Starting phenix.real_space_refine on Mon Mar 18 11:01:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/03_2024/8sew_40431_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/03_2024/8sew_40431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/03_2024/8sew_40431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/03_2024/8sew_40431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/03_2024/8sew_40431_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sew_40431/03_2024/8sew_40431_updated.pdb" } resolution = 2.89 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= -0.003 sd= 0.151 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 8 5.49 5 S 160 5.16 5 C 13448 2.51 5 N 3296 2.21 5 O 3800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20716 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5151 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 4 Chain: "B" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5151 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 4 Chain: "C" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5151 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 4 Chain: "D" Number of atoms: 5151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5151 Classifications: {'peptide': 629} Link IDs: {'PTRANS': 15, 'TRANS': 613} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4477 SG CYS A4958 57.159 83.295 88.728 1.00 36.39 S ATOM 4502 SG CYS A4961 59.556 83.860 91.636 1.00 36.10 S ATOM 9628 SG CYS B4958 60.961 57.159 88.728 1.00 36.39 S ATOM 9653 SG CYS B4961 60.396 59.556 91.636 1.00 36.10 S ATOM 14779 SG CYS C4958 87.097 60.961 88.728 1.00 36.39 S ATOM 14804 SG CYS C4961 84.700 60.396 91.636 1.00 36.10 S ATOM 19930 SG CYS D4958 83.295 87.097 88.728 1.00 36.39 S ATOM 19955 SG CYS D4961 83.860 84.700 91.636 1.00 36.10 S Time building chain proxies: 10.48, per 1000 atoms: 0.51 Number of scatterers: 20716 At special positions: 0 Unit cell: (145.544, 145.544, 133.952, 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 8 15.00 O 3800 8.00 N 3296 7.00 C 13448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.78 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5102 " pdb="ZN ZN A5102 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5102 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5102 " - pdb=" SG CYS A4958 " pdb=" ZN B5102 " pdb="ZN ZN B5102 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5102 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5102 " - pdb=" SG CYS B4958 " pdb=" ZN C5102 " pdb="ZN ZN C5102 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5102 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5102 " - pdb=" SG CYS C4958 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4958 " Number of angles added : 8 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 8 sheets defined 69.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 3951 through 3969 removed outlier: 3.554A pdb=" N GLN A3960 " --> pdb=" O SER A3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A3969 " --> pdb=" O LEU A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3974 through 3981 Processing helix chain 'A' and resid 3985 through 4005 removed outlier: 3.611A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4010 through 4030 Processing helix chain 'A' and resid 4039 through 4050 Processing helix chain 'A' and resid 4052 through 4059 removed outlier: 3.680A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) Processing helix chain 'A' and resid 4199 through 4206 Processing helix chain 'A' and resid 4208 through 4224 Processing helix chain 'A' and resid 4230 through 4251 Processing helix chain 'A' and resid 4541 through 4557 Processing helix chain 'A' and resid 4559 through 4579 removed outlier: 3.604A pdb=" N LEU A4578 " --> pdb=" O ASN A4574 " (cutoff:3.500A) removed outlier: 4.418A 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 4682 Processing helix chain 'A' and resid 4697 through 4704 removed outlier: 4.261A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) Processing helix chain 'A' and resid 4720 through 4732 removed outlier: 5.226A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4735 through 4740 Processing helix chain 'A' and resid 4745 through 4749 removed outlier: 4.005A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4745 through 4749' Processing helix chain 'A' and resid 4773 through 4784 Processing helix chain 'A' and resid 4787 through 4804 removed outlier: 3.983A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4819 removed outlier: 3.734A pdb=" N LEU A4814 " --> pdb=" O ALA A4811 " (cutoff:3.500A) Processing helix chain 'A' and resid 4821 through 4832 removed outlier: 3.784A pdb=" N SER A4829 " --> pdb=" O THR A4825 " (cutoff:3.500A) removed outlier: 3.982A 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 4863 removed outlier: 3.571A pdb=" N TYR A4863 " --> pdb=" O ARG A4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4860 through 4863' Processing helix chain 'A' and resid 4879 through 4889 Processing helix chain 'A' and resid 4910 through 4923 Processing helix chain 'A' and resid 4927 through 4956 removed outlier: 4.134A pdb=" N ILE A4932 " --> pdb=" O LEU A4928 " (cutoff:3.500A) Processing helix chain 'A' and resid 4965 through 4970 removed outlier: 4.086A pdb=" N THR A4970 " --> pdb=" O ASP A4966 " (cutoff:3.500A) Processing helix chain 'A' and resid 4974 through 4980 Processing helix chain 'A' and resid 4985 through 4997 Processing helix chain 'A' and resid 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 5031 No H-bonds generated for 'chain 'A' and resid 5028 through 5031' Processing helix chain 'A' and resid 5033 through 5036 No H-bonds generated for 'chain 'A' and resid 5033 through 5036' Processing helix chain 'B' and resid 3951 through 3969 removed outlier: 3.554A pdb=" N GLN B3960 " --> pdb=" O SER B3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B3969 " --> pdb=" O LEU B3965 " (cutoff:3.500A) Processing helix chain 'B' and resid 3974 through 3981 Processing helix chain 'B' and resid 3985 through 4005 removed outlier: 3.611A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4010 through 4030 Processing helix chain 'B' and resid 4039 through 4050 Processing helix chain 'B' and resid 4052 through 4059 removed outlier: 3.680A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) Processing helix chain 'B' and resid 4199 through 4206 Processing helix chain 'B' and resid 4208 through 4224 Processing helix chain 'B' and resid 4230 through 4251 Processing helix chain 'B' and resid 4541 through 4557 Processing helix chain 'B' and resid 4559 through 4579 removed outlier: 3.604A pdb=" N LEU B4578 " --> pdb=" O ASN B4574 " (cutoff:3.500A) removed outlier: 4.418A 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 4682 Processing helix chain 'B' and resid 4697 through 4704 removed outlier: 4.261A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) Processing helix chain 'B' and resid 4720 through 4732 removed outlier: 5.226A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4735 through 4740 Processing helix chain 'B' and resid 4745 through 4749 removed outlier: 4.005A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4745 through 4749' Processing helix chain 'B' and resid 4773 through 4784 Processing helix chain 'B' and resid 4787 through 4804 removed outlier: 3.983A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4819 removed outlier: 3.734A pdb=" N LEU B4814 " --> pdb=" O ALA B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4821 through 4832 removed outlier: 3.784A pdb=" N SER B4829 " --> pdb=" O THR B4825 " (cutoff:3.500A) removed outlier: 3.982A 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 4863 removed outlier: 3.571A pdb=" N TYR B4863 " --> pdb=" O ARG B4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4860 through 4863' Processing helix chain 'B' and resid 4879 through 4889 Processing helix chain 'B' and resid 4910 through 4923 Processing helix chain 'B' and resid 4927 through 4956 removed