Starting phenix.real_space_refine on Mon Mar 18 10:12:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sex_40432/03_2024/8sex_40432_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sex_40432/03_2024/8sex_40432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sex_40432/03_2024/8sex_40432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sex_40432/03_2024/8sex_40432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sex_40432/03_2024/8sex_40432_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sex_40432/03_2024/8sex_40432_updated.pdb" } resolution = 2.84 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= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 160 5.16 5 C 13344 2.51 5 N 3280 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4579": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20568 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5118 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "B" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5118 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "C" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5118 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "D" Number of atoms: 5118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5118 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 15, 'TRANS': 610} Chain breaks: 4 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' ZN': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4444 SG CYS A4958 56.003 81.965 85.909 1.00 45.49 S ATOM 4469 SG CYS A4961 58.285 82.520 88.873 1.00 43.92 S ATOM 9562 SG CYS B4958 59.715 56.003 85.909 1.00 45.49 S ATOM 9587 SG CYS B4961 59.160 58.285 88.873 1.00 43.92 S ATOM 14680 SG CYS C4958 85.677 59.715 85.909 1.00 45.49 S ATOM 14705 SG CYS C4961 83.395 59.160 88.873 1.00 43.92 S ATOM 19798 SG CYS D4958 81.965 85.677 85.909 1.00 45.49 S ATOM 19823 SG CYS D4961 82.520 83.395 88.873 1.00 43.92 S Time building chain proxies: 10.59, per 1000 atoms: 0.51 Number of scatterers: 20568 At special positions: 0 Unit cell: (142.968, 142.968, 130.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 160 16.00 P 4 15.00 O 3776 8.00 N 3280 7.00 C 13344 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: 8.25 Conformation dependent library (CDL) restraints added in 3.6 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 A4958 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " 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 B4958 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " 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 C4958 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " 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 D4958 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " 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: 4712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 71.4% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 3951 through 3969 Processing helix chain 'A' and resid 3974 through 3982 Processing helix chain 'A' and resid 3985 through 4005 removed outlier: 3.619A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4007 through 4030 removed outlier: 4.068A pdb=" N ILE A4010 " --> pdb=" O SER A4007 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU A4011 " --> pdb=" O SER A4008 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A4018 " --> pdb=" O GLU A4015 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A4019 " --> pdb=" O LEU A4016 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A4025 " --> pdb=" O ASP A4022 " (cutoff:3.500A) Processing helix chain 'A' and resid 4039 through 4050 Processing helix chain 'A' and resid 4052 through 4058 removed outlier: 4.151A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 4.092A 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 4229 through 4251 Processing helix chain 'A' and resid 4543 through 4557 Processing helix chain 'A' and resid 4559 through 4579 removed outlier: 3.507A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE A4579 " --> pdb=" O PHE A4575 " (cutoff:3.500A) Processing helix chain 'A' and resid 4638 through 4664 Processing helix chain 'A' and resid 4666 through 4683 Processing helix chain 'A' and resid 4697 through 4706 removed outlier: 3.697A pdb=" N ARG A4703 " --> pdb=" O GLY A4699 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) Processing helix chain 'A' and resid 4720 through 4732 removed outlier: 5.245A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.311A 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 No H-bonds generated for 'chain 'A' and resid 4745 through 4748' Processing helix chain 'A' and resid 4773 through 4784 Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.991A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.690A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.966A 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: 4.209A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) Processing helix chain 'A' and resid 4910 through 4923 Processing helix chain 'A' and resid 4927 through 4956 Processing helix chain 'A' and resid 4965 through 4970 removed outlier: 3.906A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4981 Processing helix chain 'A' and resid 4985 through 4997 Processing helix chain 'A' and resid 5000 through 5002 No H-bonds generated for 'chain 'A' and resid 5000 through 5002' Processing helix chain 'A' and resid 5005 through 5015 Processing helix chain 'A' and resid 5028 through 5036 removed outlier: 5.845A pdb=" N ASP A5034 " --> pdb=" O LYS A5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) Processing helix chain 'B' and resid 3951 through 3969 Processing helix chain 'B' and resid 3974 through 3982 Processing helix chain 'B' and resid 3985 through 4005 removed outlier: 3.619A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4007 through 4030 removed outlier: 4.068A pdb=" N ILE B4010 " --> pdb=" O SER B4007 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU B4011 " --> pdb=" O SER B4008 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B4018 " --> pdb=" O GLU B4015 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B4019 " --> pdb=" O LEU B4016 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B4025 " --> pdb=" O ASP B4022 " (cutoff:3.500A) Processing helix chain 'B' and resid 4039 through 4050 Processing helix chain 'B' and resid 4052 through 4058 removed outlier: 4.151A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 4.092A 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 4229 through 4251 Processing helix chain 'B' and resid 4543 through 4557 Processing helix chain 'B' and resid 4559 through 4579 removed outlier: 3.507A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE B4579 " --> pdb=" O PHE B4575 " (cutoff:3.500A) Processing helix chain 'B' and resid 4638 through 4664 Processing helix chain 'B' and resid 4666 through 4683 Processing helix chain 'B' and resid 4697 through 4706 removed outlier: 3.697A pdb=" N ARG B4703 " --> pdb=" O GLY B4699 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) Processing helix chain 'B' and resid 4720 through 4732 removed outlier: 5.245A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.311A 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 No H-bonds generated for 'chain 'B' and resid 4745 through 4748' Processing helix chain 'B' and resid 4773 through 4784 Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.991A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4819 Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.690A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.966A 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: 4.209A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) Processing helix chain 'B' and