ... (remaining 168688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.990 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 53.730 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.150 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.002 0.029 21048 Z= 0.145 Angle : 0.461 4.812 28412 Z= 0.258 Chirality : 0.036 0.146 3088 Planarity : 0.003 0.041 3592 Dihedral : 12.753 83.436 7640 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.17), residues: 2464 helix: 2.01 (0.13), residues: 1652 sheet: -1.32 (0.52), residues: 112 loop : -0.49 (0.22), residues: 700 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.398 Fit side-chains outliers start: 0 outliers final: 4 residues processed: 349 average time/residue: 1.4269 time to fit residues: 557.6656 Evaluate side-chains 256 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.9894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0070 chunk 187 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3950 ASN A4020 GLN B3950 ASN B4020 GLN C3950 ASN C4020 GLN D3950 ASN D4020 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 21048 Z= 0.157 Angle : 0.458 10.396 28412 Z= 0.241 Chirality : 0.035 0.130 3088 Planarity : 0.003 0.039 3592 Dihedral : 3.958 29.030 2696 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.17), residues: 2464 helix: 2.28 (0.12), residues: 1672 sheet: -1.59 (0.50), residues: 112 loop : -0.34 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 268 time to evaluate : 2.301 Fit side-chains outliers start: 64 outliers final: 15 residues processed: 311 average time/residue: 1.4594 time to fit residues: 508.5556 Evaluate side-chains 280 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 265 time to evaluate : 2.417 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 2.9510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 223 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21048 Z= 0.214 Angle : 0.451 5.989 28412 Z= 0.242 Chirality : 0.036 0.130 3088 Planarity : 0.003 0.049 3592 Dihedral : 3.977 30.445 2696 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2464 helix: 2.19 (0.12), residues: 1672 sheet: -1.84 (0.49), residues: 112 loop : -0.33 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 260 time to evaluate : 2.318 Fit side-chains outliers start: 56 outliers final: 19 residues processed: 294 average time/residue: 1.5288 time to fit residues: 501.4218 Evaluate side-chains 258 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 239 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 3 average time/residue: 0.3644 time to fit residues: 4.8758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 21048 Z= 0.371 Angle : 0.525 6.737 28412 Z= 0.280 Chirality : 0.039 0.122 3088 Planarity : 0.004 0.069 3592 Dihedral : 4.212 32.750 2696 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2464 helix: 1.86 (0.12), residues: 1668 sheet: -1.82 (0.51), residues: 112 loop : -0.48 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 2.419 Fit side-chains outliers start: 61 outliers final: 30 residues processed: 318 average time/residue: 1.5923 time to fit residues: 562.8655 Evaluate side-chains 294 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 264 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.3587 time to fit residues: 5.3644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 0.0370 chunk 60 optimal weight: 2.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 21048 Z= 0.207 Angle : 0.473 8.959 28412 Z= 0.250 Chirality : 0.036 0.139 3088 Planarity : 0.003 0.055 3592 Dihedral : 4.072 32.378 2696 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.17), residues: 2464 helix: 2.07 (0.12), residues: 1668 sheet: -1.96 (0.50), residues: 112 loop : -0.49 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 262 time to evaluate : 2.325 Fit side-chains revert: symmetry clash outliers start: 73 outliers final: 25 residues processed: 316 average time/residue: 1.5011 time to fit residues: 529.8899 Evaluate side-chains 279 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 254 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 3.1668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 111 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21048 Z= 0.169 Angle : 0.448 8.468 28412 Z= 0.237 Chirality : 0.035 0.155 3088 Planarity : 0.003 0.048 3592 Dihedral : 3.972 31.223 2696 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.17), residues: 2464 helix: 2.21 (0.12), residues: 1668 sheet: -1.95 (0.50), residues: 112 loop : -0.50 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 271 time to evaluate : 2.580 Fit side-chains outliers start: 64 outliers final: 32 residues processed: 323 average time/residue: 1.5010 time to fit residues: 542.5414 Evaluate side-chains 289 