outlier: 4.134A pdb=" N ILE B4932 " --> pdb=" O LEU B4928 " (cutoff:3.500A) Processing helix chain 'B' and resid 4965 through 4970 removed outlier: 4.086A pdb=" N THR B4970 " --> pdb=" O ASP B4966 " (cutoff:3.500A) Processing helix chain 'B' and resid 4974 through 4980 Processing helix chain 'B' and resid 4985 through 4997 Processing helix chain 'B' and resid 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 5031 No H-bonds generated for 'chain 'B' and resid 5028 through 5031' Processing helix chain 'B' and resid 5033 through 5036 No H-bonds generated for 'chain 'B' and resid 5033 through 5036' Processing helix chain 'C' and resid 3951 through 3969 removed outlier: 3.554A pdb=" N GLN C3960 " --> pdb=" O SER C3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C3969 " --> pdb=" O LEU C3965 " (cutoff:3.500A) Processing helix chain 'C' and resid 3974 through 3981 Processing helix chain 'C' and resid 3985 through 4005 removed outlier: 3.611A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4010 through 4030 Processing helix chain 'C' and resid 4039 through 4050 Processing helix chain 'C' and resid 4052 through 4059 removed outlier: 3.680A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) Processing helix chain 'C' and resid 4199 through 4206 Processing helix chain 'C' and resid 4208 through 4224 Processing helix chain 'C' and resid 4230 through 4251 Processing helix chain 'C' and resid 4541 through 4557 Processing helix chain 'C' and resid 4559 through 4579 removed outlier: 3.604A pdb=" N LEU C4578 " --> pdb=" O ASN C4574 " (cutoff:3.500A) removed outlier: 4.418A 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 4682 Processing helix chain 'C' and resid 4697 through 4704 removed outlier: 4.261A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) Processing helix chain 'C' and resid 4720 through 4732 removed outlier: 5.226A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4735 through 4740 Processing helix chain 'C' and resid 4745 through 4749 removed outlier: 4.005A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4745 through 4749' Processing helix chain 'C' and resid 4773 through 4784 Processing helix chain 'C' and resid 4787 through 4804 removed outlier: 3.983A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4819 removed outlier: 3.734A pdb=" N LEU C4814 " --> pdb=" O ALA C4811 " (cutoff:3.500A) Processing helix chain 'C' and resid 4821 through 4832 removed outlier: 3.784A pdb=" N SER C4829 " --> pdb=" O THR C4825 " (cutoff:3.500A) removed outlier: 3.982A 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 4863 removed outlier: 3.571A pdb=" N TYR C4863 " --> pdb=" O ARG C4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4860 through 4863' Processing helix chain 'C' and resid 4879 through 4889 Processing helix chain 'C' and resid 4910 through 4923 Processing helix chain 'C' and resid 4927 through 4956 removed outlier: 4.134A pdb=" N ILE C4932 " --> pdb=" O LEU C4928 " (cutoff:3.500A) Processing helix chain 'C' and resid 4965 through 4970 removed outlier: 4.086A pdb=" N THR C4970 " --> pdb=" O ASP C4966 " (cutoff:3.500A) Processing helix chain 'C' and resid 4974 through 4980 Processing helix chain 'C' and resid 4985 through 4997 Processing helix chain 'C' and resid 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 5031 No H-bonds generated for 'chain 'C' and resid 5028 through 5031' Processing helix chain 'C' and resid 5033 through 5036 No H-bonds generated for 'chain 'C' and resid 5033 through 5036' Processing helix chain 'D' and resid 3951 through 3969 removed outlier: 3.554A pdb=" N GLN D3960 " --> pdb=" O SER D3956 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE D3969 " --> pdb=" O LEU D3965 " (cutoff:3.500A) Processing helix chain 'D' and resid 3974 through 3981 Processing helix chain 'D' and resid 3985 through 4005 removed outlier: 3.611A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4010 through 4030 Processing helix chain 'D' and resid 4039 through 4050 Processing helix chain 'D' and resid 4052 through 4059 removed outlier: 3.680A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) Processing helix chain 'D' and resid 4199 through 4206 Processing helix chain 'D' and resid 4208 through 4224 Processing helix chain 'D' and resid 4230 through 4251 Processing helix chain 'D' and resid 4541 through 4557 Processing helix chain 'D' and resid 4559 through 4579 removed outlier: 3.604A pdb=" N LEU D4578 " --> pdb=" O ASN D4574 " (cutoff:3.500A) removed outlier: 4.418A 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 4682 Processing helix chain 'D' and resid 4697 through 4704 removed outlier: 4.261A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) Processing helix chain 'D' and resid 4720 through 4732 removed outlier: 5.226A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4735 through 4740 Processing helix chain 'D' and resid 4745 through 4749 removed outlier: 4.005A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4745 through 4749' Processing helix chain 'D' and resid 4773 through 4784 Processing helix chain 'D' and resid 4787 through 4804 removed outlier: 3.983A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4819 removed outlier: 3.734A pdb=" N LEU D4814 " --> pdb=" O ALA D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4821 through 4832 removed outlier: 3.784A pdb=" N SER D4829 " --> pdb=" O THR D4825 " (cutoff:3.500A) removed outlier: 3.982A 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 4863 removed outlier: 3.571A pdb=" N TYR D4863 " --> pdb=" O ARG D4860 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4860 through 4863' Processing helix chain 'D' and resid 4879 through 4889 Processing helix chain 'D' and resid 4910 through 4923 Processing helix chain 'D' and resid 4927 through 4956 removed outlier: 4.134A pdb=" N ILE D4932 " --> pdb=" O LEU D4928 " (cutoff:3.500A) Processing helix chain 'D' and resid 4965 through 4970 removed outlier: 4.086A pdb=" N THR D4970 " --> pdb=" O ASP D4966 " (cutoff:3.500A) Processing helix chain 'D' and resid 4974 through 4980 Processing helix chain 'D' and resid 4985 through 4997 Processing helix chain 'D' and resid 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 5031 No H-bonds generated for 'chain 'D' and resid 5028 through 5031' Processing helix chain 'D' and resid 5033 through 5036 No H-bonds generated for 'chain 'D' and resid 5033 through 5036' 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 1200 hydrogen bonds defined for protein. 3468 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: 6.19 Time building geometry restraints manager: 8.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6512 1.34 - 1.46: 4856 1.46 - 1.58: 9552 1.58 - 1.69: 12 1.69 - 1.81: 276 Bond restraints: 21208 Sorted by residual: bond pdb=" C4 ADP B5101 " pdb=" C5 ADP B5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP C5101 " pdb=" C5 ADP C5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP A5101 " pdb=" C5 ADP A5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP D5101 " pdb=" C5 ADP D5101 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C5 ADP A5101 " pdb=" C6 ADP A5101 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.87e+01 ... (remaining 21203 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.83: 488 106.83 - 113.68: 11404 113.68 - 120.53: 9216 120.53 - 127.38: 7348 127.38 - 134.24: 188 Bond angle restraints: 28644 Sorted by residual: angle pdb=" C LYS A4665 " pdb=" N VAL A4666 " pdb=" CA VAL A4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS B4665 " pdb=" N VAL B4666 " pdb=" CA VAL B4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS D4665 " pdb=" N VAL D4666 " pdb=" CA VAL D4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" C LYS C4665 " pdb=" N VAL C4666 " pdb=" CA VAL C4666 " ideal model delta sigma weight residual 120.24 123.16 -2.92 6.30e-01 2.52e+00 2.14e+01 angle pdb=" PA ADP C5101 " pdb=" O3A ADP C5101 " pdb=" PB ADP C5101 " ideal model delta sigma weight residual 120.50 134.24 -13.74 3.00e+00 