resid 4910 through 4923 Processing helix chain 'B' and resid 4927 through 4956 Processing helix chain 'B' and resid 4965 through 4970 removed outlier: 3.906A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4974 through 4981 Processing helix chain 'B' and resid 4985 through 4997 Processing helix chain 'B' and resid 5000 through 5002 No H-bonds generated for 'chain 'B' and resid 5000 through 5002' Processing helix chain 'B' and resid 5005 through 5015 Processing helix chain 'B' and resid 5028 through 5036 removed outlier: 5.845A pdb=" N ASP B5034 " --> pdb=" O LYS B5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) Processing helix chain 'C' and resid 3951 through 3969 Processing helix chain 'C' and resid 3974 through 3982 Processing helix chain 'C' and resid 3985 through 4005 removed outlier: 3.619A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4007 through 4030 removed outlier: 4.068A pdb=" N ILE C4010 " --> pdb=" O SER C4007 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU C4011 " --> pdb=" O SER C4008 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP C4018 " --> pdb=" O GLU C4015 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C4019 " --> pdb=" O LEU C4016 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL C4025 " --> pdb=" O ASP C4022 " (cutoff:3.500A) Processing helix chain 'C' and resid 4039 through 4050 Processing helix chain 'C' and resid 4052 through 4058 removed outlier: 4.151A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 4.092A 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 4229 through 4251 Processing helix chain 'C' and resid 4543 through 4557 Processing helix chain 'C' and resid 4559 through 4579 removed outlier: 3.507A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE C4579 " --> pdb=" O PHE C4575 " (cutoff:3.500A) Processing helix chain 'C' and resid 4638 through 4664 Processing helix chain 'C' and resid 4666 through 4683 Processing helix chain 'C' and resid 4697 through 4706 removed outlier: 3.697A pdb=" N ARG C4703 " --> pdb=" O GLY C4699 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) Processing helix chain 'C' and resid 4720 through 4732 removed outlier: 5.245A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.311A 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 No H-bonds generated for 'chain 'C' and resid 4745 through 4748' Processing helix chain 'C' and resid 4773 through 4784 Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.991A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4819 Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.690A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.966A 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: 4.209A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) Processing helix chain 'C' and resid 4910 through 4923 Processing helix chain 'C' and resid 4927 through 4956 Processing helix chain 'C' and resid 4965 through 4970 removed outlier: 3.906A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4981 Processing helix chain 'C' and resid 4985 through 4997 Processing helix chain 'C' and resid 5000 through 5002 No H-bonds generated for 'chain 'C' and resid 5000 through 5002' Processing helix chain 'C' and resid 5005 through 5015 Processing helix chain 'C' and resid 5028 through 5036 removed outlier: 5.845A pdb=" N ASP C5034 " --> pdb=" O LYS C5030 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) Processing helix chain 'D' and resid 3951 through 3969 Processing helix chain 'D' and resid 3974 through 3982 Processing helix chain 'D' and resid 3985 through 4005 removed outlier: 3.619A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4007 through 4030 removed outlier: 4.068A pdb=" N ILE D4010 " --> pdb=" O SER D4007 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU D4011 " --> pdb=" O SER D4008 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP D4018 " --> pdb=" O GLU D4015 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D4019 " --> pdb=" O LEU D4016 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D4025 " --> pdb=" O ASP D4022 " (cutoff:3.500A) Processing helix chain 'D' and resid 4039 through 4050 Processing helix chain 'D' and resid 4052 through 4058 removed outlier: 4.151A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) removed outlier: 4.092A 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 4229 through 4251 Processing helix chain 'D' and resid 4543 through 4557 Processing helix chain 'D' and resid 4559 through 4579 removed outlier: 3.507A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE D4579 " --> pdb=" O PHE D4575 " (cutoff:3.500A) Processing helix chain 'D' and resid 4638 through 4664 Processing helix chain 'D' and resid 4666 through 4683 Processing helix chain 'D' and resid 4697 through 4706 removed outlier: 3.697A pdb=" N ARG D4703 " --> pdb=" O GLY D4699 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) Processing helix chain 'D' and resid 4720 through 4732 removed outlier: 5.245A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.311A 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 No H-bonds generated for 'chain 'D' and resid 4745 through 4748' Processing helix chain 'D' and resid 4773 through 4784 Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.991A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.690A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.966A 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: 4.209A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) Processing helix chain 'D' and resid 4910 through 4923 Processing helix chain 'D' and resid 4927 through 4956 Processing helix chain 'D' and resid 4965 through 4970 removed outlier: 3.906A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4974 through 4981 Processing helix chain 'D' and resid 4985 through 4997 Processing helix chain 'D' and resid 5000 through 5002 No H-bonds generated for 'chain 'D' and resid 5000 through 5002' Processing helix chain 'D' and resid 5005 through 5015 Processing helix chain 'D' and resid 5028 through 5036 removed outlier: 5.845A pdb=" N ASP D5034 " --> pdb=" O LYS D5030 " (cutoff:3.500A) removed outlier: 6.152A 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 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 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 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 Processing sheet with id= H, first strand: chain 'D' and resid 4580 through 4583 1236 hydrogen bonds defined for protein. 3372 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: 6.03 Time building geometry restraints manager: 8.