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.3592 time to fit residues: 5.2719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 136 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN A4054 ASN B4020 GLN ** B4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4020 GLN ** C4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4020 GLN ** D4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 21048 Z= 0.163 Angle : 0.461 8.792 28412 Z= 0.241 Chirality : 0.035 0.169 3088 Planarity : 0.003 0.046 3592 Dihedral : 3.904 30.628 2696 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.17), residues: 2464 helix: 2.25 (0.12), residues: 1668 sheet: -1.95 (0.50), residues: 112 loop : -0.46 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 265 time to evaluate : 2.349 Fit side-chains outliers start: 64 outliers final: 28 residues processed: 321 average time/residue: 1.4759 time to fit residues: 530.9443 Evaluate side-chains 293 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 265 time to evaluate : 2.455 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 3.1732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4054 ASN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4054 ASN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4054 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 21048 Z= 0.160 Angle : 0.454 8.398 28412 Z= 0.238 Chirality : 0.035 0.170 3088 Planarity : 0.003 0.046 3592 Dihedral : 3.867 30.051 2696 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.17), residues: 2464 helix: 2.28 (0.12), residues: 1668 sheet: -1.94 (0.49), residues: 112 loop : -0.49 (0.24), residues: 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 277 time to evaluate : 2.449 Fit side-chains outliers start: 45 outliers final: 31 residues processed: 314 average time/residue: 1.4179 time to fit residues: 501.2369 Evaluate side-chains 299 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 1.2989 time to fit residues: 7.6117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.0970 chunk 208 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 210 optimal weight: 0.4980 chunk 221 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 21048 Z= 0.137 Angle : 0.457 9.036 28412 Z= 0.238 Chirality : 0.035 0.167 3088 Planarity : 0.003 0.040 3592 Dihedral : 3.812 29.356 2696 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.17), residues: 2464 helix: 2.37 (0.12), residues: 1672 sheet: -1.87 (0.49), residues: 112 loop : -0.50 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 266 time to evaluate : 2.409 Fit side-chains outliers start: 54 outliers final: 36 residues processed: 307 average time/residue: 1.4987 time to fit residues: 515.3286 Evaluate side-chains 293 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 257 time to evaluate : 2.462 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.2339 time to fit residues: 4.8596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4020 GLN B4054 ASN C4020 GLN C4054 ASN D4020 GLN D4054 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 21048 Z= 0.177 Angle : 0.477 10.943 28412 Z= 0.247 Chirality : 0.036 0.169 3088 Planarity : 0.003 0.045 3592 Dihedral : 3.831 29.419 2696 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.17), residues: 2464 helix: 2.27 (0.12), residues: 1672 sheet: -1.85 (0.50), residues: 112 loop : -0.53 (0.24), residues: 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 275 time to evaluate : 2.337 Fit side-chains outliers start: 39 outliers final: 35 residues processed: 307 average time/residue: 1.4381 time to fit residues: 495.0106 Evaluate side-chains 303 residues out of total 2236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 268 time to evaluate : 2.170 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 1.1337 time to fit residues: 6.8101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3950 ASN A4020 GLN ** A4054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3950 ASN ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3950 ASN ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3950 ASN ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108262 restraints weight = 26592.009| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.43 r_work: 0.2963 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 21048 Z= 0.315 Angle : 0.541 12.126 28412 Z= 0.280 Chirality : 0.038 0.167 3088 Planarity : 0.004 0.051 3592 Dihedral : 4.067 31.765 2696 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2464 helix: 1.98 (0.12), residues: 1672 sheet: -1.91 (0.50), residues: 112 loop : -0.51 (0.24), residues: 680 =============================================================================== Job complete usr+sys time: 7711.93 seconds wall clock time: 137 minutes 28.62 seconds (8248.62 seconds total)