1.11e-01 2.10e+01 ... (remaining 28639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 12212 30.20 - 60.41: 228 60.41 - 90.61: 12 90.61 - 120.81: 4 120.81 - 151.01: 4 Dihedral angle restraints: 12460 sinusoidal: 5112 harmonic: 7348 Sorted by residual: dihedral pdb=" C2' ADP A5101 " pdb=" C1' ADP A5101 " pdb=" N9 ADP A5101 " pdb=" C4 ADP A5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C2' ADP D5101 " pdb=" C1' ADP D5101 " pdb=" N9 ADP D5101 " pdb=" C4 ADP D5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" C2' ADP C5101 " pdb=" C1' ADP C5101 " pdb=" N9 ADP C5101 " pdb=" C4 ADP C5101 " ideal model delta sinusoidal sigma weight residual 91.55 -59.47 151.01 1 2.00e+01 2.50e-03 4.50e+01 ... (remaining 12457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1724 0.029 - 0.058: 1004 0.058 - 0.087: 288 0.087 - 0.116: 68 0.116 - 0.144: 12 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C3' ADP C5101 " pdb=" C2' ADP C5101 " pdb=" C4' ADP C5101 " pdb=" O3' ADP C5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C3' ADP D5101 " pdb=" C2' ADP D5101 " pdb=" C4' ADP D5101 " pdb=" O3' ADP D5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" C3' ADP A5101 " pdb=" C2' ADP A5101 " pdb=" C4' ADP A5101 " pdb=" O3' ADP A5101 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3093 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B4913 " 0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG B4913 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B4913 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B4913 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B4913 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A4913 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG A4913 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A4913 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A4913 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A4913 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D4913 " -0.124 9.50e-02 1.11e+02 5.56e-02 1.93e+00 pdb=" NE ARG D4913 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D4913 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D4913 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D4913 " -0.006 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 0.27 - 1.19: 16 1.19 - 2.12: 36 2.12 - 3.05: 13796 3.05 - 3.97: 55176 3.97 - 4.90: 102782 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171806 Sorted by model distance: nonbonded pdb=" NH2 ARG B4944 " pdb=" OD1 ASP C4938 " model vdw 0.267 2.520 nonbonded pdb=" NH2 ARG C4944 " pdb=" OD1 ASP D4938 " model vdw 0.267 2.520 nonbonded pdb=" OD1 ASP A4938 " pdb=" NH2 ARG D4944 " model vdw 0.267 2.520 nonbonded pdb=" NH2 ARG A4944 " pdb=" OD1 ASP B4938 " model vdw 0.267 2.520 nonbonded pdb=" NZ LYS B4581 " pdb=" CB ASP C4878 " model vdw 0.440 3.520 ... (remaining 171801 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: 3.980 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: 14.200 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 56.710 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.130 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 21208 Z= 0.274 Angle : 0.591 13.737 28644 Z= 0.295 Chirality : 0.038 0.144 3096 Planarity : 0.004 0.056 3612 Dihedral : 12.563 151.014 7712 Min Nonbonded Distance : 0.267 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.14 % Allowed : 4.28 % Favored : 93.58 % 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: 1.93 (0.17), residues: 2476 helix: 1.99 (0.12), residues: 1644 sheet: 0.31 (0.51), residues: 112 loop : -0.16 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C5019 HIS 0.005 0.001 HIS D4886 PHE 0.020 0.002 PHE C4916 TYR 0.012 0.001 TYR C4994 ARG 0.003 0.001 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 464 time to evaluate : 2.524 Fit side-chains REVERT: A 3992 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7633 (m-80) REVERT: A 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: A 4580 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6354 (t80) REVERT: A 4644 TRP cc_start: 0.7187 (t60) cc_final: 0.6975 (t-100) REVERT: A 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6792 (m-30) REVERT: A 4844 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8096 (tp) REVERT: B 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: B 4196 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5993 (tp30) REVERT: B 4580 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6353 (t80) REVERT: B 4644 TRP cc_start: 0.7185 (t60) cc_final: 0.6971 (t-100) REVERT: B 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6788 (m-30) REVERT: B 4844 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (tp) REVERT: C 3992 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: C 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5992 (tp30) REVERT: C 4580 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6347 (t80) REVERT: C 4644 TRP cc_start: 0.7186 (t60) cc_final: 0.6975 (t-100) REVERT: C 4726 ASP cc_start: 0.7010 (m-30) cc_final: 0.6790 (m-30) REVERT: C 4844 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8091 (tp) REVERT: D 3992 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: D 4196 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5991 (tp30) REVERT: D 4580 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6348 (t80) REVERT: D 4644 TRP cc_start: 0.7186 (t60) cc_final: 0.6975 (t-100) REVERT: D 4726 ASP cc_start: 0.7011 (m-30) cc_final: 0.6792 (m-30) REVERT: D 4844 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8094 (tp) outliers start: 48 outliers final: 16 residues processed: 508 average time/residue: 1.2519 time to fit residues: 721.3090 Evaluate side-chains 396 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 364 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3992 PHE Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain B residue 3992 PHE Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain C residue 3992 PHE Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain D residue 3992 PHE Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4844 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4626 ASN A4973 HIS ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4626 ASN B4973 HIS ** B5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4626 ASN C4973 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4626 ASN D4973 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21208 Z= 0.188 Angle : 0.525 7.383 28644 Z= 0.265 Chirality : 0.037 0.132 3096 Planarity : 0.004 0.048 3612 Dihedral : 10.148 146.549 2812 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 3.92 % Allowed : 12.66 % Favored : 83.42 % 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: 2.17 (0.17), residues: 2476 helix: 2.18 (0.12), residues: 1664 sheet: 0.18 (0.48), residues: 112 loop : -0.14 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D4701 HIS 0.004 0.001 HIS D3994 PHE 0.019 0.001 PHE C4916 TYR 0.012 0.001 TYR D5032 ARG 0.008 0.001 ARG C4189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 380 time to evaluate : 2.227 Fit side-chains REVERT: A 3969 ILE cc_start: 0.8744 (pt) cc_final: 0.8529 (pt) REVERT: A 4001 MET cc_start: 0.6740 (mmm) cc_final: 0.6512 (mmm) REVERT: A 4023 MET cc_start: 0.7577 (ttp) cc_final: 0.7009 (tpp) REVERT: A 4042 ARG cc_start: 0.6832 (mtm110) cc_final: 0.6335 (mtm180) REVERT: A 4196 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5956 (tp30) REVERT: A 4209 GLN cc_start: 0.7860 (pt0) cc_final: 0.7551 (pm20) REVERT: A 4212 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 4224 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: A 4580 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6284 (t80) REVERT: A 4736 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6663 (ttp-110) REVERT: A 4992 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 3969 ILE cc_start: 0.8744 (pt) cc_final: 0.8529 (pt) REVERT: B 4001 MET cc_start: 0.6732 (mmm) cc_final: 0.6501 (mmm) REVERT: B 4023 MET cc_start: 