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6484 1.34 - 1.46: 4196 1.46 - 1.57: 10088 1.57 - 1.69: 4 1.69 - 1.81: 276 Bond restraints: 21048 Sorted by residual: bond pdb=" C4 AMP C5101 " pdb=" C5 AMP C5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP D5101 " pdb=" C5 AMP D5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP A5101 " pdb=" C5 AMP A5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C4 AMP B5101 " pdb=" C5 AMP B5101 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C5 AMP A5101 " pdb=" C6 AMP A5101 " ideal model delta sigma weight residual 1.490 1.405 0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 21043 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.43: 464 106.43 - 113.33: 11100 113.33 - 120.23: 8004 120.23 - 127.12: 8672 127.12 - 134.02: 176 Bond angle restraints: 28416 Sorted by residual: angle pdb=" C LYS D4665 " pdb=" N VAL D4666 " pdb=" CA VAL D4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS C4665 " pdb=" N VAL C4666 " pdb=" CA VAL C4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS A4665 " pdb=" N VAL A4666 " pdb=" CA VAL A4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" C LYS B4665 " pdb=" N VAL B4666 " pdb=" CA VAL B4666 " ideal model delta sigma weight residual 120.24 122.66 -2.42 6.30e-01 2.52e+00 1.47e+01 angle pdb=" N1 AMP A5101 " pdb=" C2 AMP A5101 " pdb=" N3 AMP A5101 " ideal model delta sigma weight residual 120.00 129.33 -9.33 3.00e+00 1.11e-01 9.66e+00 ... (remaining 28411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 12100 30.78 - 61.57: 280 61.57 - 92.35: 8 92.35 - 123.13: 0 123.13 - 153.92: 4 Dihedral angle restraints: 12392 sinusoidal: 5080 harmonic: 7312 Sorted by residual: dihedral pdb=" C2' AMP C5101 " pdb=" C1' AMP C5101 " pdb=" N9 AMP C5101 " pdb=" C4 AMP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C2' AMP B5101 " pdb=" C1' AMP B5101 " pdb=" N9 AMP B5101 " pdb=" C4 AMP B5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" C2' AMP A5101 " pdb=" C1' AMP A5101 " pdb=" N9 AMP A5101 " pdb=" C4 AMP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -62.36 153.92 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 12389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1952 0.035 - 0.070: 928 0.070 - 0.104: 160 0.104 - 0.139: 36 0.139 - 0.174: 4 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA PRO A3972 " pdb=" N PRO A3972 " pdb=" C PRO A3972 " pdb=" CB PRO A3972 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA PRO B3972 " pdb=" N PRO B3972 " pdb=" C PRO B3972 " pdb=" CB PRO B3972 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA PRO D3972 " pdb=" N PRO D3972 " pdb=" C PRO D3972 " pdb=" CB PRO D3972 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.57e-01 ... (remaining 3077 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A3971 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO A3972 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO A3972 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A3972 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B3971 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO B3972 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO B3972 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO B3972 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C3971 " -0.083 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C3972 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C3972 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO C3972 " -0.065 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 0.42 - 1.31: 16 1.31 - 2.21: 28 2.21 - 3.11: 15428 3.11 - 4.00: 54764 4.00 - 4.90: 101672 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171908 Sorted by model distance: nonbonded pdb=" NH2 ARG A4944 " pdb=" OD1 ASP B4938 " model vdw 0.419 2.520 nonbonded pdb=" NH2 ARG B4944 " pdb=" OD1 ASP C4938 " model vdw 0.419 2.520 nonbonded pdb=" OD1 ASP A4938 " pdb=" NH2 ARG D4944 " model vdw 0.419 2.520 nonbonded pdb=" NH2 ARG C4944 " pdb=" OD1 ASP D4938 " model vdw 0.419 2.520 nonbonded pdb=" NH2 ARG A4944 " pdb=" CG ASP B4938 " model vdw 1.035 3.350 ... (remaining 171903 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: 3.010 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: 0.020 Extract box with map and model: 14.260 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 56.430 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.120 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 0.005 0.110 21048 Z= 0.329 Angle : 0.556 9.326 28416 Z= 0.294 Chirality : 0.038 0.174 3080 Planarity : 0.005 0.126 3592 Dihedral : 12.782 153.916 7668 Min Nonbonded Distance : 0.419 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.76 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 6.45 % Favored : 91.40 % 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: 1.60 (0.17), residues: 2464 helix: 1.56 (0.12), residues: 1664 sheet: -0.11 (0.54), residues: 104 loop : 0.20 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A4716 HIS 0.003 0.001 HIS C4650 PHE 0.020 0.002 PHE D4916 TYR 0.017 0.002 TYR D4994 ARG 0.002 0.001 ARG D4673 *********************** 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 440 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 392 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4047 MET cc_start: 0.6927 (tmm) cc_final: 0.6382 (tmm) REVERT: A 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6265 (t80) REVERT: A 4629 TYR cc_start: 0.7423 (m-80) cc_final: 0.7091 (m-80) REVERT: A 4698 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7719 (ttmm) REVERT: A 4949 GLN cc_start: 0.8113 (tp40) cc_final: 0.7646 (mp10) REVERT: A 5006 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: A 5030 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7527 (ttpt) REVERT: B 4047 MET cc_start: 0.6926 (tmm) cc_final: 0.6382 (tmm) REVERT: B 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6263 (t80) REVERT: B 4629 TYR cc_start: 0.7419 (m-80) cc_final: 0.7089 (m-80) REVERT: B 4698 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7722 (ttmm) REVERT: B 4949 GLN cc_start: 0.8112 (tp40) cc_final: 0.7646 (mp10) REVERT: B 5006 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: B 5030 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7532 (ttpt) REVERT: C 4047 MET cc_start: 0.6927 (tmm) cc_final: 0.6380 (tmm) REVERT: C 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6269 (t80) REVERT: C 4629 TYR cc_start: 0.7422 (m-80) cc_final: 0.7093 (m-80) REVERT: C 4698 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7719 (ttmm) REVERT: C 4949 GLN cc_start: 0.8110 (tp40) cc_final: 0.7646 (mp10) REVERT: C 5006 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: C 5030 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7528 (ttpt) REVERT: D 4047 MET cc_start: 0.6924 (tmm) cc_final: 0.6380 (tmm) REVERT: D 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6266 (t80) REVERT: D 4629 TYR cc_start: 0.7426 (m-80) cc_final: 0.7094 (m-80) REVERT: D 4698 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7720 (ttmm) REVERT: D 4949 GLN cc_start: 0.8113 (tp40) cc_final: 0.7649 (mp10) REVERT: D 5006 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: D 5030 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7528 (ttpt) outliers start: 48 outliers final: 24 residues processed: 436 average time/residue: 1.3245 time to fit residues: 651.0502 Evaluate side-chains 332 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4027 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4027 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4027 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4027 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 194 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 chunk 225 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3963 ASN A3978 GLN A3982 HIS A4997 ASN B3963 ASN B3978 GLN B4020 GLN B4997 ASN C3963 ASN C3978 GLN C4020 GLN C4997 ASN D3963 ASN D3978 GLN D4997 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 21048 Z= 0.184 Angle : 0.497 7.536 28416 Z= 0.261 Chirality : 0.037 0.171 3080 Planarity : 0.006 0.122 3592 Dihedral : 8.245 149.750 2784 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.79 % Favored : 98.05 % Rotamer: Outliers : 3.94 % Allowed : 10.57 % Favored : 85.48 % 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: 2.06 (0.17), residues: 2464 helix: 1.95 (0.12), residues: 1660 sheet: -0.66 (0.49), residues: 104 loop : 0.40 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C4716 HIS 0.004 0.001 HIS D4973 PHE 0.016 0.001 PHE D4916 TYR 0.013 0.001 TYR A4687 ARG 0.008 0.001 ARG B4188 *********************** 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 416 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 328 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.7116 (m-30) cc_final: 0.6810 (m-30) REVERT: A 4030 LEU cc_start: 0.8940 (mt) cc_final: 0.8655 (mp) REVERT: A 4047 MET cc_start: 0.6748 (tmm) cc_final: 0.6063 (tmm) REVERT: A 4196 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.3834 (tp30) REVERT: A 4580 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6243 (t80) REVERT: A 4933 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: A 4949 GLN cc_start: 0.8101 (tp40) cc_final: 0.7707 (mp10) REVERT: A 5002 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7071 (mp0) REVERT: A 5030 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7479 (ttpt) REVERT: B 4022 ASP cc_start: 0.7111 (m-30) cc_final: 0.6804 (m-30) REVERT: B 4030 LEU cc_start: 0.8938 (mt) cc_final: 0.8653 (mp) REVERT: B 4047 MET cc_start: 0.6747 (tmm) cc_final: 0.6064 (tmm) REVERT: B 4196 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.3832 (tp30) REVERT: B 4580 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.6242 (t80) REVERT: B 4933 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: B 4949 GLN cc_start: 0.8102 (tp40) cc_final: 0.7708 (mp10) REVERT: B 5002 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7069 (mp0) REVERT: B 5030 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7481 (ttpt) REVERT: C 4022 ASP cc_start: 0.7110 (m-30) cc_final: 0.6800 (m-30) REVERT: C 4030 LEU cc_start: 0.8939 (mt) cc_final: 0.8653 (mp) REVERT: C 4047 MET cc_start: 0.6751 (tmm) cc_final: 0.6068 (tmm) REVERT: C 4196 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.3837 (tp30) REVERT: C 4580 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.6244 (t80) REVERT: C 4933 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: C 4949 GLN cc_start: 0.8100 (tp40) cc_final: 0.7709 (mp10) REVERT: C 5002 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7069 (mp0) REVERT: C 5030 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7480 (ttpt) REVERT: D 4022 ASP cc_start: 0.7112 (m-30) cc_final: 0.6802 (m-30) REVERT: D 4030 LEU cc_start: 0.8943 (mt) cc_final: 0.8656 (mp) REVERT: D 4047 MET cc_start: 0.6751 (tmm) cc_final: 0.6068 (tmm) REVERT: D 4196 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.3832 (tp30) REVERT: D 4580 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6243 (t80) REVERT: D 4933 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7277 (mt0) REVERT: D 4949 GLN cc_start: 0.8101 (tp40) cc_final: 0.7708 (mp10) REVERT: D 5002 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7069 (mp0) REVERT: D 5030 LYS cc_start: 0.8145 (ttmt) cc_final: 0.7476 (ttpt) outliers start: 88 outliers final: 32 residues processed: 380 average time/residue: 1.2908 time to fit residues: 554.4764 Evaluate side-chains 356 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 312 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 200 optimal weight: 0.6980 chunk 223 optimal weight: 0.0870 chunk 76 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 overall best weight: 0.9338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A5031 GLN B5031 GLN C5031 GLN D5031 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21048 Z= 0.203 Angle : 0.486 7.300 28416 Z= 0.252 Chirality : 0.036 0.174 3080 Planarity : 0.005 0.120 3592 Dihedral : 7.857 146.398 2748 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.21 % Rotamer: Outliers : 4.66 % Allowed : 12.37 % Favored : 82.97 % 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: 2.05 (0.17), residues: 2464 helix: 1.99 (0.12), residues: 1660 sheet: -0.92 (0.49), residues: 104 loop : 0.29 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D4716 HIS 0.003 0.001 HIS C4973 PHE 0.016 0.001 PHE C4916 TYR 0.012 0.001 TYR D4994 ARG 0.008 0.001 ARG B4042 *********************** 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 428 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 324 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.7008 (m-30) cc_final: 0.6651 (m-30) REVERT: A 4030 LEU cc_start: 0.8925 (mt) cc_final: 0.8643 (mp) REVERT: A 4047 MET cc_start: 0.6624 (tmm) cc_final: 0.5975 (tmm) REVERT: A 4188 ARG cc_start: 0.7465 (mmm160) cc_final: 0.6891 (tpt170) REVERT: A 4580 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.6301 (t80) REVERT: A 4844 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8380 (tp) REVERT: A 4933 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7129 (mt0) REVERT: A 4949 GLN cc_start: 0.8148 (tp40) cc_final: 0.7545 (mp10) REVERT: A 5026 ASP cc_start: 0.8130 (t0) cc_final: 0.7901 (t70) REVERT: A 5030 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7345 (ttpt) REVERT: B 4022 ASP cc_start: 0.7153 (m-30) cc_final: 0.6773 (m-30) REVERT: B 4030 LEU cc_start: 0.8925 (mt) cc_final: 0.8643 (mp) REVERT: B 4047 MET cc_start: 0.6622 (tmm) cc_final: 0.5973 (tmm) REVERT: B 4188 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6890 (tpt170) REVERT: B 4580 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.6299 (t80) REVERT: B 4844 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8376 (tp) REVERT: B 4933 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: B 4949 GLN cc_start: 0.8147 (tp40) cc_final: 0.7545 (mp10) REVERT: B 5026 ASP cc_start: 0.8131 (t0) cc_final: 0.7898 (t70) REVERT: B 5030 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7349 (ttpt) REVERT: C 4022 ASP cc_start: 0.7150 (m-30) cc_final: 0.6769 (m-30) REVERT: C 4030 LEU cc_start: 0.8924 (mt) cc_final: 0.8642 (mp) REVERT: C 4047 MET cc_start: 0.6627 (tmm) cc_final: 0.5976 (tmm) REVERT: C 4188 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6891 (tpt170) REVERT: C 4580 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.6303 (t80) REVERT: C 4844 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8377 (tp) REVERT: C 4933 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: C 4949 GLN cc_start: 0.8149 (tp40) cc_final: 0.7546 (mp10) REVERT: C 5026 ASP cc_start: 0.8130 (t0) cc_final: 0.7902 (t70) REVERT: C 5030 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7347 (ttpt) REVERT: D 4022 ASP cc_start: 0.7000 (m-30) cc_final: 0.6643 (m-30) REVERT: D 4030 LEU cc_start: 0.8926 (mt) cc_final: 0.8644 (mp) REVERT: D 4047 MET cc_start: 0.6631 (tmm) cc_final: 0.5979 (tmm) REVERT: D 4188 ARG cc_start: 0.7462 (mmm160) cc_final: 0.6892 (tpt170) REVERT: D 4580 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.6301 (t80) REVERT: D 4844 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8381 (tp) REVERT: D 4933 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7128 (mt0) REVERT: D 4949 GLN cc_start: 0.8148 (tp40) cc_final: 0.7547 (mp10) REVERT: D 5026 ASP cc_start: 0.8132 (t0) cc_final: 0.7904 (t70) REVERT: D 5030 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7345 (ttpt) outliers start: 104 outliers final: 52 residues processed: 392 average time/residue: 1.3192 time to fit residues: 584.1691 Evaluate side-chains 372 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 308 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4818 MET Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4951 LYS Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4818 MET Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4951 LYS Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4818 MET Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4951 LYS Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4818 MET Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4951 LYS Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 117 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 239 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21048 Z= 0.168 Angle : 0.465 6.568 28416 Z= 0.240 Chirality : 0.035 0.177 3080 Planarity : 0.005 0.116 3592 Dihedral : 7.680 143.643 2748 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % Rotamer: Outliers : 3.58 % Allowed : 13.80 % Favored : 82.62 % 