0.7574 (ttp) cc_final: 0.7007 (tpp) REVERT: B 4042 ARG cc_start: 0.6833 (mtm110) cc_final: 0.6338 (mtm180) REVERT: B 4184 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7446 (ttp) REVERT: B 4196 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5956 (tp30) REVERT: B 4209 GLN cc_start: 0.7859 (pt0) cc_final: 0.7552 (pm20) REVERT: B 4212 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: B 4224 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: B 4580 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6283 (t80) REVERT: B 4736 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6665 (ttp-110) REVERT: B 4992 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8338 (mt) REVERT: C 3969 ILE cc_start: 0.8744 (pt) cc_final: 0.8529 (pt) REVERT: C 4001 MET cc_start: 0.6731 (mmm) cc_final: 0.6501 (mmm) REVERT: C 4023 MET cc_start: 0.7575 (ttp) cc_final: 0.7006 (tpp) REVERT: C 4042 ARG cc_start: 0.6835 (mtm110) cc_final: 0.6339 (mtm180) REVERT: C 4184 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7448 (ttp) REVERT: C 4196 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5956 (tp30) REVERT: C 4209 GLN cc_start: 0.7865 (pt0) cc_final: 0.7551 (pm20) REVERT: C 4212 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: C 4224 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: C 4580 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6278 (t80) REVERT: C 4736 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6664 (ttp-110) REVERT: C 4992 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8338 (mt) REVERT: D 3969 ILE cc_start: 0.8746 (pt) cc_final: 0.8528 (pt) REVERT: D 4001 MET cc_start: 0.6738 (mmm) cc_final: 0.6507 (mmm) REVERT: D 4023 MET cc_start: 0.7577 (ttp) cc_final: 0.7007 (tpp) REVERT: D 4042 ARG cc_start: 0.6834 (mtm110) cc_final: 0.6338 (mtm180) REVERT: D 4196 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5957 (tp30) REVERT: D 4209 GLN cc_start: 0.7862 (pt0) cc_final: 0.7549 (pm20) REVERT: D 4212 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: D 4224 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: D 4580 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6277 (t80) REVERT: D 4736 ARG cc_start: 0.6954 (ttp-110) cc_final: 0.6662 (ttp-110) REVERT: D 4992 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8340 (mt) outliers start: 88 outliers final: 36 residues processed: 432 average time/residue: 1.2490 time to fit residues: 611.3754 Evaluate side-chains 414 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 356 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4626 ASN Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4626 ASN Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4626 ASN Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4626 ASN Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4626 ASN A4973 HIS ** A5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4626 ASN B4973 HIS C4626 ASN C4973 HIS ** C5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4626 ASN D4973 HIS ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21208 Z= 0.158 Angle : 0.494 6.319 28644 Z= 0.248 Chirality : 0.036 0.118 3096 Planarity : 0.004 0.047 3612 Dihedral : 9.647 148.927 2796 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 3.74 % Allowed : 14.44 % Favored : 81.82 % 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: 2.25 (0.17), residues: 2476 helix: 2.25 (0.12), residues: 1664 sheet: -0.06 (0.48), residues: 112 loop : -0.07 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A4701 HIS 0.005 0.001 HIS C3982 PHE 0.018 0.001 PHE C4916 TYR 0.011 0.001 TYR D4629 ARG 0.009 0.001 ARG C4189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 364 time to evaluate : 2.418 Fit side-chains REVERT: A 3969 ILE cc_start: 0.8694 (pt) cc_final: 0.8474 (pt) REVERT: A 3980 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8298 (mt) REVERT: A 3999 MET cc_start: 0.7902 (mmm) cc_final: 0.7559 (tpt) REVERT: A 4023 MET cc_start: 0.7444 (ttp) cc_final: 0.6978 (tpp) REVERT: A 4042 ARG cc_start: 0.6742 (mtm110) cc_final: 0.6213 (mtm180) REVERT: A 4196 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.5825 (tp30) REVERT: A 4209 GLN cc_start: 0.7830 (pt0) cc_final: 0.7563 (pm20) REVERT: A 4580 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6248 (t80) REVERT: A 4992 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8336 (mt) REVERT: B 3969 ILE cc_start: 0.8695 (pt) cc_final: 0.8475 (pt) REVERT: B 3980 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 3999 MET cc_start: 0.7899 (mmm) cc_final: 0.7558 (tpt) REVERT: B 4023 MET cc_start: 0.7441 (ttp) cc_final: 0.6977 (tpp) REVERT: B 4042 ARG cc_start: 0.6739 (mtm110) cc_final: 0.6214 (mtm180) REVERT: B 4196 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5826 (tp30) REVERT: B 4209 GLN cc_start: 0.7828 (pt0) cc_final: 0.7561 (pm20) REVERT: B 4580 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6246 (t80) REVERT: B 4992 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8336 (mt) REVERT: C 3969 ILE cc_start: 0.8695 (pt) cc_final: 0.8474 (pt) REVERT: C 3980 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8293 (mt) REVERT: C 3999 MET cc_start: 0.7902 (mmm) cc_final: 0.7566 (tpt) REVERT: C 4023 MET cc_start: 0.7445 (ttp) cc_final: 0.6980 (tpp) REVERT: C 4042 ARG cc_start: 0.6739 (mtm110) cc_final: 0.6215 (mtm180) REVERT: C 4196 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5825 (tp30) REVERT: C 4209 GLN cc_start: 0.7834 (pt0) cc_final: 0.7561 (pm20) REVERT: C 4580 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.6243 (t80) REVERT: C 4992 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8334 (mt) REVERT: D 3969 ILE cc_start: 0.8695 (pt) cc_final: 0.8473 (pt) REVERT: D 3980 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8295 (mt) REVERT: D 3999 MET cc_start: 0.7900 (mmm) cc_final: 0.7561 (tpt) REVERT: D 4023 MET cc_start: 0.7445 (ttp) cc_final: 0.6979 (tpp) REVERT: D 4042 ARG cc_start: 0.6742 (mtm110) cc_final: 0.6217 (mtm180) REVERT: D 4196 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5825 (tp30) REVERT: D 4209 GLN cc_start: 0.7832 (pt0) cc_final: 0.7560 (pm20) REVERT: D 4580 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6241 (t80) REVERT: D 4992 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8336 (mt) outliers start: 84 outliers final: 24 residues processed: 412 average time/residue: 1.2707 time to fit residues: 592.5946 Evaluate side-chains 400 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 360 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3980 LEU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 239 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS A5031 GLN B4973 HIS B5031 GLN ** C4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4973 HIS C5031 GLN ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4973 HIS D5031 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21208 Z= 0.264 Angle : 0.554 7.855 28644 Z= 0.280 Chirality : 0.039 0.116 3096 Planarity : 0.004 0.061 3612 Dihedral : 9.467 151.817 2780 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 4.81 % Allowed : 14.26 % Favored : 80.93 % 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: 1.88 (0.17), residues: 2476 helix: 1.97 (0.12), residues: 1652 sheet: -0.42 (0.47), residues: 112 loop : -0.11 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C5019 HIS 0.004 0.001 HIS D3994 PHE 0.021 0.002 PHE D4916 TYR 0.013 0.002 TYR C5032 ARG 0.010 0.001 ARG C4189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 380 time to evaluate : 2.355 Fit side-chains REVERT: A 3969 ILE cc_start: 0.8731 (pt) cc_final: 0.8521 (pt) REVERT: A 3986 TRP cc_start: 0.8580 (m100) cc_final: 0.8067 (m100) REVERT: A 3999 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: A 4023 MET cc_start: 0.7579 (ttp) cc_final: 0.7156 (tpp) REVERT: A 4042 ARG cc_start: 0.6690 (mtm110) cc_final: 0.6151 (mtm180) REVERT: A 4196 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6125 (tp30) REVERT: A 4209 GLN cc_start: 0.7925 (pt0) cc_final: 0.7598 (pm20) REVERT: A 4580 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6298 (t80) REVERT: A 4957 LYS cc_start: 0.8883 (ptmt) cc_final: 0.8629 (ptmm) REVERT: B 3969 ILE cc_start: 0.8730 (pt) cc_final: 0.8523 (pt) REVERT: B 3986 TRP cc_start: 0.8579 (m100) cc_final: 0.8064 (m100) REVERT: B 3999 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7485 (tpt) REVERT: B 4023 MET cc_start: 0.7577 (ttp) cc_final: 0.7156 (tpp) REVERT: B 4042 ARG cc_start: 0.6688 (mtm110) cc_final: 0.6153 (mtm180) REVERT: B 4196 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6126 (tp30) REVERT: B 4209 GLN cc_start: 0.7920 (pt0) cc_final: 0.7597 (pm20) REVERT: B 4580 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6296 (t80) REVERT: B 4957 LYS cc_start: 0.8885 (ptmt) cc_final: 0.8629 (ptmm) REVERT: C 3969 ILE cc_start: 0.8731 (pt) cc_final: 0.8521 (pt) REVERT: C 3986 TRP cc_start: 0.8581 (m100) cc_final: 0.8067 (m100) REVERT: C 3999 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: C 4023 MET cc_start: 0.7578 (ttp) cc_final: 0.7155 (tpp) REVERT: C 4042 ARG cc_start: 0.6691 (mtm110) cc_final: 0.6154 (mtm180) REVERT: C 4196 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6125 (tp30) REVERT: C 4209 GLN cc_start: 0.7929 (pt0) cc_final: 0.7597 (pm20) REVERT: C 4580 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.6292 (t80) REVERT: C 4957 LYS cc_start: 0.8888 (ptmt) cc_final: 0.8630 (ptmm) REVERT: D 3969 ILE cc_start: 0.8734 (pt) cc_final: 0.8520 (pt) REVERT: D 3986 TRP cc_start: 0.8579 (m100) cc_final: 0.8066 (m100) REVERT: D 3999 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7491 (tpt) REVERT: D 4023 MET cc_start: 0.7579 (ttp) cc_final: 0.7156 (tpp) REVERT: D 4042 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6152 (mtm180) REVERT: D 4196 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6124 (tp30) REVERT: D 4209 GLN cc_start: 0.7927 (pt0) cc_final: 0.7597 (pm20) REVERT: D 4580 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6291 (t80) REVERT: D 4957 LYS cc_start: 0.8886 (ptmt) cc_final: 0.8628 (ptmm) outliers start: 108 outliers final: 46 residues processed: 436 average time/residue: 1.1751 time to fit residues: 584.7046 Evaluate side-chains 422 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 364 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4773 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4773 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4773 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4773 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4043 GLN A4973 HIS B4043 GLN ** B4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4973 HIS C4973 HIS D4043 GLN ** D4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4973 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21208 Z= 0.353 Angle : 0.601 6.800 28644 Z= 0.307 Chirality : 0.041 0.122 3096 Planarity : 0.005 0.094 3612 Dihedral : 9.584 153.160 2780 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 4.63 % Allowed : 15.02 % Favored : 80.35 % 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: 1.32 (0.16), residues: 2476 helix: 1.48 (0.12), residues: 1676 sheet: -0.50 (0.46), residues: 112 loop : -0.25 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C4541 HIS 0.005 0.001 HIS A4886 PHE 0.028 0.002 PHE D4916 TYR 0.012 0.002 TYR B4994 ARG 0.008 0.001 ARG D4736 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 360 time to evaluate : 2.316 Fit side-chains REVERT: A 3969 ILE cc_start: 0.8747 (pt) cc_final: 0.8545 (pt) REVERT: A 3980 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7860 (mm) REVERT: A 3986 TRP cc_start: 0.8544 (m100) cc_final: 0.8124 (m100) REVERT: A 3999 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: A 4023 MET cc_start: 0.7809 (ttp) cc_final: 0.7345 (ttp) REVERT: A 4042 ARG cc_start: 0.6713 (mtm110) cc_final: 0.6106 (mtm180) REVERT: A 4048 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6661 (mp) REVERT: A 4196 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.5976 (tp30) REVERT: A 4209 GLN cc_start: 0.7955 (pt0) cc_final: 0.7602 (pm20) REVERT: A 4212 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: A 4224 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7368 (pt0) REVERT: A 4554 TYR cc_start: 0.8651 (t80) cc_final: 0.8370 (t80) REVERT: A 4580 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6455 (t80) REVERT: B 3969 ILE cc_start: 0.8746 (pt) cc_final: 0.8546 (pt) REVERT: B 3980 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7858 (mm) REVERT: B 3986 TRP cc_start: 0.8543 (m100) cc_final: 0.8122 (m100) REVERT: B 3999 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7502 (tpt) REVERT: B 4023 MET cc_start: 0.7802 (ttp) cc_final: 0.7343 (ttp) REVERT: B 4042 ARG cc_start: 0.6715 (mtm110) cc_final: 0.6108 (mtm180) REVERT: B 4048 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6661 (mp) REVERT: B 4196 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5966 (tp30) REVERT: B 4209 GLN cc_start: 0.7948 (pt0) cc_final: 0.7602 (pm20) REVERT: B 4212 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: B 4224 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: B 4554 TYR cc_start: 0.8650 (t80) cc_final: 0.8369 (t80) REVERT: B 4580 TYR cc_start: 0.7540 (OUTLIER) cc_final: 0.6457 (t80) REVERT: C 3969 ILE cc_start: 0.8749 (pt) cc_final: 0.8547 (pt) REVERT: C 3980 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7859 (mm) REVERT: C 3986 TRP cc_start: 0.8546 (m100) cc_final: 0.8128 (m100) REVERT: C 3999 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7506 (tpt) REVERT: C 4023 MET cc_start: 0.7810 (ttp) cc_final: 0.7349 (ttp) REVERT: C 4042 ARG cc_start: 0.6716 (mtm110) cc_final: 0.6102 (mtm180) REVERT: C 4048 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6663 (mp) REVERT: C 4196 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.5972 (tp30) REVERT: C 4209 GLN cc_start: 0.7959 (pt0) cc_final: 0.7601 (pm20) REVERT: C 4212 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: C 4224 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: C 4554 TYR cc_start: 0.8651 (t80) cc_final: 0.8372 (t80) REVERT: C 4580 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6452 (t80) REVERT: D 3969 ILE cc_start: 0.8749 (pt) cc_final: 0.8545 (pt) REVERT: D 3980 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.7859 (mm) REVERT: D 3986 TRP cc_start: 0.8546 (m100) cc_final: 0.8125 (m100) REVERT: D 3999 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7509 (tpt) REVERT: D 4023 MET cc_start: 0.7809 (ttp) cc_final: 0.7344 (ttp) REVERT: D 4042 ARG cc_start: 0.6716 (mtm110) cc_final: 0.6112 (mtm180) REVERT: D 4048 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6660 (mp) REVERT: D 4196 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5970 (tp30) REVERT: D 4209 GLN cc_start: 0.7958 (pt0) cc_final: 0.7603 (pm20) REVERT: D 4212 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: D 4224 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: D 4554 TYR cc_start: 0.8651 (t80) cc_final: 0.8368 (t80) REVERT: D 4580 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6452 (t80) outliers start: 104 outliers final: 51 residues processed: 420 average time/residue: 1.2008 time to fit residues: 574.6924 Evaluate side-chains 431 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 352 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4048 LEU Chi-restraints excluded: chain A residue 4183 ILE Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4212 GLU Chi-restraints excluded: chain A residue 4224 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4773 VAL Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4976 GLU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4048 LEU Chi-restraints excluded: chain B residue 4183 ILE Chi-restraints excluded: chain B residue 4184 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4212 GLU Chi-restraints excluded: chain B residue 4224 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4773 VAL Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4976 