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: 2.16 (0.17), residues: 2464 helix: 2.12 (0.12), residues: 1672 sheet: -1.15 (0.49), residues: 104 loop : 0.23 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C4716 HIS 0.002 0.001 HIS D3998 PHE 0.014 0.001 PHE D4916 TYR 0.012 0.001 TYR D4687 ARG 0.008 0.001 ARG A4042 *********************** 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 391 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 311 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.7040 (m-30) cc_final: 0.6701 (m-30) REVERT: A 4030 LEU cc_start: 0.8903 (mt) cc_final: 0.8638 (mp) REVERT: A 4047 MET cc_start: 0.6480 (tmm) cc_final: 0.5862 (tmm) REVERT: A 4188 ARG cc_start: 0.7443 (mmm160) cc_final: 0.6876 (tpt170) REVERT: A 4580 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 4639 MET cc_start: 0.7800 (mmm) cc_final: 0.7428 (mtm) REVERT: A 4844 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8375 (tp) REVERT: A 4933 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 4949 GLN cc_start: 0.8138 (tp40) cc_final: 0.7535 (mp10) REVERT: A 4956 THR cc_start: 0.8795 (p) cc_final: 0.8576 (p) REVERT: B 4022 ASP cc_start: 0.7031 (m-30) cc_final: 0.6692 (m-30) REVERT: B 4030 LEU cc_start: 0.8904 (mt) cc_final: 0.8639 (mp) REVERT: B 4047 MET cc_start: 0.6478 (tmm) cc_final: 0.5862 (tmm) REVERT: B 4188 ARG cc_start: 0.7442 (mmm160) cc_final: 0.6875 (tpt170) REVERT: B 4580 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.6228 (t80) REVERT: B 4639 MET cc_start: 0.7803 (mmm) cc_final: 0.7433 (mtm) REVERT: B 4844 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8370 (tp) REVERT: B 4933 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: B 4949 GLN cc_start: 0.8137 (tp40) cc_final: 0.7535 (mp10) REVERT: B 4956 THR cc_start: 0.8799 (p) cc_final: 0.8580 (p) REVERT: C 4022 ASP cc_start: 0.7029 (m-30) cc_final: 0.6685 (m-30) REVERT: C 4030 LEU cc_start: 0.8901 (mt) cc_final: 0.8637 (mp) REVERT: C 4047 MET cc_start: 0.6484 (tmm) cc_final: 0.5866 (tmm) REVERT: C 4188 ARG cc_start: 0.7440 (mmm160) cc_final: 0.6876 (tpt170) REVERT: C 4580 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.6231 (t80) REVERT: C 4639 MET cc_start: 0.7798 (mmm) cc_final: 0.7428 (mtm) REVERT: C 4844 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8369 (tp) REVERT: C 4933 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: C 4949 GLN cc_start: 0.8137 (tp40) cc_final: 0.7536 (mp10) REVERT: C 4956 THR cc_start: 0.8800 (p) cc_final: 0.8583 (p) REVERT: D 4022 ASP cc_start: 0.7035 (m-30) cc_final: 0.6695 (m-30) REVERT: D 4030 LEU cc_start: 0.8901 (mt) cc_final: 0.8638 (mp) REVERT: D 4047 MET cc_start: 0.6483 (tmm) cc_final: 0.5866 (tmm) REVERT: D 4188 ARG cc_start: 0.7443 (mmm160) cc_final: 0.6877 (tpt170) REVERT: D 4580 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.6229 (t80) REVERT: D 4639 MET cc_start: 0.7796 (mmm) cc_final: 0.7426 (mtm) REVERT: D 4844 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8373 (tp) REVERT: D 4933 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: D 4949 GLN cc_start: 0.8140 (tp40) cc_final: 0.7538 (mp10) REVERT: D 4956 THR cc_start: 0.8802 (p) cc_final: 0.8584 (p) outliers start: 80 outliers final: 36 residues processed: 371 average time/residue: 1.2361 time to fit residues: 521.0280 Evaluate side-chains 358 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 310 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3998 HIS B3998 HIS C3998 HIS D3998 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 21048 Z= 0.399 Angle : 0.575 7.285 28416 Z= 0.298 Chirality : 0.041 0.177 3080 Planarity : 0.006 0.117 3592 Dihedral : 7.902 142.870 2748 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.11 % Favored : 97.73 % Rotamer: Outliers : 5.38 % Allowed : 12.63 % Favored : 81.99 % 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: 1.37 (0.17), residues: 2464 helix: 1.49 (0.12), residues: 1676 sheet: -1.12 (0.48), residues: 104 loop : -0.05 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B4716 HIS 0.005 0.001 HIS B4650 PHE 0.023 0.002 PHE B4916 TYR 0.020 0.002 TYR D4994 ARG 0.011 0.001 ARG A4042 *********************** 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 422 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 302 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4022 ASP cc_start: 0.7065 (m-30) cc_final: 0.6713 (m-30) REVERT: A 4047 MET cc_start: 0.6533 (tmm) cc_final: 0.5892 (tmm) REVERT: A 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6323 (t80) REVERT: A 4725 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6428 (tp) REVERT: A 4933 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: A 4949 GLN cc_start: 0.8158 (tp40) cc_final: 0.7499 (mp10) REVERT: A 5006 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: B 4022 ASP cc_start: 0.7232 (m-30) cc_final: 0.6886 (m-30) REVERT: B 4047 MET cc_start: 0.6534 (tmm) cc_final: 0.5895 (tmm) REVERT: B 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6319 (t80) REVERT: B 4725 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6427 (tp) REVERT: B 4933 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7224 (mt0) REVERT: B 4949 GLN cc_start: 0.8159 (tp40) cc_final: 0.7498 (mp10) REVERT: B 5006 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: C 4022 ASP cc_start: 0.7235 (m-30) cc_final: 0.6886 (m-30) REVERT: C 4047 MET cc_start: 0.6536 (tmm) cc_final: 0.5893 (tmm) REVERT: C 4580 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.6324 (t80) REVERT: C 4725 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6427 (tp) REVERT: C 4933 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7226 (mt0) REVERT: C 4949 GLN cc_start: 0.8155 (tp40) cc_final: 0.7498 (mp10) REVERT: C 5006 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7393 (pt0) REVERT: D 4022 ASP cc_start: 0.7061 (m-30) cc_final: 0.6708 (m-30) REVERT: D 4047 MET cc_start: 0.6539 (tmm) cc_final: 0.5897 (tmm) REVERT: D 4580 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.6321 (t80) REVERT: D 4725 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6423 (tp) REVERT: D 4933 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: D 4949 GLN cc_start: 0.8156 (tp40) cc_final: 0.7498 (mp10) REVERT: D 5006 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7393 (pt0) outliers start: 120 outliers final: 68 residues processed: 386 average time/residue: 1.1644 time to fit residues: 515.6725 Evaluate side-chains 372 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 288 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4036 VAL Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4207 MET Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4549 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4036 VAL Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4549 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4036 VAL Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4549 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4036 VAL Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4549 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 111 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21048 Z= 0.163 Angle : 0.472 5.999 28416 Z= 0.243 Chirality : 0.035 0.179 3080 Planarity : 0.005 0.110 3592 Dihedral : 7.595 141.310 2748 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % Rotamer: Outliers : 3.58 % Allowed : 15.77 % Favored : 80.65 % 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: 1.81 (0.17), residues: 2464 helix: 1.90 (0.12), residues: 1696 sheet: -1.17 (0.49), residues: 104 loop : -0.14 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D4716 HIS 0.002 0.001 HIS A3998 PHE 0.015 0.001 PHE B4916 TYR 0.010 0.001 TYR D4687 ARG 0.008 0.001 ARG A4188 *********************** 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 378 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 298 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4573 (tpt) cc_final: 0.3969 (mmm) REVERT: A 4022 ASP cc_start: 0.7057 (m-30) cc_final: 0.6693 (m-30) REVERT: A 4047 MET cc_start: 0.6582 (tmm) cc_final: 0.5929 (tmm) REVERT: A 4188 ARG cc_start: 0.7490 (mmm160) cc_final: 0.6889 (tpt170) REVERT: A 4580 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6239 (t80) REVERT: A 4735 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6480 (pm20) REVERT: A 4844 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8262 (tp) REVERT: A 4933 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: A 4949 GLN cc_start: 0.8142 (tp40) cc_final: 0.7528 (mp10) REVERT: A 4956 THR cc_start: 0.8801 (p) cc_final: 0.8597 (p) REVERT: B 4000 MET cc_start: 0.5009 (tpt) cc_final: 0.4382 (mmm) REVERT: B 4022 ASP cc_start: 0.7039 (m-30) cc_final: 0.6671 (m-30) REVERT: B 4047 MET cc_start: 0.6576 (tmm) cc_final: 0.5929 (tmm) REVERT: B 4188 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6889 (tpt170) REVERT: B 4580 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.6239 (t80) REVERT: B 4735 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6480 (pm20) REVERT: B 4844 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 4933 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 4949 GLN cc_start: 0.8141 (tp40) cc_final: 0.7528 (mp10) REVERT: B 4956 THR cc_start: 0.8804 (p) cc_final: 0.8602 (p) REVERT: C 4000 MET cc_start: 0.5008 (tpt) cc_final: 0.4379 (mmm) REVERT: C 4022 ASP cc_start: 0.7042 (m-30) cc_final: 0.6670 (m-30) REVERT: C 4047 MET cc_start: 0.6579 (tmm) cc_final: 0.5929 (tmm) REVERT: C 4188 ARG cc_start: 0.7486 (mmm160) cc_final: 0.6890 (tpt170) REVERT: C 4580 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.6240 (t80) REVERT: C 4735 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6484 (pm20) REVERT: C 4844 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8256 (tp) REVERT: C 4933 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: C 4949 GLN cc_start: 0.8140 (tp40) cc_final: 0.7529 (mp10) REVERT: C 4956 THR cc_start: 0.8804 (p) cc_final: 0.8603 (p) REVERT: D 4000 MET cc_start: 0.5009 (tpt) cc_final: 0.4379 (mmm) REVERT: D 4022 ASP cc_start: 0.7051 (m-30) cc_final: 0.6688 (m-30) REVERT: D 4047 MET cc_start: 0.6579 (tmm) cc_final: 0.5931 (tmm) REVERT: D 4188 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6893 (tpt170) REVERT: D 4580 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.6241 (t80) REVERT: D 4735 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6481 (pm20) REVERT: D 4844 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8261 (tp) REVERT: D 4933 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: D 4949 GLN cc_start: 0.8142 (tp40) cc_final: 0.7530 (mp10) REVERT: D 4956 THR cc_start: 0.8806 (p) cc_final: 0.8602 (p) outliers start: 80 outliers final: 40 residues processed: 362 average time/residue: 1.0738 time to fit residues: 450.1103 Evaluate side-chains 344 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 292 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.1980 chunk 133 optimal weight: 5.9990 chunk 239 optimal weight: 0.2980 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21048 Z= 0.166 Angle : 0.474 7.348 28416 Z= 0.244 Chirality : 0.035 0.179 3080 Planarity : 0.005 0.107 3592 Dihedral : 7.538 140.947 2748 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.63 % Allowed : 16.08 % Favored : 80.29 % 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: 2.10 (0.17), residues: 2464 helix: 2.10 (0.12), residues: 1664 sheet: -1.19 (0.50), residues: 104 loop : 0.16 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D4716 HIS 0.003 0.001 HIS A3998 PHE 0.014 0.001 PHE B4916 TYR 0.012 0.001 TYR D4554 ARG 0.008 0.001 ARG D4188 *********************** 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 377 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 296 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4644 (tpt) cc_final: 0.4011 (mmm) REVERT: A 4022 ASP cc_start: 0.7237 (m-30) cc_final: 0.6867 (m-30) REVERT: A 4030 LEU cc_start: 0.8915 (mt) cc_final: 0.8611 (mp) REVERT: A 4047 MET cc_start: 0.6484 (tmm) cc_final: 0.5835 (tmm) REVERT: A 4188 ARG cc_start: 0.7501 (mmm160) cc_final: 0.6929 (tpt170) REVERT: A 4580 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.6204 (t80) REVERT: A 4725 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6590 (tp) REVERT: A 4824 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.7127 (mmt180) REVERT: A 4844 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8291 (tp) REVERT: A 4933 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: A 4949 GLN cc_start: 0.8141 (tp40) cc_final: 0.7521 (mp10) REVERT: A 4953 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7869 (t0) REVERT: B 4000 MET cc_start: 0.4652 (tpt) cc_final: 0.4017 (mmm) REVERT: B 4022 ASP cc_start: 0.7220 (m-30) cc_final: 0.6848 (m-30) REVERT: B 4030 LEU cc_start: 0.8917 (mt) cc_final: 0.8612 (mp) REVERT: B 4047 MET cc_start: 0.6478 (tmm) cc_final: 0.5834 (tmm) REVERT: B 4188 ARG cc_start: 0.7498 (mmm160) cc_final: 0.6926 (tpt170) REVERT: B 4580 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.6198 (t80) REVERT: B 4725 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6591 (tp) REVERT: B 4824 ARG cc_start: 0.7431 (ttp-170) cc_final: 0.7129 (mmt180) REVERT: B 4844 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 4933 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: B 4949 GLN cc_start: 0.8139 (tp40) cc_final: 0.7521 (mp10) REVERT: B 4953 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7868 (t0) REVERT: C 4000 MET cc_start: 0.4645 (tpt) cc_final: 0.4010 (mmm) REVERT: C 4022 ASP cc_start: 0.7219 (m-30) cc_final: 0.6847 (m-30) REVERT: C 4030 LEU cc_start: 0.8915 (mt) cc_final: 0.8612 (mp) REVERT: C 4047 MET cc_start: 0.6480 (tmm) cc_final: 0.5834 (tmm) REVERT: C 4188 ARG cc_start: 0.7495 (mmm160) cc_final: 0.6927 (tpt170) REVERT: C 4580 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.6201 (t80) REVERT: C 4725 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6591 (tp) REVERT: C 4824 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.7131 (mmt180) REVERT: C 4844 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8286 (tp) REVERT: C 4933 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: C 4949 GLN cc_start: 0.8141 (tp40) cc_final: 0.7523 (mp10) REVERT: C 4953 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7867 (t0) REVERT: D 4000 MET cc_start: 0.4647 (tpt) cc_final: 0.4015 (mmm) REVERT: D 4022 ASP cc_start: 0.7233 (m-30) cc_final: 0.6864 (m-30) REVERT: D 4030 LEU cc_start: 0.8915 (mt) cc_final: 0.8611 (mp) REVERT: D 4047 MET cc_start: 0.6496 (tmm) cc_final: 0.5834 (tmm) REVERT: D 4188 ARG cc_start: 0.7498 (mmm160) cc_final: 0.6928 (tpt170) REVERT: D 4580 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.6200 (t80) REVERT: D 4725 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6587 (tp) REVERT: D 4824 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7131 (mmt180) REVERT: D 4844 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8291 (tp) REVERT: D 4933 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: D 4949 GLN cc_start: 0.8142 (tp40) cc_final: 0.7523 (mp10) REVERT: D 4953 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7869 (t0) outliers start: 81 outliers final: 52 residues processed: 365 average time/residue: 1.1953 time to fit residues: 498.1073 Evaluate side-chains 363 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 291 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4953 ASP Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4953 