GLU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3980 LEU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4183 ILE Chi-restraints excluded: chain C residue 4184 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4212 GLU Chi-restraints excluded: chain C residue 4224 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4773 VAL Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4976 GLU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4048 LEU Chi-restraints excluded: chain D residue 4183 ILE Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4212 GLU Chi-restraints excluded: chain D residue 4224 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4773 VAL Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4976 GLU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21208 Z= 0.171 Angle : 0.528 8.324 28644 Z= 0.261 Chirality : 0.036 0.117 3096 Planarity : 0.004 0.073 3612 Dihedral : 9.321 153.308 2776 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.52 % Allowed : 17.34 % Favored : 79.14 % 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: 1.84 (0.17), residues: 2476 helix: 1.99 (0.12), residues: 1644 sheet: -0.62 (0.46), residues: 112 loop : -0.23 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C4701 HIS 0.004 0.001 HIS C3994 PHE 0.019 0.001 PHE C4916 TYR 0.010 0.001 TYR D5032 ARG 0.011 0.001 ARG C4736 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 368 time to evaluate : 2.355 Fit side-chains REVERT: A 3986 TRP cc_start: 0.8475 (m100) cc_final: 0.7971 (m100) REVERT: A 3999 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7523 (tpt) REVERT: A 4023 MET cc_start: 0.7478 (ttp) cc_final: 0.7100 (ttt) REVERT: A 4042 ARG cc_start: 0.6686 (mtm110) cc_final: 0.6205 (mtm180) REVERT: A 4184 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7134 (ttp) REVERT: A 4196 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5947 (tp30) REVERT: A 4209 GLN cc_start: 0.7862 (pt0) cc_final: 0.7567 (pm20) REVERT: A 4580 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6434 (t80) REVERT: A 4992 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 3986 TRP cc_start: 0.8472 (m100) cc_final: 0.7965 (m100) REVERT: B 3999 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7511 (tpt) REVERT: B 4023 MET cc_start: 0.7474 (ttp) cc_final: 0.7097 (ttt) REVERT: B 4042 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6210 (mtm180) REVERT: B 4196 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5952 (tp30) REVERT: B 4209 GLN cc_start: 0.7850 (pt0) cc_final: 0.7604 (pm20) REVERT: B 4580 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6433 (t80) REVERT: B 4992 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8362 (mt) REVERT: C 3986 TRP cc_start: 0.8549 (m100) cc_final: 0.8033 (m100) REVERT: C 3999 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7522 (tpt) REVERT: C 4023 MET cc_start: 0.7477 (ttp) cc_final: 0.7101 (ttt) REVERT: C 4042 ARG cc_start: 0.6682 (mtm110) cc_final: 0.6201 (mtm180) REVERT: C 4196 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5952 (tp30) REVERT: C 4209 GLN cc_start: 0.7861 (pt0) cc_final: 0.7596 (pm20) REVERT: C 4580 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6431 (t80) REVERT: C 4992 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (mt) REVERT: D 3986 TRP cc_start: 0.8475 (m100) cc_final: 0.7972 (m100) REVERT: D 3999 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7515 (tpt) REVERT: D 4023 MET cc_start: 0.7479 (ttp) cc_final: 0.7101 (ttt) REVERT: D 4042 ARG cc_start: 0.6688 (mtm110) cc_final: 0.6209 (mtm180) REVERT: D 4184 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7136 (ttp) REVERT: D 4196 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5948 (tp30) REVERT: D 4209 GLN cc_start: 0.7861 (pt0) cc_final: 0.7566 (pm20) REVERT: D 4580 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6432 (t80) REVERT: D 4992 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8363 (mt) outliers start: 79 outliers final: 35 residues processed: 419 average time/residue: 1.1883 time to fit residues: 569.4411 Evaluate side-chains 405 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 352 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 239 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21208 Z= 0.169 Angle : 0.522 7.593 28644 Z= 0.259 Chirality : 0.036 0.118 3096 Planarity : 0.004 0.074 3612 Dihedral : 9.296 154.041 2776 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.66 % Favored : 98.18 % Rotamer: Outliers : 3.16 % Allowed : 18.05 % Favored : 78.79 % 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: 1.96 (0.17), residues: 2476 helix: 2.07 (0.12), residues: 1656 sheet: -0.57 (0.46), residues: 112 loop : -0.16 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B5011 HIS 0.003 0.001 HIS C3994 PHE 0.019 0.001 PHE D4922 TYR 0.009 0.001 TYR B5032 ARG 0.012 0.001 ARG B4736 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 380 time to evaluate : 2.262 Fit side-chains REVERT: A 3986 TRP cc_start: 0.8418 (m100) cc_final: 0.7800 (m100) REVERT: A 3999 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: A 4023 MET cc_start: 0.7453 (ttp) cc_final: 0.7096 (ttt) REVERT: A 4042 ARG cc_start: 0.6626 (mtm110) cc_final: 0.6126 (mtm180) REVERT: A 4045 VAL cc_start: 0.7554 (OUTLIER) cc_final: 0.7265 (m) REVERT: A 4184 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7055 (ttp) REVERT: A 4196 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5924 (tp30) REVERT: A 4209 GLN cc_start: 0.7815 (pt0) cc_final: 0.7533 (pm20) REVERT: A 4580 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 4992 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 3986 TRP cc_start: 0.8416 (m100) cc_final: 0.7796 (m100) REVERT: B 3999 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7501 (tpt) REVERT: B 4023 MET cc_start: 0.7448 (ttp) cc_final: 0.7094 (ttt) REVERT: B 4042 ARG cc_start: 0.6629 (mtm110) cc_final: 0.6130 (mtm180) REVERT: B 4045 VAL cc_start: 0.7556 (OUTLIER) cc_final: 0.7265 (m) REVERT: B 4196 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5925 (tp30) REVERT: B 4209 GLN cc_start: 0.7811 (pt0) cc_final: 0.7535 (pm20) REVERT: B 4580 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6423 (t80) REVERT: B 4992 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8350 (mt) REVERT: C 3986 TRP cc_start: 0.8484 (m100) cc_final: 0.7912 (m100) REVERT: C 3999 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7509 (tpt) REVERT: C 4023 MET cc_start: 0.7449 (ttp) cc_final: 0.7092 (ttt) REVERT: C 4042 ARG cc_start: 0.6509 (mtm110) cc_final: 0.5987 (mtm180) REVERT: C 4045 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7308 (m) REVERT: C 4196 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.5929 (tp30) REVERT: C 4209 GLN cc_start: 0.7819 (pt0) cc_final: 0.7534 (pm20) REVERT: C 4580 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6422 (t80) REVERT: C 4992 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8351 (mt) REVERT: D 3986 TRP cc_start: 0.8417 (m100) cc_final: 0.7802 (m100) REVERT: D 3999 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7503 (tpt) REVERT: D 4023 MET cc_start: 0.7453 (ttp) cc_final: 0.7096 (ttt) REVERT: D 4042 ARG cc_start: 0.6630 (mtm110) cc_final: 0.6131 (mtm180) REVERT: D 4045 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (m) REVERT: D 4184 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7063 (ttp) REVERT: D 4196 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5927 (tp30) REVERT: D 4209 GLN cc_start: 0.7815 (pt0) cc_final: 0.7532 (pm20) REVERT: D 4580 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6421 (t80) REVERT: D 4992 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8353 (mt) outliers start: 71 outliers final: 36 residues processed: 422 average time/residue: 1.1402 time to fit residues: 549.2318 Evaluate side-chains 434 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 376 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4184 MET Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4184 MET Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.0010 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4034 ASN A4973 HIS B4034 ASN B4973 HIS C4034 ASN C4973 HIS D4034 ASN D4973 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21208 Z= 0.155 Angle : 0.520 8.996 28644 Z= 0.256 Chirality : 0.036 0.122 3096 Planarity : 0.004 0.069 3612 Dihedral : 9.269 154.828 2776 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.66 % Favored : 98.18 % Rotamer: Outliers : 3.34 % Allowed : 18.09 % Favored : 78.57 % 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: 2.02 (0.17), residues: 2476 helix: 2.14 (0.12), residues: 1656 sheet: -0.58 (0.46), residues: 112 loop : -0.23 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A5019 HIS 0.003 0.001 HIS C3994 PHE 0.021 0.001 PHE A4922 TYR 0.012 0.001 TYR B4629 ARG 0.014 0.001 ARG D4736 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 383 time to evaluate : 2.295 Fit side-chains REVERT: A 3980 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 3986 TRP cc_start: 0.8460 (m100) cc_final: 0.7887 (m100) REVERT: A 3999 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7496 (tpt) REVERT: A 4023 MET cc_start: 0.7438 (ttp) cc_final: 0.7122 (ttp) REVERT: A 4042 ARG cc_start: 0.6580 (mtm110) cc_final: 0.6021 (mtm180) REVERT: A 4196 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5996 (tp30) REVERT: A 4209 GLN cc_start: 0.7795 (pt0) cc_final: 0.7512 (pm20) REVERT: A 4554 TYR cc_start: 0.8423 (t80) cc_final: 0.8082 (t80) REVERT: A 4580 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6415 (t80) REVERT: A 4992 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8319 (mt) REVERT: B 3980 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 3986 TRP cc_start: 0.8458 (m100) cc_final: 0.7881 (m100) REVERT: B 3999 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7487 (tpt) REVERT: B 4023 MET cc_start: 0.7438 (ttp) cc_final: 0.7123 (ttp) REVERT: B 4042 ARG cc_start: 0.6581 (mtm110) cc_final: 0.6023 (mtm180) REVERT: B 4196 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5997 (tp30) REVERT: B 4209 GLN cc_start: 0.7789 (pt0) cc_final: 0.7514 (pm20) REVERT: B 4554 TYR cc_start: 0.8422 (t80) cc_final: 0.8080 (t80) REVERT: B 4580 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6414 (t80) REVERT: B 4992 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8319 (mt) REVERT: C 3986 TRP cc_start: 0.8460 (m100) cc_final: 0.7916 (m100) REVERT: C 3999 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7493 (tpt) REVERT: C 4023 MET cc_start: 0.7453 (ttp) cc_final: 0.7128 (ttp) REVERT: C 4042 ARG cc_start: 0.6538 (mtm110) cc_final: 0.6051 (mtm180) REVERT: C 4196 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5995 (tp30) REVERT: C 4209 GLN cc_start: 0.7798 (pt0) cc_final: 0.7513 (pm20) REVERT: C 4554 TYR cc_start: 0.8427 (t80) cc_final: 0.8083 (t80) REVERT: C 4580 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6412 (t80) REVERT: C 4992 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8317 (mt) REVERT: D 3980 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8216 (mt) REVERT: D 3986 TRP cc_start: 0.8459 (m100) cc_final: 0.7886 (m100) REVERT: D 3999 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7486 (tpt) REVERT: D 4023 MET cc_start: 0.7441 (ttp) cc_final: 0.7124 (ttp) REVERT: D 4042 ARG cc_start: 0.6582 (mtm110) cc_final: 0.6023 (mtm180) REVERT: D 4196 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.5996 (tp30) REVERT: D 4209 GLN cc_start: 0.7794 (pt0) cc_final: 0.7511 (pm20) REVERT: D 4554 TYR cc_start: 0.8422 (t80) cc_final: 0.8079 (t80) REVERT: D 4580 TYR cc_start: 0.7427 (OUTLIER) cc_final: 0.6409 (t80) REVERT: D 4992 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8320 (mt) outliers start: 75 outliers final: 38 residues processed: 422 average time/residue: 1.2161 time to fit residues: 584.4462 Evaluate side-chains 433 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 376 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21208 Z= 0.165 Angle : 0.528 7.622 28644 Z= 0.260 Chirality : 0.036 0.119 3096 Planarity : 0.004 0.071 3612 Dihedral : 9.260 155.304 2776 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % Rotamer: Outliers : 2.72 % Allowed : 18.89 % Favored : 78.39 % 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: 2476 helix: 2.18 (0.12), residues: 1652 sheet: -0.58 (0.46), residues: 112 loop : -0.24 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C5019 HIS 0.003 0.001 HIS D3994 PHE 0.023 0.001 PHE A4922 TYR 0.008 0.001 TYR A5032 ARG 0.013 0.001 ARG A4736 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 379 time to evaluate : 2.242 Fit side-chains REVERT: A 3986 TRP cc_start: 0.8390 (m100) cc_final: 0.7873 (m100) REVERT: A 3999 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7468 (tpt) REVERT: A 4023 MET cc_start: 0.7363 (ttp) cc_final: 0.7122 (ttp) REVERT: A 4034 ASN cc_start: 0.6557 (t0) cc_final: 0.6279 (t0) REVERT: A 4042 ARG cc_start: 0.6580 (mtm110) cc_final: 0.6009 (mtm180) REVERT: A 4196 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.5965 (tp30) REVERT: A 4209 GLN cc_start: 0.7790 (pt0) cc_final: 0.7512 (pm20) REVERT: A 4554 TYR cc_start: 0.8441 (t80) cc_final: 0.8072 (t80) REVERT: A 4580 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6424 (t80) REVERT: A 4992 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8314 (mt) REVERT: B 3986 TRP cc_start: 0.8389 (m100) cc_final: 0.7869 (m100) REVERT: B 3999 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7460 (tpt) REVERT: B 4023 MET cc_start: 0.7365 (ttp) cc_final: 0.7122 (ttp) REVERT: B 4034 ASN cc_start: 0.6552 (t0) cc_final: 0.6273 (t0) REVERT: B 4042 ARG cc_start: 0.6577 (mtm110) cc_final: 0.6012 (mtm180) REVERT: B 4196 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6006 (tp30) REVERT: B 4209 GLN cc_start: 0.7784 (pt0) cc_final: 0.7513 (pm20) REVERT: B 4554 TYR cc_start: 0.8440 (t80) cc_final: 0.8072 (t80) REVERT: B 4580 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6423 (t80) REVERT: B 4992 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8312 (mt) REVERT: C 3980 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.7760 (mm) REVERT: C 3986 TRP cc_start: 0.8513 (m100) cc_final: 0.7882 (m100) REVERT: C 3999 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7464 (tpt) REVERT: C 4023 MET cc_start: 0.7346 (ttp) cc_final: 0.7118 (ttp) REVERT: C 4034 ASN cc_start: 0.6579 (t0) cc_final: 0.6304 (t0) REVERT: C 4042 ARG cc_start: 0.6548 (mtm110) cc_final: 0.6046 (mtm180) REVERT: C 4048 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6612 (mp) REVERT: C 4196 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6005 (tp30) REVERT: C 4209 GLN cc_start: 0.7791 (pt0) cc_final: 0.7513 (pm20) REVERT: C 4554 TYR cc_start: 0.8444 (t80) cc_final: 0.8073 (t80) REVERT: C 4580 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6416 (t80) REVERT: C 4992 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (mt) REVERT: D 3986 TRP cc_start: 0.8391 (m100) cc_final: 0.7874 (m100) REVERT: D 3999 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7457 (tpt) REVERT: D 4023 MET cc_start: 0.7365 (ttp) cc_final: 0.7122 (ttp) REVERT: D 4034 ASN cc_start: 0.6552 (t0) cc_final: 0.6275 (t0) REVERT: D 4042 ARG cc_start: 0.6582 (mtm110) cc_final: 0.6014 (mtm180) REVERT: D 4196 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5964 (tp30) REVERT: D 4209 GLN cc_start: 0.7790 (pt0) cc_final: 0.7511 (pm20) REVERT: D 4554 TYR cc_start: 0.8441 (t80) cc_final: 0.8072 (t80) REVERT: D 4580 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6420 (t80) REVERT: D 4992 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8314 (mt) outliers start: 61 outliers final: 39 residues processed: 411 average time/residue: 1.2111 time to fit residues: 566.3353 Evaluate side-chains 426 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 369 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3980 LEU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 156 