ASP Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4953 ASP Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4953 ASP Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 46 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 187 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21048 Z= 0.178 Angle : 0.477 6.338 28416 Z= 0.244 Chirality : 0.036 0.183 3080 Planarity : 0.005 0.103 3592 Dihedral : 7.513 140.801 2748 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % Rotamer: Outliers : 4.30 % Allowed : 15.28 % Favored : 80.42 % 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: 2.01 (0.17), residues: 2464 helix: 2.06 (0.12), residues: 1684 sheet: -1.17 (0.49), residues: 104 loop : -0.03 (0.26), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D4716 HIS 0.003 0.001 HIS D3998 PHE 0.015 0.001 PHE D4916 TYR 0.010 0.001 TYR A4994 ARG 0.005 0.000 ARG D4188 *********************** 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 409 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 313 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4482 (tpt) cc_final: 0.3803 (mmm) REVERT: A 4022 ASP cc_start: 0.7021 (m-30) cc_final: 0.6654 (m-30) REVERT: A 4047 MET cc_start: 0.6502 (tmm) cc_final: 0.5853 (tmm) REVERT: A 4188 ARG cc_start: 0.7549 (mmm160) cc_final: 0.6939 (tpt170) REVERT: A 4580 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.6220 (t80) REVERT: A 4725 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6608 (tp) REVERT: A 4824 ARG cc_start: 0.7348 (ttp-170) cc_final: 0.7018 (mmt180) REVERT: A 4933 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: A 4949 GLN cc_start: 0.8137 (tp40) cc_final: 0.7519 (mp10) REVERT: A 5006 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: B 4000 MET cc_start: 0.4489 (tpt) cc_final: 0.3804 (mmm) REVERT: B 4022 ASP cc_start: 0.7194 (m-30) cc_final: 0.6825 (m-30) REVERT: B 4047 MET cc_start: 0.6498 (tmm) cc_final: 0.5852 (tmm) REVERT: B 4188 ARG cc_start: 0.7547 (mmm160) cc_final: 0.6938 (tpt170) REVERT: B 4580 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.6208 (t80) REVERT: B 4725 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6608 (tp) REVERT: B 4824 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7018 (mmt180) REVERT: B 4933 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: B 4949 GLN cc_start: 0.8136 (tp40) cc_final: 0.7517 (mp10) REVERT: B 5006 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: C 4000 MET cc_start: 0.4482 (tpt) cc_final: 0.3798 (mmm) REVERT: C 4022 ASP cc_start: 0.7194 (m-30) cc_final: 0.6823 (m-30) REVERT: C 4047 MET cc_start: 0.6500 (tmm) cc_final: 0.5853 (tmm) REVERT: C 4188 ARG cc_start: 0.7544 (mmm160) cc_final: 0.6938 (tpt170) REVERT: C 4580 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.6219 (t80) REVERT: C 4725 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6610 (tp) REVERT: C 4824 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.7001 (mmt180) REVERT: C 4933 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: C 4949 GLN cc_start: 0.8138 (tp40) cc_final: 0.7521 (mp10) REVERT: C 5006 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7378 (pt0) REVERT: D 4000 MET cc_start: 0.4483 (tpt) cc_final: 0.3799 (mmm) REVERT: D 4022 ASP cc_start: 0.7016 (m-30) cc_final: 0.6652 (m-30) REVERT: D 4047 MET cc_start: 0.6590 (tmm) cc_final: 0.5961 (tmm) REVERT: D 4188 ARG cc_start: 0.7546 (mmm160) cc_final: 0.6939 (tpt170) REVERT: D 4580 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.6214 (t80) REVERT: D 4725 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6607 (tp) REVERT: D 4824 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.7003 (mmt180) REVERT: D 4933 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: D 4949 GLN cc_start: 0.8137 (tp40) cc_final: 0.7519 (mp10) REVERT: D 5006 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7375 (pt0) outliers start: 96 outliers final: 68 residues processed: 389 average time/residue: 1.1522 time to fit residues: 515.7305 Evaluate side-chains 390 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 306 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3983 SER Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 3983 SER Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4933 GLN Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 3983 SER Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4933 GLN Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 3983 SER Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21048 Z= 0.181 Angle : 0.467 5.468 28416 Z= 0.241 Chirality : 0.036 0.184 3080 Planarity : 0.004 0.099 3592 Dihedral : 7.507 140.750 2748 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 3.94 % Allowed : 15.77 % Favored : 80.29 % 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: 2.03 (0.17), residues: 2464 helix: 2.06 (0.12), residues: 1688 sheet: -1.21 (0.50), residues: 104 loop : -0.01 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B4716 HIS 0.003 0.001 HIS C3998 PHE 0.015 0.001 PHE B4916 TYR 0.011 0.001 TYR A4554 ARG 0.005 0.000 ARG C4188 *********************** 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 405 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 317 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4476 (tpt) cc_final: 0.3822 (mmm) REVERT: A 4022 ASP cc_start: 0.7020 (m-30) cc_final: 0.6645 (m-30) REVERT: A 4047 MET cc_start: 0.6526 (tmm) cc_final: 0.5835 (tmm) REVERT: A 4188 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7022 (tpt170) REVERT: A 4580 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.6246 (t80) REVERT: A 4725 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6614 (tp) REVERT: A 4824 ARG cc_start: 0.7496 (ttp-170) cc_final: 0.7124 (mmt180) REVERT: A 4933 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: A 4949 GLN cc_start: 0.8151 (tp40) cc_final: 0.7495 (mp10) REVERT: A 5006 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: B 4000 MET cc_start: 0.4484 (tpt) cc_final: 0.3829 (mmm) REVERT: B 4022 ASP cc_start: 0.6999 (m-30) cc_final: 0.6620 (m-30) REVERT: B 4047 MET cc_start: 0.6520 (tmm) cc_final: 0.5845 (tmm) REVERT: B 4188 ARG cc_start: 0.7552 (mmm160) cc_final: 0.7020 (tpt170) REVERT: B 4580 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.6244 (t80) REVERT: B 4725 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6615 (tp) REVERT: B 4824 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7124 (mmt180) REVERT: B 4949 GLN cc_start: 0.8151 (tp40) cc_final: 0.7495 (mp10) REVERT: B 5006 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: C 4000 MET cc_start: 0.4485 (tpt) cc_final: 0.3830 (mmm) REVERT: C 4022 ASP cc_start: 0.6999 (m-30) cc_final: 0.6615 (m-30) REVERT: C 4047 MET cc_start: 0.6522 (tmm) cc_final: 0.5843 (tmm) REVERT: C 4188 ARG cc_start: 0.7551 (mmm160) cc_final: 0.7021 (tpt170) REVERT: C 4580 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.6246 (t80) REVERT: C 4725 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6614 (tp) REVERT: C 4824 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7125 (mmt180) REVERT: C 4949 GLN cc_start: 0.8151 (tp40) cc_final: 0.7498 (mp10) REVERT: C 5006 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7363 (pt0) REVERT: D 4000 MET cc_start: 0.4476 (tpt) cc_final: 0.3823 (mmm) REVERT: D 4022 ASP cc_start: 0.7020 (m-30) cc_final: 0.6647 (m-30) REVERT: D 4047 MET cc_start: 0.6526 (tmm) cc_final: 0.5845 (tmm) REVERT: D 4188 ARG cc_start: 0.7553 (mmm160) cc_final: 0.7023 (tpt170) REVERT: D 4580 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.6242 (t80) REVERT: D 4725 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6617 (tp) REVERT: D 4824 ARG cc_start: 0.7500 (ttp-170) cc_final: 0.7125 (mmt180) REVERT: D 4933 