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4812 HIS B4973 HIS C4812 HIS C4973 HIS D4812 HIS D4973 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21208 Z= 0.195 Angle : 0.555 9.007 28644 Z= 0.274 Chirality : 0.037 0.117 3096 Planarity : 0.004 0.073 3612 Dihedral : 9.286 155.728 2776 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 3.16 % Allowed : 18.72 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.17), residues: 2476 helix: 2.11 (0.12), residues: 1652 sheet: -0.61 (0.46), residues: 112 loop : -0.25 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A5019 HIS 0.004 0.001 HIS A4886 PHE 0.027 0.001 PHE B4922 TYR 0.011 0.001 TYR C4629 ARG 0.016 0.001 ARG B4189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 363 time to evaluate : 2.335 Fit side-chains REVERT: A 3980 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8215 (mt) REVERT: A 3986 TRP cc_start: 0.8455 (m100) cc_final: 0.7858 (m100) REVERT: A 3999 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7470 (tpt) REVERT: A 4015 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: A 4023 MET cc_start: 0.7504 (ttp) cc_final: 0.7192 (ttt) REVERT: A 4034 ASN cc_start: 0.6597 (t0) cc_final: 0.6315 (t0) REVERT: A 4042 ARG cc_start: 0.6652 (mtm110) cc_final: 0.6066 (mtm180) REVERT: A 4196 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6033 (tp30) REVERT: A 4209 GLN cc_start: 0.7808 (pt0) cc_final: 0.7537 (pm20) REVERT: A 4554 TYR cc_start: 0.8465 (t80) cc_final: 0.8073 (t80) REVERT: A 4580 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6425 (t80) REVERT: A 4992 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8339 (mt) REVERT: B 3980 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 3986 TRP cc_start: 0.8453 (m100) cc_final: 0.7853 (m100) REVERT: B 3999 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7462 (tpt) REVERT: B 4015 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: B 4023 MET cc_start: 0.7504 (ttp) cc_final: 0.7195 (ttt) REVERT: B 4034 ASN cc_start: 0.6594 (t0) cc_final: 0.6314 (t0) REVERT: B 4042 ARG cc_start: 0.6650 (mtm110) cc_final: 0.6066 (mtm180) REVERT: B 4196 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6025 (tp30) REVERT: B 4209 GLN cc_start: 0.7807 (pt0) cc_final: 0.7540 (pm20) REVERT: B 4554 TYR cc_start: 0.8464 (t80) cc_final: 0.8071 (t80) REVERT: B 4580 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6424 (t80) REVERT: B 4992 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8337 (mt) REVERT: C 3986 TRP cc_start: 0.8531 (m100) cc_final: 0.8065 (m100) REVERT: C 3999 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7466 (tpt) REVERT: C 4015 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: C 4023 MET cc_start: 0.7494 (ttp) cc_final: 0.7162 (ttp) REVERT: C 4034 ASN cc_start: 0.6641 (t0) cc_final: 0.6360 (t0) REVERT: C 4042 ARG cc_start: 0.6518 (mtm110) cc_final: 0.5995 (mtm180) REVERT: C 4048 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6619 (mp) REVERT: C 4196 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6019 (tp30) REVERT: C 4209 GLN cc_start: 0.7813 (pt0) cc_final: 0.7541 (pm20) REVERT: C 4554 TYR cc_start: 0.8469 (t80) cc_final: 0.8075 (t80) REVERT: C 4580 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6420 (t80) REVERT: C 4992 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8337 (mt) REVERT: D 3980 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8211 (mt) REVERT: D 3986 TRP cc_start: 0.8454 (m100) cc_final: 0.7858 (m100) REVERT: D 3999 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7461 (tpt) REVERT: D 4015 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: D 4023 MET cc_start: 0.7504 (ttp) cc_final: 0.7194 (ttt) REVERT: D 4034 ASN cc_start: 0.6592 (t0) cc_final: 0.6312 (t0) REVERT: D 4042 ARG cc_start: 0.6653 (mtm110) cc_final: 0.6067 (mtm180) REVERT: D 4196 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6032 (tp30) REVERT: D 4209 GLN cc_start: 0.7810 (pt0) cc_final: 0.7538 (pm20) REVERT: D 4554 TYR cc_start: 0.8466 (t80) cc_final: 0.8071 (t80) REVERT: D 4580 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6422 (t80) REVERT: D 4992 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (mt) outliers start: 71 outliers final: 43 residues processed: 408 average time/residue: 1.1753 time to fit residues: 547.9981 Evaluate side-chains 430 residues out of total 2244 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 363 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3980 LEU Chi-restraints excluded: chain A residue 3999 MET Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4039 MET Chi-restraints excluded: chain A residue 4045 VAL Chi-restraints excluded: chain A residue 4196 GLU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4658 ILE Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4743 MET Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4844 LEU Chi-restraints excluded: chain A residue 4889 VAL Chi-restraints excluded: chain A residue 4992 LEU Chi-restraints excluded: chain A residue 5002 GLU Chi-restraints excluded: chain B residue 3980 LEU Chi-restraints excluded: chain B residue 3999 MET Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4039 MET Chi-restraints excluded: chain B residue 4045 VAL Chi-restraints excluded: chain B residue 4196 GLU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4658 ILE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4743 MET Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4844 LEU Chi-restraints excluded: chain B residue 4889 VAL Chi-restraints excluded: chain B residue 4992 LEU Chi-restraints excluded: chain B residue 5002 GLU Chi-restraints excluded: chain C residue 3999 MET Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4045 VAL Chi-restraints excluded: chain C residue 4048 LEU Chi-restraints excluded: chain C residue 4196 GLU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4658 ILE Chi-restraints excluded: chain C residue 4666 VAL Chi-restraints excluded: chain C residue 4743 MET Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4844 LEU Chi-restraints excluded: chain C residue 4889 VAL Chi-restraints excluded: chain C residue 4992 LEU Chi-restraints excluded: chain C residue 5002 GLU Chi-restraints excluded: chain D residue 3980 LEU Chi-restraints excluded: chain D residue 3999 MET Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4039 MET Chi-restraints excluded: chain D residue 4045 VAL Chi-restraints excluded: chain D residue 4196 GLU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4658 ILE Chi-restraints excluded: chain D residue 4666 VAL Chi-restraints excluded: chain D residue 4743 MET Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4844 LEU Chi-restraints excluded: chain D residue 4889 VAL Chi-restraints excluded: chain D residue 4992 LEU Chi-restraints excluded: chain D residue 5002 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 202 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 173 optimal weight: 0.0980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4973 HIS B4973 HIS C4973 HIS D4973 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.174041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.140085 restraints weight = 24241.413| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.91 r_work: 0.3341 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21208 Z= 0.154 Angle : 0.544 8.602 28644 Z= 0.268 Chirality : 0.036 0.219 3096 Planarity : 0.005 0.067 3612 Dihedral : 9.232 155.606 2776 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.76 % Allowed : 19.25 % Favored : 77.99 % 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: 2.05 (0.17), residues: 2476 helix: 2.20 (0.12), residues: 1652 sheet: -0.60 (0.46), residues: 112 loop : -0.28 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C5019 HIS 0.003 0.001 HIS D3994 PHE 0.027 0.001 PHE D4922 TYR 0.008 0.001 TYR B5032 ARG 0.016 0.001 ARG B4189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8814.44 seconds wall clock time: 157 minutes 22.38 seconds (9442.38 seconds total)