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: D 4949 GLN cc_start: 0.8150 (tp40) cc_final: 0.7497 (mp10) REVERT: D 5006 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7358 (pt0) outliers start: 88 outliers final: 60 residues processed: 389 average time/residue: 1.1263 time to fit residues: 504.5069 Evaluate side-chains 379 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 305 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4933 GLN Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 247 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 196 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4204 GLN B4204 GLN C4204 GLN D4204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21048 Z= 0.165 Angle : 0.490 10.095 28416 Z= 0.247 Chirality : 0.036 0.186 3080 Planarity : 0.004 0.095 3592 Dihedral : 7.460 140.345 2748 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % Rotamer: Outliers : 3.14 % Allowed : 17.29 % Favored : 79.57 % 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: 2.15 (0.17), residues: 2464 helix: 2.17 (0.12), residues: 1664 sheet: -1.22 (0.50), residues: 104 loop : 0.08 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D4716 HIS 0.003 0.001 HIS A3998 PHE 0.014 0.001 PHE C4916 TYR 0.010 0.001 TYR D4177 ARG 0.004 0.000 ARG A4188 ********************** 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 379 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 309 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4000 MET cc_start: 0.4499 (tpt) cc_final: 0.3838 (mmm) REVERT: A 4022 ASP cc_start: 0.7017 (m-30) cc_final: 0.6640 (m-30) REVERT: A 4047 MET cc_start: 0.6530 (tmm) cc_final: 0.5847 (tmm) REVERT: A 4188 ARG cc_start: 0.7551 (mmm160) cc_final: 0.6997 (tpt170) REVERT: A 4580 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6172 (t80) REVERT: A 4639 MET cc_start: 0.8239 (tpt) cc_final: 0.7880 (mmt) REVERT: A 4725 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6616 (tp) REVERT: A 4824 ARG cc_start: 0.7368 (ttp-170) cc_final: 0.7130 (mmt180) REVERT: A 4949 GLN cc_start: 0.8132 (tp40) cc_final: 0.7508 (mp10) REVERT: A 5006 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: B 4000 MET cc_start: 0.4506 (tpt) cc_final: 0.3845 (mmm) REVERT: B 4022 ASP cc_start: 0.6991 (m-30) cc_final: 0.6611 (m-30) REVERT: B 4047 MET cc_start: 0.6524 (tmm) cc_final: 0.5845 (tmm) REVERT: B 4188 ARG cc_start: 0.7553 (mmm160) cc_final: 0.6997 (tpt170) REVERT: B 4580 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.6175 (t80) REVERT: B 4639 MET cc_start: 0.8240 (tpt) cc_final: 0.7887 (mmt) REVERT: B 4725 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6614 (tp) REVERT: B 4824 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.7131 (mmt180) REVERT: B 4949 GLN cc_start: 0.8134 (tp40) cc_final: 0.7509 (mp10) REVERT: B 5006 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7374 (pt0) REVERT: C 4000 MET cc_start: 0.4503 (tpt) cc_final: 0.3845 (mmm) REVERT: C 4022 ASP cc_start: 0.6989 (m-30) cc_final: 0.6604 (m-30) REVERT: C 4047 MET cc_start: 0.6524 (tmm) cc_final: 0.5840 (tmm) REVERT: C 4188 ARG cc_start: 0.7553 (mmm160) cc_final: 0.6998 (tpt170) REVERT: C 4580 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6172 (t80) REVERT: C 4639 MET cc_start: 0.8238 (tpt) cc_final: 0.7885 (mmt) REVERT: C 4725 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6615 (tp) REVERT: C 4824 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.7130 (mmt180) REVERT: C 4949 GLN cc_start: 0.8133 (tp40) cc_final: 0.7510 (mp10) REVERT: C 5006 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: D 4000 MET cc_start: 0.4499 (tpt) cc_final: 0.3836 (mmm) REVERT: D 4022 ASP cc_start: 0.7018 (m-30) cc_final: 0.6637 (m-30) REVERT: D 4047 MET cc_start: 0.6531 (tmm) cc_final: 0.5843 (tmm) REVERT: D 4188 ARG cc_start: 0.7549 (mmm160) cc_final: 0.6997 (tpt170) REVERT: D 4580 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.6169 (t80) REVERT: D 4639 MET cc_start: 0.8237 (tpt) cc_final: 0.7885 (mmt) REVERT: D 4725 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6617 (tp) REVERT: D 4824 ARG cc_start: 0.7366 (ttp-170) cc_final: 0.7130 (mmt180) REVERT: D 4949 GLN cc_start: 0.8132 (tp40) cc_final: 0.7509 (mp10) REVERT: D 5006 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7352 (pt0) outliers start: 70 outliers final: 52 residues processed: 371 average time/residue: 1.1095 time to fit residues: 475.1106 Evaluate side-chains 369 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4221 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4584 ASP Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4689 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4725 LEU Chi-restraints excluded: chain A residue 4737 ILE Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4952 GLU Chi-restraints excluded: chain A residue 4980 LEU Chi-restraints excluded: chain A residue 5004 THR Chi-restraints excluded: chain A residue 5006 GLN Chi-restraints excluded: chain A residue 5034 ASP Chi-restraints excluded: chain B residue 4221 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4584 ASP Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4689 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4725 LEU Chi-restraints excluded: chain B residue 4737 ILE Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4952 GLU Chi-restraints excluded: chain B residue 4980 LEU Chi-restraints excluded: chain B residue 5004 THR Chi-restraints excluded: chain B residue 5006 GLN Chi-restraints excluded: chain B residue 5034 ASP Chi-restraints excluded: chain C residue 4221 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4584 ASP Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4689 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4725 LEU Chi-restraints excluded: chain C residue 4737 ILE Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4952 GLU Chi-restraints excluded: chain C residue 4980 LEU Chi-restraints excluded: chain C residue 5004 THR Chi-restraints excluded: chain C residue 5006 GLN Chi-restraints excluded: chain C residue 5034 ASP Chi-restraints excluded: chain D residue 4221 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4584 ASP Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4689 THR Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4725 LEU Chi-restraints excluded: chain D residue 4737 ILE Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4952 GLU Chi-restraints excluded: chain D residue 4980 LEU Chi-restraints excluded: chain D residue 5004 THR Chi-restraints excluded: chain D residue 5006 GLN Chi-restraints excluded: chain D residue 5034 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0010 chunk 60 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 173 optimal weight: 0.4980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.178723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143159 restraints weight = 23684.044| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.95 r_work: 0.3280 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21048 Z= 0.163 Angle : 0.477 9.984 28416 Z= 0.242 Chirality : 0.035 0.186 3080 Planarity : 0.004 0.092 3592 Dihedral : 7.425 139.939 2748 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.79 % Favored : 98.05 % Rotamer: Outliers : 3.63 % Allowed : 16.76 % Favored : 79.61 % 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: 2.17 (0.17), residues: 2464 helix: 2.20 (0.12), residues: 1664 sheet: -1.22 (0.50), residues: 104 loop : 0.06 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A4716 HIS 0.003 0.001 HIS D3998 PHE 0.014 0.001 PHE D4916 TYR 0.010 0.001 TYR C4687 ARG 0.004 0.000 ARG D4188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8238.98 seconds wall clock time: 145 minutes 49.65 seconds (8749.65 seconds total)